- Chimera-users - RBVI Mailing Lists

Fwd: [Chimera] Request for download link: UCSF Chimera for macOS High Sierra
by Elaine Meng 17 Dec '25

17 Dec '25

> Begin forwarded message: > > Subject: [Chimera] Request for download link: UCSF Chimera for macOS High Sierra > Date: December 16, 2025 at 10:10:53 PM PST > Cc: Oleg Murashko <o.murashko(a)gmail.com> > > Dear Chimera Team, > > I hope you are well. > > Could you please provide a download link for the last version of UCSF Chimera > that is compatible with macOS 10.13 (High Sierra)? > > We are currently maintaining a legacy macOS system for compatibility reasons, > and newer versions of Chimera / ChimeraX are not supported on this OS. > > Thank you very much for your time and assistance. > > Best regards, > Oleg >

2 2

chimera display window issue
by Rechiche, Othman 09 Dec '25

09 Dec '25

Hi Chimera team, I’d like to bring to your attention an issue I’m encountering with the model display window (see attached images). As shown, the window appears incomplete. This problem started only after upgrading to the new macOS Tahoe—I did not experience it on macOS Sequoia. I’m currently using chimera-alpha-mac64.dmg (MD5: 555a52a5b12e1a617013213bf0f66c8d), the latest daily build. Could someone please take a look and advise on a possible solution? I would greatly appreciate your help. Thank you very much. Best regards, Othman ______________________________________ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.

2 3

Write_DMS was not found
by 肖磊 09 Dec '25

09 Dec '25

Greetings, I can not find WRITE_DMS in ChimeraX. Is WRITE_DMS removed?

2 1

CHIMERA X1.11 RELEASE - 12.01.25
by Laura Oliveira Gomes 01 Dec '25

01 Dec '25

Dear ChimeraX Support Team, I am writing to ask about the release of *ChimeraX version 1.11*, which is expected today. Is it already available for download? Since I need to use the software today, would you recommend waiting for the new release or downloading the previous version for now? Thank you, Laura Oliveira Gomes

2 2

About present the result of DiffDock using Chimera
by galxj 18 Nov '25

18 Nov '25

Dear Sir/Madam, I am a user of the Chimera software. I have obtained some molecular docking results from DiffDock, where the ligand molecules are in SDF format and the receptor protein is in PDB format. May I ask if it's possible to view the docking results using Chimera? I have tried many times but keep encountering errors. I also attempted to convert the SDF file to PDB format and opened both files together. Although both molecules are displayed, it is clear that the docking has not been performed correctly. Best Regards, Alei Geng

2 1

Chimera and ChimerX issues after update to MacOS Tahoe
by Rechiche, Othman 25 Sep '25

25 Sep '25

Hi everyone, I recently updated to MacOS Tahoe, Since then I encountered several issues with Chimera, ChmieraX and python. I installed and removed and reinstalled the apps but I still get the same error. For chimera I get this error: [Screenshot 2025-09-24 at 12.08.51 AM.png] FOr ChimeraX, when I try to open a session, it complains that the session was created with another version of python. I opened that session successfully several times before to the update of MacOS and I have never seen this error before. Failed opening file /Users/x/x/x/x/x/x/x/x.pyc: Python code was compiled for a different version of Python Can you please help me fix this? Best Regards, Othman Dr. Othman Rechiche Herbert Irving Comprehensive Cancer Center Columbia University Medical Center Columbia University New York, NY 10032 email: or2296(a)cumc.columbia.edu phone: +1 (814) 880-5554

2 3

Mapping conservation onto a structure
by Shelley Copley 25 Sep '25

25 Sep '25

Has Multalign viewer been taken down? I don’t see it in ChimeraX 1.10. Is there a different way to map sequence conservation onto a structure? Thanks! Shelley

2 1

Announcement: Release of DOCK 6.13
by Scott Brozell 16 Jul '25

16 Jul '25

We are pleased to announce the release of DOCK 6.13. DOCK is a suite of programs for molecular docking. The source code for DOCK 6.13 is available for download and free for academic users at https://dock.compbio.ucsf.edu/DOCK_6/index.htm This release includes new methods for de novo design: new biasing algorithms in DOCK_DN enable the prioritization of both fragments and torsions. Combined with parallel-based clustering and pruning algorithms that enable the efficient removal of duplicate molecules during growth, these approaches lead to ensembles with more drug-like characteristics. A number of incremental improvements are also available in this release notably for DOCK's genetic algorithm DOCK_GA and for Descriptor Score. For full information on what is new in DOCK 6.13, please visit: https://dock.compbio.ucsf.edu/DOCK_6/new_in_6.13.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. https://dock.compbio.ucsf.edu

1 0

Composite map: select only voxels within a range of resolution?
by Samuel Leite Guimaraes 29 Jun '25

29 Jun '25

Hi! I recently processed a cryo-EM map using icosahedral symmetry, achieving a decent global resolution. Then, using localized reconstruction, I improved the resolution of the asymmetric unit (ASU). However, some regions of the ASU still showed poor connectivity. To address this, I generated several additional localized reconstructions, focusing on specific regions of the ASU (taking advantage of the 2-fold, 3-fold, and 5-fold symmetry axes) to improve their local resolution. Now, I want to create a composite map in Chimera by combining the best-resolved regions from each localized reconstruction. However, instead of simply using the voxel-wise maximum density values (as done with vop max), I would like to select voxels based on the best local resolution — i.e., for each voxel position, use the value from the map where that voxel has the highest resolution (lowest local resolution value), as indicated by the associated local resolution maps. Is this type of composite map creation — resolution-guided voxel selection — possible in Chimera (or ChimeraX)? Thanks in advance! Samuel L. Guimarães Aviso Legal: Esta mensagem e seus anexos podem conter informações confidenciais e/ou de uso restrito. Observe atentamente seu conteúdo e considere eventual consulta ao remetente antes de copiá-la, divulgá-la ou distribuí-la. Se você recebeu esta mensagem por engano, por favor avise o remetente e apague-a imediatamente. Disclaimer: This email and its attachments may contain confidential and/or privileged information. Observe its content carefully and consider possible querying to the sender before copying, disclosing or distributing it. If you have received this email by mistake, please notify the sender and delete it immediately.

3 5

Request for Mathematical Details or Source Code for Helix Axis and Interhelical Distace/Angle Calculations in Chimera
by pupadhyay21 24 Jun '25

24 Jun '25

Respected Sir/Madam, My name is Prashant Upadhyay, and I am currently pursuing a Ph.D. in Bioinformatics and Molecular Dynamics Simulation at the Indian Institute of Technology Kanpur (IIT Kanpur), India. As part of my research, I am analyzing the structural dynamics of helical membrane proteins using molecular dynamics simulations. I have been using UCSF Chimera extensively for structural analysis. Specifically, I have been utilizing the Structure Analysis → Axes/Planes/Centroids tool to calculate the helix axes of selected helices in my protein of interest. When I select two helices, the Reply Log provides the interhelical distance and angle between the computed axes. This functionality has been incredibly useful for analyzing static structures. To extend this to a dynamic context, I am interested in applying the same axis and angle calculation to each frame of an MD trajectory. For this, I would greatly appreciate it if you could share the mathematical methodology or the relevant portion of the source code that Chimera uses to compute: 1)The helix axis from selected residues 2)The angle and the shortest distance between two helix axes My aim is to replicate this analysis programmatically over the entire simulation trajectory. Any guidance, reference, or code snippet you could provide would be immensely helpful. Thank you, Prashant Upadhyay Ph.D. Student Department of Biological Sciences and Bioengineering Indian Institute of Technology Kanpur (IIT Kanpur)

3 3

Request for Mathematical Details or Source Code for Helix Axis and Interhelical Distace/Angle Calculations in Chimera
by pupadhyay21 22 Jun '25

22 Jun '25

Respected Sir/Madam, My name is Prashant Upadhyay, and I am currently pursuing a Ph.D. in Bioinformatics and Molecular Dynamics Simulation at the Indian Institute of Technology Kanpur (IIT Kanpur), India. As part of my research, I am analyzing the structural dynamics of helical membrane proteins using molecular dynamics simulations. I have been using UCSF Chimera extensively for structural analysis. Specifically, I have been utilizing the Structure Analysis → Axes/Planes/Centroids tool to calculate the helix axes of selected helices in my protein of interest. When I select two helices, the Reply Log provides the interhelical distance and angle between the computed axes. This functionality has been incredibly useful for analyzing static structures. To extend this to a dynamic context, I am interested in applying the same axis and angle calculation to each frame of an MD trajectory. For this, I would greatly appreciate it if you could share the mathematical methodology or the relevant portion of the source code that Chimera uses to compute: 1)The helix axis from selected residues 2)The angle and the shortest distance between two helix axes My aim is to replicate this analysis programmatically over the entire simulation trajectory. Any guidance, reference, or code snippet you could provide would be immensely helpful. Thank you, Prashant Upadhyay Ph.D. Student Department of Biological Sciences and Bioengineering Indian Institute of Technology Kanpur (IIT Kanpur)

1 0

ChimeraX menu
by Elaine Meng 13 Jun '25

13 Jun '25

Hi Mariela, Your picture #1 is Chimera. Picture #2 is ChimeraX. These are two different programs. To get ChimeraX, you have to go to the ChimeraX website and download it: <https://www.rbvi.ucsf.edu/chimerax/download.html> If you meant that you do already have ChimeraX, but the Toolbar with icons is not shown, use ChimeraX menu: Tools... General... Toolbar to show it. See ChimeraX window and Toolbar help: <https://rbvi.ucsf.edu/chimerax/docs/user/window.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html> If you have ChimeraX questions, please use address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here. The other address chimera-users[...] is for Chimera. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 13, 2025, at 5:34 AM, Mariela Urrutia via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi Eric > I send you the menu I have (adjunto 1) and the menu I would like to have in my CPU (adjunto 2). > Could you tell me please how can I add it? > Thanks you. > Mariela > > De: Eric Pettersen <pett(a)cgl.ucsf.edu> > Enviado: Jueves, 12 de Junio de 2025 14:14 > Para: Mariela Urrutia <murrutia(a)cedie.org.ar> > CC: chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu>; Alexis Rohou via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> > Asunto: Re: [Chimera-users] query > Hi Mariela, > I don’t really know what a “superior menu” is. Maybe you could clarify? If you mean a popup menu, you get that by clicking the right button on your mouse (or the equivalent on a trackpad). > Since this is a ChimeraX question, I have cc’ed the chimerax-users list and directed replies there. Chimera and ChimeraX are separate programs and have separate mailing lists. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > On Jun 12, 2025, at 9:23 AM, Mariela Urrutia via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello, > Could you give me direction to add the superior menu in ChimeraX 1.9 (2025-3-6)? > Thanks you in advance! > Mariela > Dra. Mariela Urrutia > Investigadora > Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” (CEDIE) > CONICET – FEI – División de Endocrinología, Hospital de Niños Ricardo Gutiérrez > Gallo 1330 – C1425EFD Buenos Aires – Argentina > Tel. (+54-11) 4963-5931 int 290 > murrutia(a)cedie.org.ar 🌎 www.cedie.org.ar 👥 Facebook Instagram > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/ > > _______________________________________________

1 0

query
by Mariela Urrutia 12 Jun '25

12 Jun '25

Hello, Could you give me direction to add the superior menu in ChimeraX 1.9 (2025-3-6)? Thanks you in advance! Mariela Dra. Mariela Urrutia Investigadora Centro de Investigaciones Endocrinológicas “Dr. César Bergadá” (CEDIE) CONICET – FEI – División de Endocrinología, Hospital de Niños Ricardo Gutiérrez Gallo 1330 – C1425EFD Buenos Aires – Argentina Tel. (+54-11) 4963-5931 int 290 murrutia(a)cedie.org.ar<mailto:murrutia@cedie.org.ar> 🌎 www.cedie.org.ar<https://cedie.conicet.gov.ar/> 👥 Facebook<https://www.facebook.com/CEDIE-Centro-de-Investigaciones-Endocrinol%C3%B3gi…> Instagram<https://www.instagram.com/cedie.conicet/>

3 2

Chimera on RHEL10 or Fedora 42 with Wayland
by Ben Webb 10 Jun '25

10 Jun '25

RedHat Enterprise Linux 10 has dropped Xorg in favor of Wayland, and Fedora 43 will likely do the same. Fedora 42 already uses Wayland by default. Is Chimera expected to work with Wayland? ChimeraX works fine in our environment with Wayland, but I have folks that still want to use Chimera. And they're getting a Togl failure at startup: "Display misconfiguration. Please increase the color quality (24 bit color or greater), update your display (graphics) driver, and/or upgrade your graphics card. Also see chimera installation instructions." I would love to tell them that "the Chimera folks say it doesn't work with Wayland so you need to switch to ChimeraX" (we can eke out another six months or so with Fedora 42 using Xorg) but if you think it *should* work, any clues as to where to look to tweak our configuration? Other than using the NVIDIA drivers (570.133.07), we are using a stock Fedora and Wayland install.

3 6

Add sequence logo to view
by Alexander Lee 05 May '25

05 May '25

Dear ChimeraX community, I have a consensus sequence + logo done in an outside program. Is there a way to superimpose this onto a crystal structure? When hovering my mouse over a residue in the structure viewer (or sequence viewer), I would like the logo to come up. Is there a similar feature available? Regards, Alex

2 1

Error with color byattribute
by svle＠tiscali.it 13 Apr '25

13 Apr '25

Hi, I'm using the Attribute Assignment Files tutorial with the commands: open [1] 1pho open [2] kdHydrophobicity.defattr [3] color byattribute [4] kdHydrophobicity palette ^RdYlBu select [5] ::kdHydrophobicity>2.0 I've only substituted 1pho with 1caz. For the command: color byattribute [6] kdHydrophobicity palette ^RdYlBu I receive the error "color byattribute is undefined" with different version of chimera. Any suggestions? Thanks. Saverio

3 2

Exporting PDB in correct coordinate system
by James Nettles 11 Apr '25

11 Apr '25

Hello, I have built a Chimera model of N-term and C-term folding associated with a particular dimeric crystal structure associated with HCV. The crystal structure (1zh1) is our reference and we identified theoretical low-energy folds that correlate well with our biological data. We want to be able to upload pdb’s of our folding models with the data presented in the paper so that readers can also see the interactions in 3D. I used the writePDB function and chose to Save relative to 1zh1 in Model Panel, but the results come out misaligned. I’m obviously doing something wrong, have tried various things but have not been able to figure this out. Any tips? Thanks, Jim _____________________ James Nettles, PhD nettlesconsulting(a)gmail.com +01.404.966.4617

2 2

Save PDBs relative to each other
by Elaine Meng 11 Apr '25

11 Apr '25

On Apr 11, 2025, at 9:35 AM, James Nettles <nettlesconsulting(a)gmail.com> wrote: > > Hi Elaine, I tried submitting a new question to the list, but received a response that I’m not a list member. > > I am trying to output some models in PDB format and am having problems getting the coordinates of the sports to align properly when read back in. > > I haven’t been able to figure what I'm doing wrong. > > Your help will be appreciated. > > Jim Hi Jim, That message is probably caused by sending the message from a different address than what is signed up to the list. If so, your question has to be approved by the moderator (not me) but usually it is within a day. Otherwise we would be inundated with spam messages from addresses that aren't list members. Re your question: If you moved one model relative to the other and want to maintain their relationship, you need to use the save "relative" option. Doesn't matter which model is relative to which, as long as they are all relative to the same model. This is in both the File... Save dialog and the "write" command. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> These are the address for managing list subscriptions (Chimera and ChimeraX users) <https://mail.cgl.ucsf.edu/mailman/mailman3/lists/chimera-users.cgl.ucsf.edu/> <https://mail.cgl.ucsf.edu/mailman/mailman3/lists/chimerax-users.cgl.ucsf.ed…> ChimeraX has an analogous relative saving option for PDB files in both the File... Save dialog and the "save" command (instead of Chimera's "write" command). Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Inquiry about Using UCSF Chimera for Biology Olympiad
by Oliwier Różański 02 Apr '25

02 Apr '25

Dear UCSF Chimera Team, I am a student participating in the *Biology Olympiad* and would like to ask if I am allowed to use *UCSF Chimera* for this competition. Could you please confirm if this is permitted and if there are any specific licensing requirements? Thank you for your assistance.

2 1

Re: UCSF Chimera Download
by Elaine Meng 31 Mar '25

31 Mar '25

The recommended address for asking questions about Chimera is chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> ... you do not need to send another message, I have CC'd that address on this message so that somebody else can answer. I don't know the details of Windows download. My only guess is to wait for a few minutes to be sure the download is finished before you try to open it. Maybe there is a temporary filename for the partial download that changes after the download is complete. Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 31, 2025, at 2:52 PM, Ki Kim <pkhkim(a)gmail.com> wrote: > > Hello, > I am trying to download and install the UCSF Chimera Program. I used the download site as shown below: > > > This is what I have in my download folder: > > > Now, this doesn;t seem to be the right exe file. Did I do something wrong? > I have a Window 11 and 64-bit. > Thank you for your help. > Ki > >

1 1

registration
by YELIZ KAYA 11 Mar '25

11 Mar '25

I registered to the Chimera program with my address yeliz.kaya(a)iuc.edu.tr. Can I find out if I am registered to the Chimera program? Thank you. Assoc. Prof. Dr. Yeliz KAYA IUC Chemistry Department -- *İSTANBUL ÜNİVERSİTESİ-CERRAHPAŞA <https://www.iuc.edu.tr/tr/_>* Yasal Uyarı: <https://bilgiislem.iuc.edu.tr/tr/content/e-posta-hizmetleri/%E2%96%BA-e-pos…> Bu e-posta ve beraberinde iletilen bütün dosyalar sadece göndericisi tarafından alınması amaçlanan yetkili gerçek ya da tüzel kişinin kullanımı içindir. Eğer söz konusu yetkili alıcı değilseniz bu e-postanın içeriğini açıklamanız, kopyalamanız, yönlendirmeniz ve kullanmanız kesinlikle yasaktır ve bu e-postayı derhal silmeniz gerekmektedir. İSTANBUL ÜNİVERSİTESİ-CERRAHPAŞA bu e-postanın içerdiği bilgilerin doğruluğu veya eksiksiz olduğu konusunda herhangi bir garanti vermemektedir. Bu nedenle bu bilgilerin ne şekilde olursa olsun içeriğinden, iletilmesinden, alınmasından ve saklanmasından sorumlu değildir. Bu e-postadaki görüşler yalnızca gönderen kişiye aittir ve İSTANBUL ÜNİVERSİTESİ-CERRAHPAŞA'nın görüşlerini yansıtmayabilir. *ISTANBUL UNIVERSITY-CERRAHPASA <https://www.iuc.edu.tr/tr/_>* Disclaimer <https://bilgiislem.iuc.edu.tr/tr/content/e-posta-hizmetleri/%E2%96%BA-e-pos…>: This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the intended recipient you are hereby notified that any dissemination, forwarding, copying or use of any of the information is strictly prohibited, and the e-mail should immediately be deleted. ISTANBUL UNIVERSITY-CERRAHPASA makes no warranty as to the accuracy or completeness of any information contained in this e-mail and hereby excludes any liability of any kind for the information contained therein or for the information transmission, reception, storage or use of such in any way whatsoever. The opinions expressed in this e-mail may belong to the sender alone and may not necessarily reflect the opinions of ISTANBUL UNIVERSITY-CERRAHPASA.

2 2

Problem downloading PDBs in Chimera
by Clarke, Oliver 10 Mar '25

10 Mar '25

Hi, Since this weekend, I have been unable to download PDBs from within Chimera (using "open" or Fetch by ID). The same PDBs load fine in ChimeraX or when downloaded manually. Cached PDBs load fine. Cheers Oli

4 3

Setting partial charges to a protein gives same charges in both Gasteiger and AM1-BCC methods. Is that corrects?
by teralexei＠proton.me 03 Mar '25

03 Mar '25

Dear colleagues, calculation of partial charges in Chimera looks to work improperly in my hands. After addcharge or dokprep procedures, independent on method used (am1-bcc or Gasteiger), mol2 files are just the same: @<TRIPOS>MOLECULE .... PROTEIN AMBER ff14SB @<TRIPOS>ATOM 1 N -76.5030 6.5380 -16.5070 N.4 1 ARG 0.1305 2 CA -75.2450 7.2900 -16.2110 C.3 1 ARG -0.0223 .... The problem persist in both Chimera 1.17.3 and ChimeraX. The latter gives even "NO_CHARGES" comment in both (am1-bcc and Gasteiger) cases: @<TRIPOS>MOLECULE .... PROTEIN NO_CHARGES @<TRIPOS>ATOM 1 N -76.5030 6.5380 -16.5070 N.4 1 ARG 0.1305 2 CA -75.2450 7.2900 -16.2110 C.3 1 ARG -0.0223 .... I am not an expert in molecular modeling, sorry. But I think that I am doing something wrong. Could you please help me with setting charges properly? Thank you in advance! PS. I am a newbie here. Please don't hurt me too much. Yours sincerely, Al.

2 1

registration
by YELIZ KAYA 27 Feb '25

27 Feb '25

Dear Sir, As I have attached the image, I registered to the Chimera program. However, I did not receive any e-mail. Can you help me with this? Thank you. Assoc. Prof. Dr. Yeliz KAYA IUC Chemistry Department -- *İSTANBUL ÜNİVERSİTESİ-CERRAHPAŞA <https://www.iuc.edu.tr/tr/_>* Yasal Uyarı: <https://bilgiislem.iuc.edu.tr/tr/content/e-posta-hizmetleri/%E2%96%BA-e-pos…> Bu e-posta ve beraberinde iletilen bütün dosyalar sadece göndericisi tarafından alınması amaçlanan yetkili gerçek ya da tüzel kişinin kullanımı içindir. Eğer söz konusu yetkili alıcı değilseniz bu e-postanın içeriğini açıklamanız, kopyalamanız, yönlendirmeniz ve kullanmanız kesinlikle yasaktır ve bu e-postayı derhal silmeniz gerekmektedir. İSTANBUL ÜNİVERSİTESİ-CERRAHPAŞA bu e-postanın içerdiği bilgilerin doğruluğu veya eksiksiz olduğu konusunda herhangi bir garanti vermemektedir. Bu nedenle bu bilgilerin ne şekilde olursa olsun içeriğinden, iletilmesinden, alınmasından ve saklanmasından sorumlu değildir. Bu e-postadaki görüşler yalnızca gönderen kişiye aittir ve İSTANBUL ÜNİVERSİTESİ-CERRAHPAŞA'nın görüşlerini yansıtmayabilir. *ISTANBUL UNIVERSITY-CERRAHPASA <https://www.iuc.edu.tr/tr/_>* Disclaimer <https://bilgiislem.iuc.edu.tr/tr/content/e-posta-hizmetleri/%E2%96%BA-e-pos…>: This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the intended recipient you are hereby notified that any dissemination, forwarding, copying or use of any of the information is strictly prohibited, and the e-mail should immediately be deleted. ISTANBUL UNIVERSITY-CERRAHPASA makes no warranty as to the accuracy or completeness of any information contained in this e-mail and hereby excludes any liability of any kind for the information contained therein or for the information transmission, reception, storage or use of such in any way whatsoever. The opinions expressed in this e-mail may belong to the sender alone and may not necessarily reflect the opinions of ISTANBUL UNIVERSITY-CERRAHPASA.

2 1

UCSF chimera problems when fetching PDB id's
by Charles-Alexandre Mattelaer 26 Feb '25

26 Feb '25

Hi all I just wanted to ask if it is normal my Chimera installs have begun throwing errors when fetching PDB’s by ID (eg 1EHZ)? It does work for other PDB codes, eg 6NP2. I used to do this regularly but since a few days I have noticed these errors pop up. It typically returns: “Error reading $PDBcode: No such id: $PDBcode” I am aware Chimera is deprecated and not supported anymore, but I used it for simple tasks eg Autodock Vina which is not supported in ChimeraX and teaching thereof. Kind regards Charles-Alexandre

2 1

I would like to inquire about the way to make the ligand file pdbqt.
by Healer Choi 20 Feb '25

20 Feb '25

Dear UCSF Hello, I'm Choi Hwan. I'm a college student majoring in molecular design research in Korea. I'm inquiring about a problem in the process of making a pdbqt file during the research project. First of all, the contents are as follows. I made a total of two ligand.pdbqt. (1) Called Lingand(4YZN) to chimera as sdf file and ran autodock vina. That way, I can see that 4YZN.pdb and 4YZN.pdbqt are created. (2) We also used Autodock tools to make 4YZN.pdbqt of 4YZN.pdb generated in the process above. Autodock tools used here directly used prepare_ligand4.py in the path where chimera was installed. As a result, the format of the three pdbqt made was different. The 4YZN.pdbqt made in chimera had 6 active torsions and the 4YZN.pdbqt made using Autodock tools had 7 active torsions. The result was that the vina docking results were different. As a result of docking, the (1) pdbqt made in chimera was better suited for vina docking. I want to create the pdbqt format generated by chimera. Since we need to make a large amount of compound into pdbqt, could you tell me how to get pdbqt without using chimera GUI? I am using linux. Or I would like to know if I missed anything in the process of making sdf -> pdb -> pdbqt in chimera. (using chimera 1.17.3)

3 2

script for clashes
by valerio chiarini 18 Feb '25

18 Feb '25

Dear Responsible, I am working on a script that should iterate through several structures, check the structures for clashes among all atoms, and eliminate the pdb in any clashes are found. Here is what I have worked out so far: # -*- coding: utf-8 -*- import os from chimera import runCommand as rc from chimera import replyobj import chimera # Specify folder folder_path = "/gporq3/store_0/usr/chiarini/chroma/chroma/" # String to be found search_string = "xxx" # List of files in the folder file_names = [fn for fn in os.listdir(folder_path) if fn.endswith(".pdb")] print("File trovati nella cartella:" + str(file_names)) # Loop on every file containing 'search_string' in the name for pdb_file in file_names: if search_string in pdb_file: pdb_path = os.path.join(folder_path, pdb_file) # Open the PDB rc("open {}".format(pdb_path)) # Calculates clashes rc("findclash") rc("wait") # Verify if any clashes are found clashes = chimera.clashClashList() if clashes: # If clashes are found eliminates the file os.remove(pdb_path) print("Clash trovati, il file {} è stato eliminato.".format(pdb_file)) else: # If no clash, exit normally print("Nessun clash trovato per {}.".format(pdb_file)) But no analisys is done at all. I have been searching through the script page (https://www.rbvi.ucsf.edu/trac/chimera/wiki/Scripts) in order to found some clue on this function but so far I have found none. Could you help me on this issue? Thank you in advance Valerio Chiarini

3 3

smart boards or mobile devices
by Wendy Tomamichel 12 Feb '25

12 Feb '25

Good afternoon. We have a VIBE board that we would like to utilize your software for. The only issue is that it is a smart board that can't download traditional software. Do you have a software download that I could try to see if it could work? Thank you! Wendy -- Wendy Tomamichel DePauw Chemistry Lab Manager Julian Science and Mathematics Center 2 E. Hanna St. Room 348 Greencastle, IN 46135 765-658-4606

3 2

Chimera 1.X PDB downloads are broken
by Eric Pettersen 12 Feb '25

12 Feb '25

Hi all, The RCSB made a change to their web site this morning that broke the fetching of PDB files by ID code in Chimera. We have committed a fix to Chimera that re-enables PDB fetching, and that fix will be in tomorrow's daily build. Note that this problem only really affects you if you are trying to access PDB files you've never used before, because Chimera caches fetched PDB files on your machine. We hope to make a production release that incorporates this fix sooner rather than later, but aren't yet sure exactly when that will be. --Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

Contributor
by Roy, Raj (MU-Student) 12 Feb '25

12 Feb '25

Dear Concern, I have used chimera for a long time, and I was wondering if I can contribute with some scripts/python code that can make chimera more beneficial to others. Regards, Raj Shekhor Roy PhD Student Electrical Engineering and Computer Science (EECS) Department University of Missouri - Columbia Email: rsr3gt(a)umsystem.edu Phone (Cell): 573-814-9512

2 1

script for clashes
by chiarini＠takisbiotech.it 12 Feb '25

12 Feb '25

Dear Responsible, I am working on a script that should iterate through several structures, check the structures for clashes among all atoms, and eliminate the pdb in any clashes are found. Here is what I have worked out so far: # -*- coding: utf-8 -*- import os from chimera import runCommand as rc from chimera import replyobj import chimera # Specify folder folder_path = "/gporq3/store_0/usr/chiarini/chroma/chroma/" # String to be found search_string = "xxx" # List of files in the folder file_names = [fn for fn in os.listdir(folder_path) if fn.endswith(".pdb")] print("File trovati nella cartella:" + str(file_names)) # Loop on every file containing 'search_string' in the name for pdb_file in file_names: if search_string in pdb_file: pdb_path = os.path.join(folder_path, pdb_file) # Open the PDB rc("open {}".format(pdb_path)) # Calculates clashes rc("findclash") rc("wait") # Verify if any clashes are found clashes = chimera.clashClashList() if clashes: # If clashes are found eliminates the file os.remove(pdb_path) print("Clash trovati, il file {} C( stato eliminato.".format(pdb_file)) else: # If no clash, exit normally print("Nessun clash trovato per {}.".format(pdb_file)) But no analisys is done at all. I have been searching through the script page (https://www.rbvi.ucsf.edu/trac/chimera/wiki/Scripts) in order to found some clue on this function but so far I have found none. Could you help me on this issue? Thank you in advance -- Dr. Valerio Chiarini _Senior Scientist_ Proteins & Monoclona Antibodies Department b Takis Biotech c/o Tecnopolo Via di Castel Romano, 100 00128 Rome, Italy Tel.: +39 06-50576077 Fax: +39 06-50576710 Email: chiarini(a)takisbiotech.it Web: http://www.takisbiotech.it 196/03_ _Le informazioni contenute in questa comunicazione e gli eventuali documenti allegati hanno carattere confidenziale, sono tutelate dal segreto professionale e sono ad uso esclusivo del destinatario. Nel caso questa comunicazione Vi sia pervenuta per errore, Vi informiamo che la sua diffusione e riproduzione C( contraria alla legge e preghiamo di darci prontamente avviso e di cancellare quanto ricevuto. __Grazie._ _This e-mail message and any files transmitted with it are subject to attorney-client privilege and contain confidential information intended only for the person(s) to whom it is addressed. If you are not the intended recipient, you are hereby notified that any use or distribution of this e-mail is strictly prohibited: please notify the sender and delete the original message. __Thank you._

1 0

key command
by Fabian Glaser 03 Feb '25

03 Feb '25

Hi, We would be interested to add more than one key color bar in the same chimerax session. But we noticed the key command allows only one color key can be present at a time. Is there a way to add more than one color key in the same session? Thanks a lot, Fabian Fabian Glaser, PhD Technion Centre for Structural Biology (TCSB), Computational Section, Head Technion Human Health Initiative (THHI) Technion - Israel Institute of Technology, Haifa, Israel fglaser(a)technion.ac.il +972 (0)48293701

2 1

Charges of 0.0 were assigned to the unknown atoms
by fateme haghighi 30 Jan '25

30 Jan '25

Hi, I tried to do docking with Chimera, but I aced an error. The process I used is: Tools - structure binding- dock prep -uncheck write mol2 file ok next step add Gasteiger charge ok I used several frames of a MD simulation of modelled 3CQU6 protein, in water for Docking and I faced the same error for all pdb files. Please let me know how to resolve the problem. Thank you in advanced Model 0 (frame_1001000_model1.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Residues with incomplete side chains: ILE 6 ILE 19 ILE 36 ILE 74 ILE 75 ILE 84 ILE 103 ILE 165 ILE 180 ILE 186 ILE 257 ILE 288 ILE 290 ILE 300 ILE 361 ILE 366 ILE 402 ILE 411 ILE 447 ILE 449 Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True' ILE 6: phi -77.4, psi 129.6 trans Chi angles for ILE 6: -55.1 ILE 19: phi -78.2, psi 162.7 trans Chi angles for ILE 19: 76.7 ILE 36: phi -122.2, psi 128.4 trans Chi angles for ILE 36: -55.1 ILE 74: phi -136.5, psi 119.3 trans Chi angles for ILE 74: -40.3 ILE 75: phi -110.2, psi 156.4 trans Chi angles for ILE 75: 61.0 ILE 84: phi -109.4, psi 143.1 trans Chi angles for ILE 84: -158.3 ILE 103: phi -57.4, psi -37.7 trans Chi angles for ILE 103: -68.6 ILE 165: phi -131.8, psi 170.4 trans Chi angles for ILE 165: 60.6 ILE 180: phi -125.3, psi 108.1 trans Chi angles for ILE 180: -55.2 ILE 186: phi -93.0, psi 145.1 trans Chi angles for ILE 186: 56.5 ILE 257: phi -67.9, psi -35.9 trans Chi angles for ILE 257: -60.0 ILE 288: phi -112.5, psi 145.4 trans Chi angles for ILE 288: 62.8 ILE 290: phi -94.7, psi 123.7 trans Chi angles for ILE 290: -48.4 ILE 300: phi -73.4, psi 134.5 trans Chi angles for ILE 300: -66.4 ILE 361: phi -79.0, psi -30.9 trans Chi angles for ILE 361: -176.4 ILE 366: phi -127.0, psi 128.1 trans Chi angles for ILE 366: -63.8 ILE 402: phi -61.0, psi -39.2 trans Chi angles for ILE 402: -52.7 ILE 411: phi -89.8, psi 134.0 trans Chi angles for ILE 411: -65.6 ILE 447: phi -79.9, psi 129.4 trans Chi angles for ILE 447: -42.2 ILE 449: phi -73.8, psi 174.9 trans Chi angles for ILE 449: 72.4 Applying ILE rotamer (chi angles: 63.1 170.6) to ILE 19 Applying ILE rotamer (chi angles: -174.1 70.6) to ILE 84 Applying ILE rotamer (chi angles: -60.3 -60.9) to ILE 300 Applying ILE rotamer (chi angles: -56.7 92.3) to ILE 74 Applying ILE rotamer (chi angles: -57.1 -63.4) to ILE 36 Applying ILE rotamer (chi angles: 62.2 171.6) to ILE 165 Applying ILE rotamer (chi angles: -68.1 168.5) to ILE 402 Applying ILE rotamer (chi angles: -67.0 169.0) to ILE 257 Applying ILE rotamer (chi angles: 62.3 170.5) to ILE 449 Applying ILE rotamer (chi angles: -162.1 168.1) to ILE 361 Applying ILE rotamer (chi angles: 61.8 170.9) to ILE 186 Applying ILE rotamer (chi angles: 60.6 171.1) to ILE 288 Applying ILE rotamer (chi angles: 61.7 170.9) to ILE 75 Applying ILE rotamer (chi angles: -61.1 170.2) to ILE 290 Applying ILE rotamer (chi angles: -58.4 -66.3) to ILE 366 Applying ILE rotamer (chi angles: -62.9 169.7) to ILE 6 Applying ILE rotamer (chi angles: -68.1 168.5) to ILE 103 Applying ILE rotamer (chi angles: -58.8 172.2) to ILE 180 Applying ILE rotamer (chi angles: -62.9 169.7) to ILE 447 Applying ILE rotamer (chi angles: -62.1 169.6) to ILE 411 No SEQRES records for frame_1001000_model1.pdb (#0) principal chain; guessing terminii instead Chain-initial residues that are actual N terminii: MET 1 Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: ALA 480 Chain-final residues that are not actual C terminii: 389 hydrogen bonds Hydrogens added Charge model: AMBER ff14SB Non-standard atom names: LEU HN (LEU 12 HN, LEU 28 HN, LEU 29 HN + 38 others) MET HN2 (MET 1 HN2) ASN HN (ASN 31 HN, ASN 53 HN, ASN 54 HN + 10 others) GLY HN (GLY 10 HN, GLY 16 HN, GLY 33 HN + 27 others) SER HN (SER 2 HN, SER 56 HN, SER 122 HN + 20 others) SER HG1 (SER 2 HG1, SER 56 HG1, SER 122 HG1 + 20 others) ARG HC (ARG 15 HC, ARG 23 HC, ARG 25 HC + 27 others) MET HN3 (MET 1 HN3) ARG 3HC (ARG 15 3HC, ARG 23 3HC, ARG 25 3HC + 27 others) ARG 6HC (ARG 15 6HC, ARG 23 6HC, ARG 25 6HC + 27 others) CYS HN (CYS 60 HN, CYS 77 HN, CYS 224 HN + 4 others) ARG 4HC (ARG 15 4HC, ARG 23 4HC, ARG 25 4HC + 27 others) TYR HN (TYR 18 HN, TYR 26 HN, TYR 38 HN + 15 others) ILE HN (ILE 6 HN, ILE 19 HN, ILE 36 HN + 17 others) ARG HN (ARG 15 HN, ARG 23 HN, ARG 25 HN + 27 others) VAL HN (VAL 4 HN, VAL 7 HN, VAL 45 HN + 25 others) TRP HN (TRP 11 HN, TRP 22 HN, TRP 80 HN + 4 others) PHE HN (PHE 27 HN, PHE 35 HN, PHE 55 HN + 24 others) LYS HN (LYS 8 HN, LYS 14 HN, LYS 20 HN + 33 others) ARG 2HC (ARG 15 2HC, ARG 23 2HC, ARG 25 2HC + 27 others) ARG 1HC (ARG 15 1HC, ARG 23 1HC, ARG 25 1HC + 27 others) ASP HN (ASP 3 HN, ASP 32 HN, ASP 44 HN + 25 others) HIS HN (HIS 13 HN, HIS 89 HN, HIS 143 HN + 10 others) MET HN1 (MET 1 HN1) ARG 5HC (ARG 15 5HC, ARG 23 5HC, ARG 25 5HC + 27 others) ARG HH (ARG 15 HH, ARG 15 HH, ARG 15 HH + 117 others) CYS HG1 (CYS 60 HG1, CYS 77 HG1, CYS 224 HG1 + 4 others) ALA HN (ALA 5 HN, ALA 50 HN, ALA 58 HN + 22 others) GLU HN (GLU 9 HN, GLU 17 HN, GLU 40 HN + 46 others) ALA OT1 (ALA 480 OT1) MET HN (MET 63 HN, MET 118 HN, MET 134 HN + 12 others) GLN HN (GLN 43 HN, GLN 47 HN, GLN 59 HN + 14 others) THR HN (THR 21 HN, THR 34 HN, THR 65 HN + 27 others) ALA OT2 (ALA 480 OT2) Total charge for #0: -206.220 The following residues had non-integral charges: MET 1 0.4048 SER 2 -0.6994 ASP 3 -1.2936 VAL 4 -0.2719 ALA 5 -0.2719 ILE 6 -0.2719 VAL 7 -0.2719 LYS 8 0.7253 GLU 9 -1.2936 GLY 10 -0.2719 TRP 11 -0.2719 LEU 12 -0.2719 HIS 13 0.7253 LYS 14 0.7253 ARG 15 -1.4817 GLY 16 -0.2719 GLU 17 -1.2936 TYR 18 -0.2719 ILE 19 -0.2719 LYS 20 0.7253 THR 21 -0.2719 TRP 22 -0.2719 ARG 23 -1.4817 ARG 25 -1.4817 TYR 26 -0.2719 PHE 27 -0.2719 LEU 28 -0.2719 LEU 29 -0.2719 LYS 30 0.7253 ASN 31 -0.2719 ASP 32 -1.2936 GLY 33 -0.2719 THR 34 -0.2719 PHE 35 -0.2719 ILE 36 -0.2719 GLY 37 -0.2719 TYR 38 -0.2719 LYS 39 0.7253 GLU 40 -1.2936 ARG 41 -1.4817 GLN 43 -0.2719 ASP 44 -1.2936 VAL 45 -0.2719 ASP 46 -1.2936 GLN 47 -0.2719 ARG 48 -1.4817 GLU 49 -1.2936 ALA 50 -0.2719 LEU 52 -0.2719 ASN 53 -0.2719 ASN 54 -0.2719 PHE 55 -0.2719 SER 56 -0.6994 VAL 57 -0.2719 ALA 58 -0.2719 GLN 59 -0.2719 CYS 60 -1.2719 GLN 61 -0.2719 LEU 62 -0.2719 MET 63 -0.2719 LYS 64 0.7253 THR 65 -0.2719 GLU 66 -1.2936 ARG 67 -1.4817 ARG 69 -1.4817 ASN 71 -0.2719 THR 72 -0.2719 PHE 73 -0.2719 ILE 74 -0.2719 ILE 75 -0.2719 ARG 76 -1.4817 CYS 77 -1.2719 LEU 78 -0.2719 GLN 79 -0.2719 TRP 80 -0.2719 THR 81 -0.2719 THR 82 -0.2719 VAL 83 -0.2719 ILE 84 -0.2719 GLU 85 -1.2936 ARG 86 -1.4817 THR 87 -0.2719 PHE 88 -0.2719 HIS 89 0.7253 VAL 90 -0.2719 GLU 91 -1.2936 THR 92 -0.2719 GLU 94 -1.2936 GLU 95 -1.2936 ARG 96 -1.4817 GLU 97 -1.2936 GLU 98 -1.2936 TRP 99 -0.2719 THR 100 -0.2719 THR 101 -0.2719 ALA 102 -0.2719 ILE 103 -0.2719 GLN 104 -0.2719 THR 105 -0.2719 VAL 106 -0.2719 ALA 107 -0.2719 ASP 108 -1.2936 GLY 109 -0.2719 LEU 110 -0.2719 LYS 111 0.7253 LYS 112 0.7253 GLN 113 -0.2719 GLU 114 -1.2936 GLU 115 -1.2936 GLU 116 -1.2936 GLU 117 -1.2936 MET 118 -0.2719 ASP 119 -1.2936 PHE 120 -0.2719 ARG 121 -1.4817 SER 122 -0.6994 GLY 123 -0.2719 SER 124 -0.6994 SER 126 -0.6994 ASP 127 -1.2936 ASN 128 -0.2719 SER 129 -0.6994 GLY 130 -0.2719 ALA 131 -0.2719 GLU 132 -1.2936 GLU 133 -1.2936 MET 134 -0.2719 GLU 135 -1.2936 VAL 136 -0.2719 SER 137 -0.6994 LEU 138 -0.2719 ALA 139 -0.2719 LYS 140 0.7253 LYS 142 0.7253 HIS 143 0.7253 ARG 144 -1.4817 VAL 145 -0.2719 THR 146 -0.2719 MET 147 -0.2719 ASN 148 -0.2719 GLU 149 -1.2936 PHE 150 -0.2719 GLU 151 -1.2936 TYR 152 -0.2719 LEU 153 -0.2719 LYS 154 0.7253 LEU 155 -0.2719 LEU 156 -0.2719 GLY 157 -0.2719 LYS 158 0.7253 GLY 159 -0.2719 THR 160 -0.2719 PHE 161 -0.2719 GLY 162 -0.2719 LYS 163 0.7253 VAL 164 -0.2719 ILE 165 -0.2719 LEU 166 -0.2719 VAL 167 -0.2719 LYS 168 0.7253 GLU 169 -1.2936 LYS 170 0.7253 ALA 171 -0.2719 THR 172 -0.2719 GLY 173 -0.2719 ARG 174 -1.4817 TYR 175 -0.2719 TYR 176 -0.2719 ALA 177 -0.2719 MET 178 -0.2719 LYS 179 0.7253 ILE 180 -0.2719 LEU 181 -0.2719 LYS 182 0.7253 LYS 183 0.7253 GLU 184 -1.2936 VAL 185 -0.2719 ILE 186 -0.2719 VAL 187 -0.2719 ALA 188 -0.2719 LYS 189 0.7253 ASP 190 -1.2936 GLU 191 -1.2936 VAL 192 -0.2719 ALA 193 -0.2719 HIS 194 0.7253 THR 195 -0.2719 LEU 196 -0.2719 THR 197 -0.2719 GLU 198 -1.2936 ASN 199 -0.2719 ARG 200 -1.4817 VAL 201 -0.2719 LEU 202 -0.2719 GLN 203 -0.2719 ASN 204 -0.2719 SER 205 -0.6994 ARG 206 -1.4817 HIS 207 0.7253 PHE 209 -0.2719 LEU 210 -0.2719 THR 211 -0.2719 ALA 212 -0.2719 LEU 213 -0.2719 LYS 214 0.7253 TYR 215 -0.2719 SER 216 -0.6994 PHE 217 -0.2719 GLN 218 -0.2719 THR 219 -0.2719 HIS 220 0.7253 ASP 221 -1.2936 ARG 222 -1.4817 LEU 223 -0.2719 CYS 224 -1.2719 PHE 225 -0.2719 VAL 226 -0.2719 MET 227 -0.2719 GLU 228 -1.2936 TYR 229 -0.2719 ALA 230 -0.2719 ASN 231 -0.2719 GLY 232 -0.2719 GLY 233 -0.2719 GLU 234 -1.2936 LEU 235 -0.2719 PHE 236 -0.2719 PHE 237 -0.2719 HIS 238 0.7253 LEU 239 -0.2719 SER 240 -0.6994 ARG 241 -1.4817 GLU 242 -1.2936 ARG 243 -1.4817 VAL 244 -0.2719 PHE 245 -0.2719 SER 246 -0.6994 GLU 247 -1.2936 ASP 248 -1.2936 ARG 249 -1.4817 ALA 250 -0.2719 ARG 251 -1.4817 PHE 252 -0.2719 TYR 253 -0.2719 GLY 254 -0.2719 ALA 255 -0.2719 GLU 256 -1.2936 ILE 257 -0.2719 VAL 258 -0.2719 SER 259 -0.6994 ALA 260 -0.2719 LEU 261 -0.2719 ASP 262 -1.2936 TYR 263 -0.2719 LEU 264 -0.2719 HIS 265 0.7253 SER 266 -0.6994 GLU 267 -1.2936 LYS 268 0.7253 ASN 269 -0.2719 VAL 270 -0.2719 VAL 271 -0.2719 TYR 272 -0.2719 ARG 273 -1.4817 ASP 274 -1.2936 LEU 275 -0.2719 LYS 276 0.7253 LEU 277 -0.2719 GLU 278 -1.2936 ASN 279 -0.2719 LEU 280 -0.2719 MET 281 -0.2719 LEU 282 -0.2719 ASP 283 -1.2936 LYS 284 0.7253 ASP 285 -1.2936 GLY 286 -0.2719 HIS 287 0.7253 ILE 288 -0.2719 LYS 289 0.7253 ILE 290 -0.2719 THR 291 -0.2719 ASP 292 -1.2936 PHE 293 -0.2719 GLY 294 -0.2719 LEU 295 -0.2719 CYS 296 -1.2719 LYS 297 0.7253 GLU 298 -1.2936 GLY 299 -0.2719 ILE 300 -0.2719 LYS 301 0.7253 ASP 302 -1.2936 GLY 303 -0.2719 ALA 304 -0.2719 THR 305 -0.2719 MET 306 -0.2719 LYS 307 0.7253 THR 308 -0.2719 PHE 309 -0.2719 CYS 310 -1.2719 GLY 311 -0.2719 THR 312 -0.2719 GLU 314 -1.2936 TYR 315 -0.2719 LEU 316 -0.2719 ALA 317 -0.2719 GLU 319 -1.2936 VAL 320 -0.2719 LEU 321 -0.2719 GLU 322 -1.2936 ASP 323 -1.2936 ASN 324 -0.2719 ASP 325 -1.2936 TYR 326 -0.2719 GLY 327 -0.2719 ARG 328 -1.4817 ALA 329 -0.2719 VAL 330 -0.2719 ASP 331 -1.2936 TRP 332 -0.2719 TRP 333 -0.2719 GLY 334 -0.2719 LEU 335 -0.2719 GLY 336 -0.2719 VAL 337 -0.2719 VAL 338 -0.2719 MET 339 -0.2719 TYR 340 -0.2719 GLU 341 -1.2936 MET 342 -0.2719 MET 343 -0.2719 CYS 344 -1.2719 GLY 345 -0.2719 ARG 346 -1.4817 LEU 347 -0.2719 PHE 349 -0.2719 TYR 350 -0.2719 ASN 351 -0.2719 GLN 352 -0.2719 ASP 353 -1.2936 HIS 354 0.7253 GLU 355 -1.2936 LYS 356 0.7253 LEU 357 -0.2719 PHE 358 -0.2719 GLU 359 -1.2936 LEU 360 -0.2719 ILE 361 -0.2719 LEU 362 -0.2719 MET 363 -0.2719 GLU 364 -1.2936 GLU 365 -1.2936 ILE 366 -0.2719 ARG 367 -1.4817 PHE 368 -0.2719 ARG 370 -1.4817 THR 371 -0.2719 LEU 372 -0.2719 GLY 373 -0.2719 GLU 375 -1.2936 ALA 376 -0.2719 LYS 377 0.7253 SER 378 -0.6994 LEU 379 -0.2719 LEU 380 -0.2719 SER 381 -0.6994 GLY 382 -0.2719 LEU 383 -0.2719 LEU 384 -0.2719 LYS 385 0.7253 LYS 386 0.7253 ASP 387 -1.2936 LYS 389 0.7253 GLN 390 -0.2719 ARG 391 -1.4817 LEU 392 -0.2719 GLY 393 -0.2719 GLY 394 -0.2719 GLY 395 -0.2719 SER 396 -0.6994 GLU 397 -1.2936 ASP 398 -1.2936 ALA 399 -0.2719 LYS 400 0.7253 GLU 401 -1.2936 ILE 402 -0.2719 MET 403 -0.2719 GLN 404 -0.2719 HIS 405 0.7253 ARG 406 -1.4817 PHE 407 -0.2719 PHE 408 -0.2719 ALA 409 -0.2719 GLY 410 -0.2719 ILE 411 -0.2719 VAL 412 -0.2719 TRP 413 -0.2719 GLN 414 -0.2719 HIS 415 0.7253 VAL 416 -0.2719 TYR 417 -0.2719 GLU 418 -1.2936 LYS 419 0.7253 LYS 420 0.7253 LEU 421 -0.2719 SER 422 -0.6994 PHE 425 -0.2719 LYS 426 0.7253 GLN 428 -0.2719 VAL 429 -0.2719 THR 430 -0.2719 SER 431 -0.6994 GLU 432 -1.2936 THR 433 -0.2719 ASP 434 -1.2936 THR 435 -0.2719 ARG 436 -1.4817 TYR 437 -0.2719 PHE 438 -0.2719 ASP 439 -1.2936 GLU 440 -1.2936 GLU 441 -1.2936 PHE 442 -0.2719 THR 443 -0.2719 ALA 444 -0.2719 GLN 445 -0.2719 MET 446 -0.2719 ILE 447 -0.2719 THR 448 -0.2719 ILE 449 -0.2719 THR 450 -0.2719 ASP 453 -1.2936 GLN 454 -0.2719 ASP 455 -1.2936 ASP 456 -1.2936 SER 457 -0.6994 MET 458 -0.2719 GLU 459 -1.2936 CYS 460 -1.2719 VAL 461 -0.2719 ASP 462 -1.2936 SER 463 -0.6994 GLU 464 -1.2936 ARG 465 -1.4817 ARG 466 -1.4817 HIS 468 0.7253 PHE 469 -0.2719 GLN 471 -0.2719 PHE 472 -0.2719 SER 473 -0.6994 TYR 474 -0.2719 SER 475 -0.6994 ALA 476 -0.2719 SER 477 -0.6994 GLY 478 -0.2719 THR 479 -0.2719 ALA 480 0.296 Correct charges are unknown for 34 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log Model 0 (frame_1001000_model1.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Residues with incomplete side chains: ILE 6 ILE 19 ILE 36 ILE 74 ILE 75 ILE 84 ILE 103 ILE 165 ILE 180 ILE 186 ILE 257 ILE 288 ILE 290 ILE 300 ILE 361 ILE 366 ILE 402 ILE 411 ILE 447 ILE 449 Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True' ILE 6: phi -77.4, psi 129.6 trans Chi angles for ILE 6: -55.1 ILE 19: phi -78.2, psi 162.7 trans Chi angles for ILE 19: 76.7 ILE 36: phi -122.2, psi 128.4 trans Chi angles for ILE 36: -55.1 ILE 74: phi -136.5, psi 119.3 trans Chi angles for ILE 74: -40.3 ILE 75: phi -110.2, psi 156.4 trans Chi angles for ILE 75: 61.0 ILE 84: phi -109.4, psi 143.1 trans Chi angles for ILE 84: -158.3 ILE 103: phi -57.4, psi -37.7 trans Chi angles for ILE 103: -68.6 ILE 165: phi -131.8, psi 170.4 trans Chi angles for ILE 165: 60.6 ILE 180: phi -125.3, psi 108.1 trans Chi angles for ILE 180: -55.2 ILE 186: phi -93.0, psi 145.1 trans Chi angles for ILE 186: 56.5 ILE 257: phi -67.9, psi -35.9 trans Chi angles for ILE 257: -60.0 ILE 288: phi -112.5, psi 145.4 trans Chi angles for ILE 288: 62.8 ILE 290: phi -94.7, psi 123.7 trans Chi angles for ILE 290: -48.4 ILE 300: phi -73.4, psi 134.5 trans Chi angles for ILE 300: -66.4 ILE 361: phi -79.0, psi -30.9 trans Chi angles for ILE 361: -176.4 ILE 366: phi -127.0, psi 128.1 trans Chi angles for ILE 366: -63.8 ILE 402: phi -61.0, psi -39.2 trans Chi angles for ILE 402: -52.7 ILE 411: phi -89.8, psi 134.0 trans Chi angles for ILE 411: -65.6 ILE 447: phi -79.9, psi 129.4 trans Chi angles for ILE 447: -42.2 ILE 449: phi -73.8, psi 174.9 trans Chi angles for ILE 449: 72.4 Applying ILE rotamer (chi angles: -174.1 70.6) to ILE 84 Applying ILE rotamer (chi angles: -60.3 -60.9) to ILE 300 Applying ILE rotamer (chi angles: -57.1 -63.4) to ILE 36 Applying ILE rotamer (chi angles: -68.1 168.5) to ILE 402 Applying ILE rotamer (chi angles: -56.7 92.3) to ILE 74 Applying ILE rotamer (chi angles: 62.2 171.6) to ILE 165 Applying ILE rotamer (chi angles: -67.0 169.0) to ILE 257 Applying ILE rotamer (chi angles: 63.1 170.6) to ILE 19 Applying ILE rotamer (chi angles: -62.1 169.6) to ILE 411 Applying ILE rotamer (chi angles: -162.1 168.1) to ILE 361 Applying ILE rotamer (chi angles: 61.8 170.9) to ILE 186 Applying ILE rotamer (chi angles: 60.6 171.1) to ILE 288 Applying ILE rotamer (chi angles: 61.7 170.9) to ILE 75 Applying ILE rotamer (chi angles: -61.1 170.2) to ILE 290 Applying ILE rotamer (chi angles: -58.4 -66.3) to ILE 366 Applying ILE rotamer (chi angles: -68.1 168.5) to ILE 103 Applying ILE rotamer (chi angles: -58.8 172.2) to ILE 180 Applying ILE rotamer (chi angles: -62.9 169.7) to ILE 447 Applying ILE rotamer (chi angles: -62.9 169.7) to ILE 6 Applying ILE rotamer (chi angles: 62.3 170.5) to ILE 449 No SEQRES records for frame_1001000_model1.pdb (#0) principal chain; guessing terminii instead Chain-initial residues that are actual N terminii: MET 1 Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: ALA 480 Chain-final residues that are not actual C terminii: 389 hydrogen bonds Hydrogens added Charge model: AMBER ff99SB Non-standard atom names: LEU HN (LEU 12 HN, LEU 28 HN, LEU 29 HN + 38 others) MET HN2 (MET 1 HN2) ASN HN (ASN 31 HN, ASN 53 HN, ASN 54 HN + 10 others) GLY HN (GLY 10 HN, GLY 16 HN, GLY 33 HN + 27 others) SER HN (SER 2 HN, SER 56 HN, SER 122 HN + 20 others) SER HG1 (SER 2 HG1, SER 56 HG1, SER 122 HG1 + 20 others) ARG HC (ARG 15 HC, ARG 23 HC, ARG 25 HC + 27 others) MET HN3 (MET 1 HN3) ARG 3HC (ARG 15 3HC, ARG 23 3HC, ARG 25 3HC + 27 others) ARG 6HC (ARG 15 6HC, ARG 23 6HC, ARG 25 6HC + 27 others) ALA OT1 (ALA 480 OT1) ARG 4HC (ARG 15 4HC, ARG 23 4HC, ARG 25 4HC + 27 others) TYR HN (TYR 18 HN, TYR 26 HN, TYR 38 HN + 15 others) ILE HN (ILE 6 HN, ILE 19 HN, ILE 36 HN + 17 others) ARG HN (ARG 15 HN, ARG 23 HN, ARG 25 HN + 27 others) VAL HN (VAL 4 HN, VAL 7 HN, VAL 45 HN + 25 others) TRP HN (TRP 11 HN, TRP 22 HN, TRP 80 HN + 4 others) PHE HN (PHE 27 HN, PHE 35 HN, PHE 55 HN + 24 others) LYS HN (LYS 8 HN, LYS 14 HN, LYS 20 HN + 33 others) ARG 2HC (ARG 15 2HC, ARG 23 2HC, ARG 25 2HC + 27 others) ARG 1HC (ARG 15 1HC, ARG 23 1HC, ARG 25 1HC + 27 others) ASP HN (ASP 3 HN, ASP 32 HN, ASP 44 HN + 25 others) HIS HN (HIS 13 HN, HIS 89 HN, HIS 143 HN + 10 others) MET HN1 (MET 1 HN1) ARG 5HC (ARG 15 5HC, ARG 23 5HC, ARG 25 5HC + 27 others) ARG HH (ARG 15 HH, ARG 15 HH, ARG 15 HH + 117 others) CYS HG1 (CYS 60 HG1, CYS 77 HG1, CYS 224 HG1 + 4 others) ALA HN (ALA 5 HN, ALA 50 HN, ALA 58 HN + 22 others) GLU HN (GLU 9 HN, GLU 17 HN, GLU 40 HN + 46 others) MET HN (MET 63 HN, MET 118 HN, MET 134 HN + 12 others) GLN HN (GLN 43 HN, GLN 47 HN, GLN 59 HN + 14 others) THR HN (THR 21 HN, THR 34 HN, THR 65 HN + 27 others) ALA OT2 (ALA 480 OT2) Total charge for #0: -204.317 The following residues had non-integral charges: MET 1 0.4048 SER 2 -0.6994 ASP 3 -1.2936 VAL 4 -0.2719 ALA 5 -0.2719 ILE 6 -0.2719 VAL 7 -0.2719 LYS 8 0.7253 GLU 9 -1.2936 GLY 10 -0.2719 TRP 11 -0.2719 LEU 12 -0.2719 HIS 13 0.7253 LYS 14 0.7253 ARG 15 -1.4817 GLY 16 -0.2719 GLU 17 -1.2936 TYR 18 -0.2719 ILE 19 -0.2719 LYS 20 0.7253 THR 21 -0.2719 TRP 22 -0.2719 ARG 23 -1.4817 ARG 25 -1.4817 TYR 26 -0.2719 PHE 27 -0.2719 LEU 28 -0.2719 LEU 29 -0.2719 LYS 30 0.7253 ASN 31 -0.2719 ASP 32 -1.2936 GLY 33 -0.2719 THR 34 -0.2719 PHE 35 -0.2719 ILE 36 -0.2719 GLY 37 -0.2719 TYR 38 -0.2719 LYS 39 0.7253 GLU 40 -1.2936 ARG 41 -1.4817 GLN 43 -0.2719 ASP 44 -1.2936 VAL 45 -0.2719 ASP 46 -1.2936 GLN 47 -0.2719 ARG 48 -1.4817 GLU 49 -1.2936 ALA 50 -0.2719 LEU 52 -0.2719 ASN 53 -0.2719 ASN 54 -0.2719 PHE 55 -0.2719 SER 56 -0.6994 VAL 57 -0.2719 ALA 58 -0.2719 GLN 59 -0.2719 GLN 61 -0.2719 LEU 62 -0.2719 MET 63 -0.2719 LYS 64 0.7253 THR 65 -0.2719 GLU 66 -1.2936 ARG 67 -1.4817 ARG 69 -1.4817 ASN 71 -0.2719 THR 72 -0.2719 PHE 73 -0.2719 ILE 74 -0.2719 ILE 75 -0.2719 ARG 76 -1.4817 LEU 78 -0.2719 GLN 79 -0.2719 TRP 80 -0.2719 THR 81 -0.2719 THR 82 -0.2719 VAL 83 -0.2719 ILE 84 -0.2719 GLU 85 -1.2936 ARG 86 -1.4817 THR 87 -0.2719 PHE 88 -0.2719 HIS 89 0.7253 VAL 90 -0.2719 GLU 91 -1.2936 THR 92 -0.2719 GLU 94 -1.2936 GLU 95 -1.2936 ARG 96 -1.4817 GLU 97 -1.2936 GLU 98 -1.2936 TRP 99 -0.2719 THR 100 -0.2719 THR 101 -0.2719 ALA 102 -0.2719 ILE 103 -0.2719 GLN 104 -0.2719 THR 105 -0.2719 VAL 106 -0.2719 ALA 107 -0.2719 ASP 108 -1.2936 GLY 109 -0.2719 LEU 110 -0.2719 LYS 111 0.7253 LYS 112 0.7253 GLN 113 -0.2719 GLU 114 -1.2936 GLU 115 -1.2936 GLU 116 -1.2936 GLU 117 -1.2936 MET 118 -0.2719 ASP 119 -1.2936 PHE 120 -0.2719 ARG 121 -1.4817 SER 122 -0.6994 GLY 123 -0.2719 SER 124 -0.6994 SER 126 -0.6994 ASP 127 -1.2936 ASN 128 -0.2719 SER 129 -0.6994 GLY 130 -0.2719 ALA 131 -0.2719 GLU 132 -1.2936 GLU 133 -1.2936 MET 134 -0.2719 GLU 135 -1.2936 VAL 136 -0.2719 SER 137 -0.6994 LEU 138 -0.2719 ALA 139 -0.2719 LYS 140 0.7253 LYS 142 0.7253 HIS 143 0.7253 ARG 144 -1.4817 VAL 145 -0.2719 THR 146 -0.2719 MET 147 -0.2719 ASN 148 -0.2719 GLU 149 -1.2936 PHE 150 -0.2719 GLU 151 -1.2936 TYR 152 -0.2719 LEU 153 -0.2719 LYS 154 0.7253 LEU 155 -0.2719 LEU 156 -0.2719 GLY 157 -0.2719 LYS 158 0.7253 GLY 159 -0.2719 THR 160 -0.2719 PHE 161 -0.2719 GLY 162 -0.2719 LYS 163 0.7253 VAL 164 -0.2719 ILE 165 -0.2719 LEU 166 -0.2719 VAL 167 -0.2719 LYS 168 0.7253 GLU 169 -1.2936 LYS 170 0.7253 ALA 171 -0.2719 THR 172 -0.2719 GLY 173 -0.2719 ARG 174 -1.4817 TYR 175 -0.2719 TYR 176 -0.2719 ALA 177 -0.2719 MET 178 -0.2719 LYS 179 0.7253 ILE 180 -0.2719 LEU 181 -0.2719 LYS 182 0.7253 LYS 183 0.7253 GLU 184 -1.2936 VAL 185 -0.2719 ILE 186 -0.2719 VAL 187 -0.2719 ALA 188 -0.2719 LYS 189 0.7253 ASP 190 -1.2936 GLU 191 -1.2936 VAL 192 -0.2719 ALA 193 -0.2719 HIS 194 0.7253 THR 195 -0.2719 LEU 196 -0.2719 THR 197 -0.2719 GLU 198 -1.2936 ASN 199 -0.2719 ARG 200 -1.4817 VAL 201 -0.2719 LEU 202 -0.2719 GLN 203 -0.2719 ASN 204 -0.2719 SER 205 -0.6994 ARG 206 -1.4817 HIS 207 0.7253 PHE 209 -0.2719 LEU 210 -0.2719 THR 211 -0.2719 ALA 212 -0.2719 LEU 213 -0.2719 LYS 214 0.7253 TYR 215 -0.2719 SER 216 -0.6994 PHE 217 -0.2719 GLN 218 -0.2719 THR 219 -0.2719 HIS 220 0.7253 ASP 221 -1.2936 ARG 222 -1.4817 LEU 223 -0.2719 PHE 225 -0.2719 VAL 226 -0.2719 MET 227 -0.2719 GLU 228 -1.2936 TYR 229 -0.2719 ALA 230 -0.2719 ASN 231 -0.2719 GLY 232 -0.2719 GLY 233 -0.2719 GLU 234 -1.2936 LEU 235 -0.2719 PHE 236 -0.2719 PHE 237 -0.2719 HIS 238 0.7253 LEU 239 -0.2719 SER 240 -0.6994 ARG 241 -1.4817 GLU 242 -1.2936 ARG 243 -1.4817 VAL 244 -0.2719 PHE 245 -0.2719 SER 246 -0.6994 GLU 247 -1.2936 ASP 248 -1.2936 ARG 249 -1.4817 ALA 250 -0.2719 ARG 251 -1.4817 PHE 252 -0.2719 TYR 253 -0.2719 GLY 254 -0.2719 ALA 255 -0.2719 GLU 256 -1.2936 ILE 257 -0.2719 VAL 258 -0.2719 SER 259 -0.6994 ALA 260 -0.2719 LEU 261 -0.2719 ASP 262 -1.2936 TYR 263 -0.2719 LEU 264 -0.2719 HIS 265 0.7253 SER 266 -0.6994 GLU 267 -1.2936 LYS 268 0.7253 ASN 269 -0.2719 VAL 270 -0.2719 VAL 271 -0.2719 TYR 272 -0.2719 ARG 273 -1.4817 ASP 274 -1.2936 LEU 275 -0.2719 LYS 276 0.7253 LEU 277 -0.2719 GLU 278 -1.2936 ASN 279 -0.2719 LEU 280 -0.2719 MET 281 -0.2719 LEU 282 -0.2719 ASP 283 -1.2936 LYS 284 0.7253 ASP 285 -1.2936 GLY 286 -0.2719 HIS 287 0.7253 ILE 288 -0.2719 LYS 289 0.7253 ILE 290 -0.2719 THR 291 -0.2719 ASP 292 -1.2936 PHE 293 -0.2719 GLY 294 -0.2719 LEU 295 -0.2719 LYS 297 0.7253 GLU 298 -1.2936 GLY 299 -0.2719 ILE 300 -0.2719 LYS 301 0.7253 ASP 302 -1.2936 GLY 303 -0.2719 ALA 304 -0.2719 THR 305 -0.2719 MET 306 -0.2719 LYS 307 0.7253 THR 308 -0.2719 PHE 309 -0.2719 GLY 311 -0.2719 THR 312 -0.2719 GLU 314 -1.2936 TYR 315 -0.2719 LEU 316 -0.2719 ALA 317 -0.2719 GLU 319 -1.2936 VAL 320 -0.2719 LEU 321 -0.2719 GLU 322 -1.2936 ASP 323 -1.2936 ASN 324 -0.2719 ASP 325 -1.2936 TYR 326 -0.2719 GLY 327 -0.2719 ARG 328 -1.4817 ALA 329 -0.2719 VAL 330 -0.2719 ASP 331 -1.2936 TRP 332 -0.2719 TRP 333 -0.2719 GLY 334 -0.2719 LEU 335 -0.2719 GLY 336 -0.2719 VAL 337 -0.2719 VAL 338 -0.2719 MET 339 -0.2719 TYR 340 -0.2719 GLU 341 -1.2936 MET 342 -0.2719 MET 343 -0.2719 GLY 345 -0.2719 ARG 346 -1.4817 LEU 347 -0.2719 PHE 349 -0.2719 TYR 350 -0.2719 ASN 351 -0.2719 GLN 352 -0.2719 ASP 353 -1.2936 HIS 354 0.7253 GLU 355 -1.2936 LYS 356 0.7253 LEU 357 -0.2719 PHE 358 -0.2719 GLU 359 -1.2936 LEU 360 -0.2719 ILE 361 -0.2719 LEU 362 -0.2719 MET 363 -0.2719 GLU 364 -1.2936 GLU 365 -1.2936 ILE 366 -0.2719 ARG 367 -1.4817 PHE 368 -0.2719 ARG 370 -1.4817 THR 371 -0.2719 LEU 372 -0.2719 GLY 373 -0.2719 GLU 375 -1.2936 ALA 376 -0.2719 LYS 377 0.7253 SER 378 -0.6994 LEU 379 -0.2719 LEU 380 -0.2719 SER 381 -0.6994 GLY 382 -0.2719 LEU 383 -0.2719 LEU 384 -0.2719 LYS 385 0.7253 LYS 386 0.7253 ASP 387 -1.2936 LYS 389 0.7253 GLN 390 -0.2719 ARG 391 -1.4817 LEU 392 -0.2719 GLY 393 -0.2719 GLY 394 -0.2719 GLY 395 -0.2719 SER 396 -0.6994 GLU 397 -1.2936 ASP 398 -1.2936 ALA 399 -0.2719 LYS 400 0.7253 GLU 401 -1.2936 ILE 402 -0.2719 MET 403 -0.2719 GLN 404 -0.2719 HIS 405 0.7253 ARG 406 -1.4817 PHE 407 -0.2719 PHE 408 -0.2719 ALA 409 -0.2719 GLY 410 -0.2719 ILE 411 -0.2719 VAL 412 -0.2719 TRP 413 -0.2719 GLN 414 -0.2719 HIS 415 0.7253 VAL 416 -0.2719 TYR 417 -0.2719 GLU 418 -1.2936 LYS 419 0.7253 LYS 420 0.7253 LEU 421 -0.2719 SER 422 -0.6994 PHE 425 -0.2719 LYS 426 0.7253 GLN 428 -0.2719 VAL 429 -0.2719 THR 430 -0.2719 SER 431 -0.6994 GLU 432 -1.2936 THR 433 -0.2719 ASP 434 -1.2936 THR 435 -0.2719 ARG 436 -1.4817 TYR 437 -0.2719 PHE 438 -0.2719 ASP 439 -1.2936 GLU 440 -1.2936 GLU 441 -1.2936 PHE 442 -0.2719 THR 443 -0.2719 ALA 444 -0.2719 GLN 445 -0.2719 MET 446 -0.2719 ILE 447 -0.2719 THR 448 -0.2719 ILE 449 -0.2719 THR 450 -0.2719 ASP 453 -1.2936 GLN 454 -0.2719 ASP 455 -1.2936 ASP 456 -1.2936 SER 457 -0.6994 MET 458 -0.2719 GLU 459 -1.2936 VAL 461 -0.2719 ASP 462 -1.2936 SER 463 -0.6994 GLU 464 -1.2936 ARG 465 -1.4817 ARG 466 -1.4817 HIS 468 0.7253 PHE 469 -0.2719 GLN 471 -0.2719 PHE 472 -0.2719 SER 473 -0.6994 TYR 474 -0.2719 SER 475 -0.6994 ALA 476 -0.2719 SER 477 -0.6994 GLY 478 -0.2719 THR 479 -0.2719 ALA 480 0.296 Correct charges are unknown for 33 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log Model 0 (frame_1001000_model1.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. The following problems occurred while reading PDB file for frame_1001000.pdb warning: Ignored bad PDB record found on line 1 warning: Ignored bad PDB record found on line 3 Model 0 (frame_1001000.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Residues with incomplete side chains: ILE 6 ILE 19 ILE 36 ILE 74 ILE 75 ILE 84 ILE 103 ILE 165 ILE 180 ILE 186 ILE 257 ILE 288 ILE 290 ILE 300 ILE 361 ILE 366 ILE 402 ILE 411 ILE 447 ILE 449 Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True' ILE 6: phi -77.4, psi 129.6 trans Chi angles for ILE 6: -55.1 ILE 19: phi -78.2, psi 162.7 trans Chi angles for ILE 19: 76.7 ILE 36: phi -122.2, psi 128.4 trans Chi angles for ILE 36: -55.1 ILE 74: phi -136.5, psi 119.3 trans Chi angles for ILE 74: -40.3 ILE 75: phi -110.2, psi 156.4 trans Chi angles for ILE 75: 61.0 ILE 84: phi -109.4, psi 143.1 trans Chi angles for ILE 84: -158.3 ILE 103: phi -57.4, psi -37.7 trans Chi angles for ILE 103: -68.6 ILE 165: phi -131.8, psi 170.4 trans Chi angles for ILE 165: 60.6 ILE 180: phi -125.3, psi 108.1 trans Chi angles for ILE 180: -55.2 ILE 186: phi -93.0, psi 145.1 trans Chi angles for ILE 186: 56.5 ILE 257: phi -67.9, psi -35.9 trans Chi angles for ILE 257: -60.0 ILE 288: phi -112.5, psi 145.4 trans Chi angles for ILE 288: 62.8 ILE 290: phi -94.7, psi 123.7 trans Chi angles for ILE 290: -48.4 ILE 300: phi -73.4, psi 134.5 trans Chi angles for ILE 300: -66.4 ILE 361: phi -79.0, psi -30.9 trans Chi angles for ILE 361: -176.4 ILE 366: phi -127.0, psi 128.1 trans Chi angles for ILE 366: -63.8 ILE 402: phi -61.0, psi -39.2 trans Chi angles for ILE 402: -52.7 ILE 411: phi -89.8, psi 134.0 trans Chi angles for ILE 411: -65.6 ILE 447: phi -79.9, psi 129.4 trans Chi angles for ILE 447: -42.2 ILE 449: phi -73.8, psi 174.9 trans Chi angles for ILE 449: 72.4 Applying ILE rotamer (chi angles: 62.2 171.6) to ILE 165 Applying ILE rotamer (chi angles: -67.0 169.0) to ILE 257 Applying ILE rotamer (chi angles: 63.1 170.6) to ILE 19 Applying ILE rotamer (chi angles: -60.3 -60.9) to ILE 300 Applying ILE rotamer (chi angles: -174.1 70.6) to ILE 84 Applying ILE rotamer (chi angles: -57.1 -63.4) to ILE 36 Applying ILE rotamer (chi angles: -56.7 92.3) to ILE 74 Applying ILE rotamer (chi angles: 60.6 171.1) to ILE 288 Applying ILE rotamer (chi angles: -58.4 -66.3) to ILE 366 Applying ILE rotamer (chi angles: -68.1 168.5) to ILE 103 Applying ILE rotamer (chi angles: -62.1 169.6) to ILE 411 Applying ILE rotamer (chi angles: -58.8 172.2) to ILE 180 Applying ILE rotamer (chi angles: -61.1 170.2) to ILE 290 Applying ILE rotamer (chi angles: -62.9 169.7) to ILE 447 Applying ILE rotamer (chi angles: 62.3 170.5) to ILE 449 Applying ILE rotamer (chi angles: -68.1 168.5) to ILE 402 Applying ILE rotamer (chi angles: -162.1 168.1) to ILE 361 Applying ILE rotamer (chi angles: 61.8 170.9) to ILE 186 Applying ILE rotamer (chi angles: -62.9 169.7) to ILE 6 Applying ILE rotamer (chi angles: 61.7 170.9) to ILE 75 No SEQRES records for frame_1001000.pdb (#0) principal chain; guessing terminii instead Chain-initial residues that are actual N terminii: MET 1 Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: ALA 480 Chain-final residues that are not actual C terminii: 395 hydrogen bonds Hydrogens added Charge model: AMBER ff14SB Non-standard atom names: LEU HN (LEU 12 HN, LEU 28 HN, LEU 29 HN + 38 others) ASN HN (ASN 31 HN, ASN 53 HN, ASN 54 HN + 10 others) GLY HN (GLY 10 HN, GLY 16 HN, GLY 33 HN + 27 others) SER HN (SER 2 HN, SER 56 HN, SER 122 HN + 20 others) SER HG1 (SER 2 HG1, SER 56 HG1, SER 122 HG1 + 20 others) ALA OT1 (ALA 480 OT1) TYR HN (TYR 18 HN, TYR 26 HN, TYR 38 HN + 15 others) ILE HN (ILE 6 HN, ILE 19 HN, ILE 36 HN + 17 others) ARG HN (ARG 15 HN, ARG 23 HN, ARG 25 HN + 27 others) VAL HN (VAL 4 HN, VAL 7 HN, VAL 45 HN + 25 others) TRP HN (TRP 11 HN, TRP 22 HN, TRP 80 HN + 4 others) PHE HN (PHE 27 HN, PHE 35 HN, PHE 55 HN + 24 others) LYS HN (LYS 8 HN, LYS 14 HN, LYS 20 HN + 33 others) ASP HN (ASP 3 HN, ASP 32 HN, ASP 44 HN + 25 others) HIS HN (HIS 13 HN, HIS 89 HN, HIS 143 HN + 10 others) CYS HG1 (CYS 60 HG1, CYS 77 HG1, CYS 224 HG1 + 4 others) ALA HN (ALA 5 HN, ALA 50 HN, ALA 58 HN + 22 others) GLU HN (GLU 9 HN, GLU 17 HN, GLU 40 HN + 46 others) CYS HN (CYS 60 HN, CYS 77 HN, CYS 224 HN + 4 others) MET HN (MET 63 HN, MET 118 HN, MET 134 HN + 12 others) GLN HN (GLN 43 HN, GLN 47 HN, GLN 59 HN + 14 others) THR HN (THR 21 HN, THR 34 HN, THR 65 HN + 27 others) ALA OT2 (ALA 480 OT2) Total charge for #0: -152.379 The following residues had non-integral charges: SER 2 -0.6994 ASP 3 -1.2936 VAL 4 -0.2719 ALA 5 -0.2719 ILE 6 -0.2719 VAL 7 -0.2719 LYS 8 0.7253 GLU 9 -1.2936 GLY 10 -0.2719 TRP 11 -0.2719 LEU 12 -0.2719 HIS 13 -0.2719 LYS 14 0.7253 ARG 15 0.7253 GLY 16 -0.2719 GLU 17 -1.2936 TYR 18 -0.2719 ILE 19 -0.2719 LYS 20 0.7253 THR 21 -0.2719 TRP 22 -0.2719 ARG 23 0.7253 ARG 25 0.7253 TYR 26 -0.2719 PHE 27 -0.2719 LEU 28 -0.2719 LEU 29 -0.2719 LYS 30 0.7253 ASN 31 -0.2719 ASP 32 -1.2936 GLY 33 -0.2719 THR 34 -0.2719 PHE 35 -0.2719 ILE 36 -0.2719 GLY 37 -0.2719 TYR 38 -0.2719 LYS 39 0.7253 GLU 40 -1.2936 ARG 41 0.7253 GLN 43 -0.2719 ASP 44 -1.2936 VAL 45 -0.2719 ASP 46 -1.2936 GLN 47 -0.2719 ARG 48 0.7253 GLU 49 -1.2936 ALA 50 -0.2719 LEU 52 -0.2719 ASN 53 -0.2719 ASN 54 -0.2719 PHE 55 -0.2719 SER 56 -0.6994 VAL 57 -0.2719 ALA 58 -0.2719 GLN 59 -0.2719 CYS 60 -1.2719 GLN 61 -0.2719 LEU 62 -0.2719 MET 63 -0.2719 LYS 64 0.7253 THR 65 -0.2719 GLU 66 -1.2936 ARG 67 0.7253 ARG 69 0.7253 ASN 71 -0.2719 THR 72 -0.2719 PHE 73 -0.2719 ILE 74 -0.2719 ILE 75 -0.2719 ARG 76 0.7253 CYS 77 -1.2719 LEU 78 -0.2719 GLN 79 -0.2719 TRP 80 -0.2719 THR 81 -0.2719 THR 82 -0.2719 VAL 83 -0.2719 ILE 84 -0.2719 GLU 85 -1.2936 ARG 86 0.7253 THR 87 -0.2719 PHE 88 -0.2719 HIS 89 -0.2719 VAL 90 -0.2719 GLU 91 -1.2936 THR 92 -0.2719 GLU 94 -1.2936 GLU 95 -1.2936 ARG 96 0.7253 GLU 97 -1.2936 GLU 98 -1.2936 TRP 99 -0.2719 THR 100 -0.2719 THR 101 -0.2719 ALA 102 -0.2719 ILE 103 -0.2719 GLN 104 -0.2719 THR 105 -0.2719 VAL 106 -0.2719 ALA 107 -0.2719 ASP 108 -1.2936 GLY 109 -0.2719 LEU 110 -0.2719 LYS 111 0.7253 LYS 112 0.7253 GLN 113 -0.2719 GLU 114 -1.2936 GLU 115 -1.2936 GLU 116 -1.2936 GLU 117 -1.2936 MET 118 -0.2719 ASP 119 -1.2936 PHE 120 -0.2719 ARG 121 0.7253 SER 122 -0.6994 GLY 123 -0.2719 SER 124 -0.6994 SER 126 -0.6994 ASP 127 -1.2936 ASN 128 -0.2719 SER 129 -0.6994 GLY 130 -0.2719 ALA 131 -0.2719 GLU 132 -1.2936 GLU 133 -1.2936 MET 134 -0.2719 GLU 135 -1.2936 VAL 136 -0.2719 SER 137 -0.6994 LEU 138 -0.2719 ALA 139 -0.2719 LYS 140 0.7253 LYS 142 0.7253 HIS 143 -0.2719 ARG 144 0.7253 VAL 145 -0.2719 THR 146 -0.2719 MET 147 -0.2719 ASN 148 -0.2719 GLU 149 -1.2936 PHE 150 -0.2719 GLU 151 -1.2936 TYR 152 -0.2719 LEU 153 -0.2719 LYS 154 0.7253 LEU 155 -0.2719 LEU 156 -0.2719 GLY 157 -0.2719 LYS 158 0.7253 GLY 159 -0.2719 THR 160 -0.2719 PHE 161 -0.2719 GLY 162 -0.2719 LYS 163 0.7253 VAL 164 -0.2719 ILE 165 -0.2719 LEU 166 -0.2719 VAL 167 -0.2719 LYS 168 0.7253 GLU 169 -1.2936 LYS 170 0.7253 ALA 171 -0.2719 THR 172 -0.2719 GLY 173 -0.2719 ARG 174 0.7253 TYR 175 -0.2719 TYR 176 -0.2719 ALA 177 -0.2719 MET 178 -0.2719 LYS 179 0.7253 ILE 180 -0.2719 LEU 181 -0.2719 LYS 182 0.7253 LYS 183 0.7253 GLU 184 -1.2936 VAL 185 -0.2719 ILE 186 -0.2719 VAL 187 -0.2719 ALA 188 -0.2719 LYS 189 0.7253 ASP 190 -1.2936 GLU 191 -1.2936 VAL 192 -0.2719 ALA 193 -0.2719 HIS 194 -0.2719 THR 195 -0.2719 LEU 196 -0.2719 THR 197 -0.2719 GLU 198 -1.2936 ASN 199 -0.2719 ARG 200 0.7253 VAL 201 -0.2719 LEU 202 -0.2719 GLN 203 -0.2719 ASN 204 -0.2719 SER 205 -0.6994 ARG 206 0.7253 HIS 207 -0.2719 PHE 209 -0.2719 LEU 210 -0.2719 THR 211 -0.2719 ALA 212 -0.2719 LEU 213 -0.2719 LYS 214 0.7253 TYR 215 -0.2719 SER 216 -0.6994 PHE 217 -0.2719 GLN 218 -0.2719 THR 219 -0.2719 HIS 220 -0.2719 ASP 221 -1.2936 ARG 222 0.7253 LEU 223 -0.2719 CYS 224 -1.2719 PHE 225 -0.2719 VAL 226 -0.2719 MET 227 -0.2719 GLU 228 -1.2936 TYR 229 -0.2719 ALA 230 -0.2719 ASN 231 -0.2719 GLY 232 -0.2719 GLY 233 -0.2719 GLU 234 -1.2936 LEU 235 -0.2719 PHE 236 -0.2719 PHE 237 -0.2719 HIS 238 -0.2719 LEU 239 -0.2719 SER 240 -0.6994 ARG 241 0.7253 GLU 242 -1.2936 ARG 243 0.7253 VAL 244 -0.2719 PHE 245 -0.2719 SER 246 -0.6994 GLU 247 -1.2936 ASP 248 -1.2936 ARG 249 0.7253 ALA 250 -0.2719 ARG 251 0.7253 PHE 252 -0.2719 TYR 253 -0.2719 GLY 254 -0.2719 ALA 255 -0.2719 GLU 256 -1.2936 ILE 257 -0.2719 VAL 258 -0.2719 SER 259 -0.6994 ALA 260 -0.2719 LEU 261 -0.2719 ASP 262 -1.2936 TYR 263 -0.2719 LEU 264 -0.2719 HIS 265 -0.2719 SER 266 -0.6994 GLU 267 -1.2936 LYS 268 0.7253 ASN 269 -0.2719 VAL 270 -0.2719 VAL 271 -0.2719 TYR 272 -0.2719 ARG 273 0.7253 ASP 274 -1.2936 LEU 275 -0.2719 LYS 276 0.7253 LEU 277 -0.2719 GLU 278 -1.2936 ASN 279 -0.2719 LEU 280 -0.2719 MET 281 -0.2719 LEU 282 -0.2719 ASP 283 -1.2936 LYS 284 0.7253 ASP 285 -1.2936 GLY 286 -0.2719 HIS 287 -0.2719 ILE 288 -0.2719 LYS 289 0.7253 ILE 290 -0.2719 THR 291 -0.2719 ASP 292 -1.2936 PHE 293 -0.2719 GLY 294 -0.2719 LEU 295 -0.2719 CYS 296 -1.2719 LYS 297 0.7253 GLU 298 -1.2936 GLY 299 -0.2719 ILE 300 -0.2719 LYS 301 0.7253 ASP 302 -1.2936 GLY 303 -0.2719 ALA 304 -0.2719 THR 305 -0.2719 MET 306 -0.2719 LYS 307 0.7253 THR 308 -0.2719 PHE 309 -0.2719 CYS 310 -1.2719 GLY 311 -0.2719 THR 312 -0.2719 GLU 314 -1.2936 TYR 315 -0.2719 LEU 316 -0.2719 ALA 317 -0.2719 GLU 319 -1.2936 VAL 320 -0.2719 LEU 321 -0.2719 GLU 322 -1.2936 ASP 323 -1.2936 ASN 324 -0.2719 ASP 325 -1.2936 TYR 326 -0.2719 GLY 327 -0.2719 ARG 328 0.7253 ALA 329 -0.2719 VAL 330 -0.2719 ASP 331 -1.2936 TRP 332 -0.2719 TRP 333 -0.2719 GLY 334 -0.2719 LEU 335 -0.2719 GLY 336 -0.2719 VAL 337 -0.2719 VAL 338 -0.2719 MET 339 -0.2719 TYR 340 -0.2719 GLU 341 -1.2936 MET 342 -0.2719 MET 343 -0.2719 CYS 344 -1.2719 GLY 345 -0.2719 ARG 346 0.7253 LEU 347 -0.2719 PHE 349 -0.2719 TYR 350 -0.2719 ASN 351 -0.2719 GLN 352 -0.2719 ASP 353 -1.2936 HIS 354 -0.2719 GLU 355 -1.2936 LYS 356 0.7253 LEU 357 -0.2719 PHE 358 -0.2719 GLU 359 -1.2936 LEU 360 -0.2719 ILE 361 -0.2719 LEU 362 -0.2719 MET 363 -0.2719 GLU 364 -1.2936 GLU 365 -1.2936 ILE 366 -0.2719 ARG 367 0.7253 PHE 368 -0.2719 ARG 370 0.7253 THR 371 -0.2719 LEU 372 -0.2719 GLY 373 -0.2719 GLU 375 -1.2936 ALA 376 -0.2719 LYS 377 0.7253 SER 378 -0.6994 LEU 379 -0.2719 LEU 380 -0.2719 SER 381 -0.6994 GLY 382 -0.2719 LEU 383 -0.2719 LEU 384 -0.2719 LYS 385 0.7253 LYS 386 0.7253 ASP 387 -1.2936 LYS 389 0.7253 GLN 390 -0.2719 ARG 391 0.7253 LEU 392 -0.2719 GLY 393 -0.2719 GLY 394 -0.2719 GLY 395 -0.2719 SER 396 -0.6994 GLU 397 -1.2936 ASP 398 -1.2936 ALA 399 -0.2719 LYS 400 0.7253 GLU 401 -1.2936 ILE 402 -0.2719 MET 403 -0.2719 GLN 404 -0.2719 HIS 405 -0.2719 ARG 406 0.7253 PHE 407 -0.2719 PHE 408 -0.2719 ALA 409 -0.2719 GLY 410 -0.2719 ILE 411 -0.2719 VAL 412 -0.2719 TRP 413 -0.2719 GLN 414 -0.2719 HIS 415 -0.2719 VAL 416 -0.2719 TYR 417 -0.2719 GLU 418 -1.2936 LYS 419 0.7253 LYS 420 0.7253 LEU 421 -0.2719 SER 422 -0.6994 PHE 425 -0.2719 LYS 426 0.7253 GLN 428 -0.2719 VAL 429 -0.2719 THR 430 -0.2719 SER 431 -0.6994 GLU 432 -1.2936 THR 433 -0.2719 ASP 434 -1.2936 THR 435 -0.2719 ARG 436 0.7253 TYR 437 -0.2719 PHE 438 -0.2719 ASP 439 -1.2936 GLU 440 -1.2936 GLU 441 -1.2936 PHE 442 -0.2719 THR 443 -0.2719 ALA 444 -0.2719 GLN 445 -0.2719 MET 446 -0.2719 ILE 447 -0.2719 THR 448 -0.2719 ILE 449 -0.2719 THR 450 -0.2719 ASP 453 -1.2936 GLN 454 -0.2719 ASP 455 -1.2936 ASP 456 -1.2936 SER 457 -0.6994 MET 458 -0.2719 GLU 459 -1.2936 CYS 460 -1.2719 VAL 461 -0.2719 ASP 462 -1.2936 SER 463 -0.6994 GLU 464 -1.2936 ARG 465 0.7253 ARG 466 0.7253 HIS 468 -0.2719 PHE 469 -0.2719 GLN 471 -0.2719 PHE 472 -0.2719 SER 473 -0.6994 TYR 474 -0.2719 SER 475 -0.6994 ALA 476 -0.2719 SER 477 -0.6994 GLY 478 -0.2719 THR 479 -0.2719 ALA 480 0.296 Correct charges are unknown for 23 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log No incomplete side chains No SEQRES records for frame_1001000.pdb (#0) principal chain; guessing terminii instead Chain-initial residues that are actual N terminii: MET 1 Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: ALA 480 Chain-final residues that are not actual C terminii: 395 hydrogen bonds Hydrogens added Charge model: AMBER ff14SB Non-standard atom names: LEU HN (LEU 12 HN, LEU 28 HN, LEU 29 HN + 38 others) ASN HN (ASN 31 HN, ASN 53 HN, ASN 54 HN + 10 others) GLY HN (GLY 10 HN, GLY 16 HN, GLY 33 HN + 27 others) SER HN (SER 2 HN, SER 56 HN, SER 122 HN + 20 others) SER HG1 (SER 2 HG1, SER 56 HG1, SER 122 HG1 + 20 others) ALA OT1 (ALA 480 OT1) TYR HN (TYR 18 HN, TYR 26 HN, TYR 38 HN + 15 others) ILE HN (ILE 6 HN, ILE 19 HN, ILE 36 HN + 17 others) ARG HN (ARG 15 HN, ARG 23 HN, ARG 25 HN + 27 others) VAL HN (VAL 4 HN, VAL 7 HN, VAL 45 HN + 25 others) TRP HN (TRP 11 HN, TRP 22 HN, TRP 80 HN + 4 others) PHE HN (PHE 27 HN, PHE 35 HN, PHE 55 HN + 24 others) LYS HN (LYS 8 HN, LYS 14 HN, LYS 20 HN + 33 others) ASP HN (ASP 3 HN, ASP 32 HN, ASP 44 HN + 25 others) HIS HN (HIS 13 HN, HIS 89 HN, HIS 143 HN + 10 others) CYS HG1 (CYS 60 HG1, CYS 77 HG1, CYS 224 HG1 + 4 others) ALA HN (ALA 5 HN, ALA 50 HN, ALA 58 HN + 22 others) GLU HN (GLU 9 HN, GLU 17 HN, GLU 40 HN + 46 others) CYS HN (CYS 60 HN, CYS 77 HN, CYS 224 HN + 4 others) MET HN (MET 63 HN, MET 118 HN, MET 134 HN + 12 others) GLN HN (GLN 43 HN, GLN 47 HN, GLN 59 HN + 14 others) THR HN (THR 21 HN, THR 34 HN, THR 65 HN + 27 others) ALA OT2 (ALA 480 OT2) Total charge for #0: -152.379 The following residues had non-integral charges: SER 2 -0.6994 ASP 3 -1.2936 VAL 4 -0.2719 ALA 5 -0.2719 ILE 6 -0.2719 VAL 7 -0.2719 LYS 8 0.7253 GLU 9 -1.2936 GLY 10 -0.2719 TRP 11 -0.2719 LEU 12 -0.2719 HIS 13 -0.2719 LYS 14 0.7253 ARG 15 0.7253 GLY 16 -0.2719 GLU 17 -1.2936 TYR 18 -0.2719 ILE 19 -0.2719 LYS 20 0.7253 THR 21 -0.2719 TRP 22 -0.2719 ARG 23 0.7253 ARG 25 0.7253 TYR 26 -0.2719 PHE 27 -0.2719 LEU 28 -0.2719 LEU 29 -0.2719 LYS 30 0.7253 ASN 31 -0.2719 ASP 32 -1.2936 GLY 33 -0.2719 THR 34 -0.2719 PHE 35 -0.2719 ILE 36 -0.2719 GLY 37 -0.2719 TYR 38 -0.2719 LYS 39 0.7253 GLU 40 -1.2936 ARG 41 0.7253 GLN 43 -0.2719 ASP 44 -1.2936 VAL 45 -0.2719 ASP 46 -1.2936 GLN 47 -0.2719 ARG 48 0.7253 GLU 49 -1.2936 ALA 50 -0.2719 LEU 52 -0.2719 ASN 53 -0.2719 ASN 54 -0.2719 PHE 55 -0.2719 SER 56 -0.6994 VAL 57 -0.2719 ALA 58 -0.2719 GLN 59 -0.2719 CYS 60 -1.2719 GLN 61 -0.2719 LEU 62 -0.2719 MET 63 -0.2719 LYS 64 0.7253 THR 65 -0.2719 GLU 66 -1.2936 ARG 67 0.7253 ARG 69 0.7253 ASN 71 -0.2719 THR 72 -0.2719 PHE 73 -0.2719 ILE 74 -0.2719 ILE 75 -0.2719 ARG 76 0.7253 CYS 77 -1.2719 LEU 78 -0.2719 GLN 79 -0.2719 TRP 80 -0.2719 THR 81 -0.2719 THR 82 -0.2719 VAL 83 -0.2719 ILE 84 -0.2719 GLU 85 -1.2936 ARG 86 0.7253 THR 87 -0.2719 PHE 88 -0.2719 HIS 89 -0.2719 VAL 90 -0.2719 GLU 91 -1.2936 THR 92 -0.2719 GLU 94 -1.2936 GLU 95 -1.2936 ARG 96 0.7253 GLU 97 -1.2936 GLU 98 -1.2936 TRP 99 -0.2719 THR 100 -0.2719 THR 101 -0.2719 ALA 102 -0.2719 ILE 103 -0.2719 GLN 104 -0.2719 THR 105 -0.2719 VAL 106 -0.2719 ALA 107 -0.2719 ASP 108 -1.2936 GLY 109 -0.2719 LEU 110 -0.2719 LYS 111 0.7253 LYS 112 0.7253 GLN 113 -0.2719 GLU 114 -1.2936 GLU 115 -1.2936 GLU 116 -1.2936 GLU 117 -1.2936 MET 118 -0.2719 ASP 119 -1.2936 PHE 120 -0.2719 ARG 121 0.7253 SER 122 -0.6994 GLY 123 -0.2719 SER 124 -0.6994 SER 126 -0.6994 ASP 127 -1.2936 ASN 128 -0.2719 SER 129 -0.6994 GLY 130 -0.2719 ALA 131 -0.2719 GLU 132 -1.2936 GLU 133 -1.2936 MET 134 -0.2719 GLU 135 -1.2936 VAL 136 -0.2719 SER 137 -0.6994 LEU 138 -0.2719 ALA 139 -0.2719 LYS 140 0.7253 LYS 142 0.7253 HIS 143 -0.2719 ARG 144 0.7253 VAL 145 -0.2719 THR 146 -0.2719 MET 147 -0.2719 ASN 148 -0.2719 GLU 149 -1.2936 PHE 150 -0.2719 GLU 151 -1.2936 TYR 152 -0.2719 LEU 153 -0.2719 LYS 154 0.7253 LEU 155 -0.2719 LEU 156 -0.2719 GLY 157 -0.2719 LYS 158 0.7253 GLY 159 -0.2719 THR 160 -0.2719 PHE 161 -0.2719 GLY 162 -0.2719 LYS 163 0.7253 VAL 164 -0.2719 ILE 165 -0.2719 LEU 166 -0.2719 VAL 167 -0.2719 LYS 168 0.7253 GLU 169 -1.2936 LYS 170 0.7253 ALA 171 -0.2719 THR 172 -0.2719 GLY 173 -0.2719 ARG 174 0.7253 TYR 175 -0.2719 TYR 176 -0.2719 ALA 177 -0.2719 MET 178 -0.2719 LYS 179 0.7253 ILE 180 -0.2719 LEU 181 -0.2719 LYS 182 0.7253 LYS 183 0.7253 GLU 184 -1.2936 VAL 185 -0.2719 ILE 186 -0.2719 VAL 187 -0.2719 ALA 188 -0.2719 LYS 189 0.7253 ASP 190 -1.2936 GLU 191 -1.2936 VAL 192 -0.2719 ALA 193 -0.2719 HIS 194 -0.2719 THR 195 -0.2719 LEU 196 -0.2719 THR 197 -0.2719 GLU 198 -1.2936 ASN 199 -0.2719 ARG 200 0.7253 VAL 201 -0.2719 LEU 202 -0.2719 GLN 203 -0.2719 ASN 204 -0.2719 SER 205 -0.6994 ARG 206 0.7253 HIS 207 -0.2719 PHE 209 -0.2719 LEU 210 -0.2719 THR 211 -0.2719 ALA 212 -0.2719 LEU 213 -0.2719 LYS 214 0.7253 TYR 215 -0.2719 SER 216 -0.6994 PHE 217 -0.2719 GLN 218 -0.2719 THR 219 -0.2719 HIS 220 -0.2719 ASP 221 -1.2936 ARG 222 0.7253 LEU 223 -0.2719 CYS 224 -1.2719 PHE 225 -0.2719 VAL 226 -0.2719 MET 227 -0.2719 GLU 228 -1.2936 TYR 229 -0.2719 ALA 230 -0.2719 ASN 231 -0.2719 GLY 232 -0.2719 GLY 233 -0.2719 GLU 234 -1.2936 LEU 235 -0.2719 PHE 236 -0.2719 PHE 237 -0.2719 HIS 238 -0.2719 LEU 239 -0.2719 SER 240 -0.6994 ARG 241 0.7253 GLU 242 -1.2936 ARG 243 0.7253 VAL 244 -0.2719 PHE 245 -0.2719 SER 246 -0.6994 GLU 247 -1.2936 ASP 248 -1.2936 ARG 249 0.7253 ALA 250 -0.2719 ARG 251 0.7253 PHE 252 -0.2719 TYR 253 -0.2719 GLY 254 -0.2719 ALA 255 -0.2719 GLU 256 -1.2936 ILE 257 -0.2719 VAL 258 -0.2719 SER 259 -0.6994 ALA 260 -0.2719 LEU 261 -0.2719 ASP 262 -1.2936 TYR 263 -0.2719 LEU 264 -0.2719 HIS 265 -0.2719 SER 266 -0.6994 GLU 267 -1.2936 LYS 268 0.7253 ASN 269 -0.2719 VAL 270 -0.2719 VAL 271 -0.2719 TYR 272 -0.2719 ARG 273 0.7253 ASP 274 -1.2936 LEU 275 -0.2719 LYS 276 0.7253 LEU 277 -0.2719 GLU 278 -1.2936 ASN 279 -0.2719 LEU 280 -0.2719 MET 281 -0.2719 LEU 282 -0.2719 ASP 283 -1.2936 LYS 284 0.7253 ASP 285 -1.2936 GLY 286 -0.2719 HIS 287 -0.2719 ILE 288 -0.2719 LYS 289 0.7253 ILE 290 -0.2719 THR 291 -0.2719 ASP 292 -1.2936 PHE 293 -0.2719 GLY 294 -0.2719 LEU 295 -0.2719 CYS 296 -1.2719 LYS 297 0.7253 GLU 298 -1.2936 GLY 299 -0.2719 ILE 300 -0.2719 LYS 301 0.7253 ASP 302 -1.2936 GLY 303 -0.2719 ALA 304 -0.2719 THR 305 -0.2719 MET 306 -0.2719 LYS 307 0.7253 THR 308 -0.2719 PHE 309 -0.2719 CYS 310 -1.2719 GLY 311 -0.2719 THR 312 -0.2719 GLU 314 -1.2936 TYR 315 -0.2719 LEU 316 -0.2719 ALA 317 -0.2719 GLU 319 -1.2936 VAL 320 -0.2719 LEU 321 -0.2719 GLU 322 -1.2936 ASP 323 -1.2936 ASN 324 -0.2719 ASP 325 -1.2936 TYR 326 -0.2719 GLY 327 -0.2719 ARG 328 0.7253 ALA 329 -0.2719 VAL 330 -0.2719 ASP 331 -1.2936 TRP 332 -0.2719 TRP 333 -0.2719 GLY 334 -0.2719 LEU 335 -0.2719 GLY 336 -0.2719 VAL 337 -0.2719 VAL 338 -0.2719 MET 339 -0.2719 TYR 340 -0.2719 GLU 341 -1.2936 MET 342 -0.2719 MET 343 -0.2719 CYS 344 -1.2719 GLY 345 -0.2719 ARG 346 0.7253 LEU 347 -0.2719 PHE 349 -0.2719 TYR 350 -0.2719 ASN 351 -0.2719 GLN 352 -0.2719 ASP 353 -1.2936 HIS 354 -0.2719 GLU 355 -1.2936 LYS 356 0.7253 LEU 357 -0.2719 PHE 358 -0.2719 GLU 359 -1.2936 LEU 360 -0.2719 ILE 361 -0.2719 LEU 362 -0.2719 MET 363 -0.2719 GLU 364 -1.2936 GLU 365 -1.2936 ILE 366 -0.2719 ARG 367 0.7253 PHE 368 -0.2719 ARG 370 0.7253 THR 371 -0.2719 LEU 372 -0.2719 GLY 373 -0.2719 GLU 375 -1.2936 ALA 376 -0.2719 LYS 377 0.7253 SER 378 -0.6994 LEU 379 -0.2719 LEU 380 -0.2719 SER 381 -0.6994 GLY 382 -0.2719 LEU 383 -0.2719 LEU 384 -0.2719 LYS 385 0.7253 LYS 386 0.7253 ASP 387 -1.2936 LYS 389 0.7253 GLN 390 -0.2719 ARG 391 0.7253 LEU 392 -0.2719 GLY 393 -0.2719 GLY 394 -0.2719 GLY 395 -0.2719 SER 396 -0.6994 GLU 397 -1.2936 ASP 398 -1.2936 ALA 399 -0.2719 LYS 400 0.7253 GLU 401 -1.2936 ILE 402 -0.2719 MET 403 -0.2719 GLN 404 -0.2719 HIS 405 -0.2719 ARG 406 0.7253 PHE 407 -0.2719 PHE 408 -0.2719 ALA 409 -0.2719 GLY 410 -0.2719 ILE 411 -0.2719 VAL 412 -0.2719 TRP 413 -0.2719 GLN 414 -0.2719 HIS 415 -0.2719 VAL 416 -0.2719 TYR 417 -0.2719 GLU 418 -1.2936 LYS 419 0.7253 LYS 420 0.7253 LEU 421 -0.2719 SER 422 -0.6994 PHE 425 -0.2719 LYS 426 0.7253 GLN 428 -0.2719 VAL 429 -0.2719 THR 430 -0.2719 SER 431 -0.6994 GLU 432 -1.2936 THR 433 -0.2719 ASP 434 -1.2936 THR 435 -0.2719 ARG 436 0.7253 TYR 437 -0.2719 PHE 438 -0.2719 ASP 439 -1.2936 GLU 440 -1.2936 GLU 441 -1.2936 PHE 442 -0.2719 THR 443 -0.2719 ALA 444 -0.2719 GLN 445 -0.2719 MET 446 -0.2719 ILE 447 -0.2719 THR 448 -0.2719 ILE 449 -0.2719 THR 450 -0.2719 ASP 453 -1.2936 GLN 454 -0.2719 ASP 455 -1.2936 ASP 456 -1.2936 SER 457 -0.6994 MET 458 -0.2719 GLU 459 -1.2936 CYS 460 -1.2719 VAL 461 -0.2719 ASP 462 -1.2936 SER 463 -0.6994 GLU 464 -1.2936 ARG 465 0.7253 ARG 466 0.7253 HIS 468 -0.2719 PHE 469 -0.2719 GLN 471 -0.2719 PHE 472 -0.2719 SER 473 -0.6994 TYR 474 -0.2719 SER 475 -0.6994 ALA 476 -0.2719 SER 477 -0.6994 GLY 478 -0.2719 THR 479 -0.2719 ALA 480 0.296 Correct charges are unknown for 23 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log The following problems occurred while reading PDB file for frame_853960.pdb warning: Ignored bad PDB record found on line 1 warning: Ignored bad PDB record found on line 3 Model 0 (frame_853960.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Residues with incomplete side chains: ILE 6 ILE 19 ILE 36 ILE 74 ILE 75 ILE 84 ILE 103 ILE 165 ILE 180 ILE 186 ILE 257 ILE 288 ILE 290 ILE 300 ILE 361 ILE 366 ILE 402 ILE 411 ILE 447 ILE 449 Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True' ILE 6: phi -107.2, psi 108.1 trans Chi angles for ILE 6: -68.8 ILE 19: phi -140.8, psi 145.1 trans Chi angles for ILE 19: -160.5 ILE 36: phi -119.2, psi 123.0 trans Chi angles for ILE 36: -36.7 ILE 74: phi -113.1, psi 135.8 trans Chi angles for ILE 74: -50.0 ILE 75: phi -140.4, psi 153.3 trans Chi angles for ILE 75: 43.5 ILE 84: phi -129.2, psi 117.8 trans Chi angles for ILE 84: -66.0 ILE 103: phi -69.8, psi -30.0 trans Chi angles for ILE 103: -59.8 ILE 165: phi -117.7, psi 158.0 trans Chi angles for ILE 165: 51.0 ILE 180: phi -103.1, psi 117.0 trans Chi angles for ILE 180: -57.2 ILE 186: phi -68.7, psi 152.2 trans Chi angles for ILE 186: 54.6 ILE 257: phi -68.8, psi -40.9 trans Chi angles for ILE 257: -56.1 ILE 288: phi -92.0, psi 124.5 trans Chi angles for ILE 288: -51.5 ILE 290: phi -121.9, psi 123.0 trans Chi angles for ILE 290: -61.5 ILE 300: phi -70.1, psi 136.1 trans Chi angles for ILE 300: -61.5 ILE 361: phi -68.8, psi -37.9 trans Chi angles for ILE 361: -56.6 ILE 366: phi -92.8, psi 158.8 trans Chi angles for ILE 366: -14.9 ILE 402: phi -67.9, psi -50.9 trans Chi angles for ILE 402: -52.7 ILE 411: phi -115.4, psi 158.5 trans Chi angles for ILE 411: 45.5 ILE 447: phi -59.2, psi 150.3 trans Chi angles for ILE 447: 45.2 ILE 449: phi -136.8, psi 151.6 trans Chi angles for ILE 449: 55.5 Applying ILE rotamer (chi angles: -67.2 169.2) to ILE 103 Applying ILE rotamer (chi angles: 60.9 170.1) to ILE 447 Applying ILE rotamer (chi angles: -171.9 70.5) to ILE 19 Applying ILE rotamer (chi angles: -67.0 169.0) to ILE 361 Applying ILE rotamer (chi angles: -57.7 -65.9) to ILE 84 Applying ILE rotamer (chi angles: 62.4 170.2) to ILE 186 Applying ILE rotamer (chi angles: -62.2 169.5) to ILE 74 Applying ILE rotamer (chi angles: -56.4 -59.2) to ILE 288 Applying ILE rotamer (chi angles: -57.4 -60.3) to ILE 366 Applying ILE rotamer (chi angles: 61.8 171.3) to ILE 165 Applying ILE rotamer (chi angles: -60.4 170.3) to ILE 180 Applying ILE rotamer (chi angles: -67.0 169.0) to ILE 257 Applying ILE rotamer (chi angles: -59.9 171.3) to ILE 290 Applying ILE rotamer (chi angles: -59.2 171.5) to ILE 6 Applying ILE rotamer (chi angles: 61.8 171.3) to ILE 411 Applying ILE rotamer (chi angles: 60.0 172.1) to ILE 449 Applying ILE rotamer (chi angles: -66.5 168.5) to ILE 402 Applying ILE rotamer (chi angles: -59.9 171.3) to ILE 36 Applying ILE rotamer (chi angles: 60.0 172.1) to ILE 75 Applying ILE rotamer (chi angles: -64.7 169.9) to ILE 300 No SEQRES records for frame_853960.pdb (#0) principal chain; guessing terminii instead Chain-initial residues that are actual N terminii: MET 1 Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: ALA 480 Chain-final residues that are not actual C terminii: 412 hydrogen bonds Hydrogens added Charge model: AMBER ff14SB Non-standard atom names: LEU HN (LEU 12 HN, LEU 28 HN, LEU 29 HN + 38 others) ASN HN (ASN 31 HN, ASN 53 HN, ASN 54 HN + 10 others) GLY HN (GLY 10 HN, GLY 16 HN, GLY 33 HN + 27 others) SER HN (SER 2 HN, SER 56 HN, SER 122 HN + 20 others) SER HG1 (SER 2 HG1, SER 56 HG1, SER 122 HG1 + 20 others) ALA OT1 (ALA 480 OT1) TYR HN (TYR 18 HN, TYR 26 HN, TYR 38 HN + 15 others) ILE HN (ILE 6 HN, ILE 19 HN, ILE 36 HN + 17 others) ARG HN (ARG 15 HN, ARG 23 HN, ARG 25 HN + 27 others) VAL HN (VAL 4 HN, VAL 7 HN, VAL 45 HN + 25 others) TRP HN (TRP 11 HN, TRP 22 HN, TRP 80 HN + 4 others) PHE HN (PHE 27 HN, PHE 35 HN, PHE 55 HN + 24 others) LYS HN (LYS 8 HN, LYS 14 HN, LYS 20 HN + 33 others) ASP HN (ASP 3 HN, ASP 32 HN, ASP 44 HN + 25 others) HIS HN (HIS 13 HN, HIS 89 HN, HIS 143 HN + 10 others) CYS HG1 (CYS 60 HG1, CYS 77 HG1, CYS 224 HG1 + 4 others) ALA HN (ALA 5 HN, ALA 50 HN, ALA 58 HN + 22 others) GLU HN (GLU 9 HN, GLU 17 HN, GLU 40 HN + 46 others) CYS HN (CYS 60 HN, CYS 77 HN, CYS 224 HN + 4 others) MET HN (MET 63 HN, MET 118 HN, MET 134 HN + 12 others) GLN HN (GLN 43 HN, GLN 47 HN, GLN 59 HN + 14 others) THR HN (THR 21 HN, THR 34 HN, THR 65 HN + 27 others) ALA OT2 (ALA 480 OT2) Total charge for #0: -152.379 The following residues had non-integral charges: SER 2 -0.6994 ASP 3 -1.2936 VAL 4 -0.2719 ALA 5 -0.2719 ILE 6 -0.2719 VAL 7 -0.2719 LYS 8 0.7253 GLU 9 -1.2936 GLY 10 -0.2719 TRP 11 -0.2719 LEU 12 -0.2719 HIS 13 -0.2719 LYS 14 0.7253 ARG 15 0.7253 GLY 16 -0.2719 GLU 17 -1.2936 TYR 18 -0.2719 ILE 19 -0.2719 LYS 20 0.7253 THR 21 -0.2719 TRP 22 -0.2719 ARG 23 0.7253 ARG 25 0.7253 TYR 26 -0.2719 PHE 27 -0.2719 LEU 28 -0.2719 LEU 29 -0.2719 LYS 30 0.7253 ASN 31 -0.2719 ASP 32 -1.2936 GLY 33 -0.2719 THR 34 -0.2719 PHE 35 -0.2719 ILE 36 -0.2719 GLY 37 -0.2719 TYR 38 -0.2719 LYS 39 0.7253 GLU 40 -1.2936 ARG 41 0.7253 GLN 43 -0.2719 ASP 44 -1.2936 VAL 45 -0.2719 ASP 46 -1.2936 GLN 47 -0.2719 ARG 48 0.7253 GLU 49 -1.2936 ALA 50 -0.2719 LEU 52 -0.2719 ASN 53 -0.2719 ASN 54 -0.2719 PHE 55 -0.2719 SER 56 -0.6994 VAL 57 -0.2719 ALA 58 -0.2719 GLN 59 -0.2719 CYS 60 -1.2719 GLN 61 -0.2719 LEU 62 -0.2719 MET 63 -0.2719 LYS 64 0.7253 THR 65 -0.2719 GLU 66 -1.2936 ARG 67 0.7253 ARG 69 0.7253 ASN 71 -0.2719 THR 72 -0.2719 PHE 73 -0.2719 ILE 74 -0.2719 ILE 75 -0.2719 ARG 76 0.7253 CYS 77 -1.2719 LEU 78 -0.2719 GLN 79 -0.2719 TRP 80 -0.2719 THR 81 -0.2719 THR 82 -0.2719 VAL 83 -0.2719 ILE 84 -0.2719 GLU 85 -1.2936 ARG 86 0.7253 THR 87 -0.2719 PHE 88 -0.2719 HIS 89 -0.2719 VAL 90 -0.2719 GLU 91 -1.2936 THR 92 -0.2719 GLU 94 -1.2936 GLU 95 -1.2936 ARG 96 0.7253 GLU 97 -1.2936 GLU 98 -1.2936 TRP 99 -0.2719 THR 100 -0.2719 THR 101 -0.2719 ALA 102 -0.2719 ILE 103 -0.2719 GLN 104 -0.2719 THR 105 -0.2719 VAL 106 -0.2719 ALA 107 -0.2719 ASP 108 -1.2936 GLY 109 -0.2719 LEU 110 -0.2719 LYS 111 0.7253 LYS 112 0.7253 GLN 113 -0.2719 GLU 114 -1.2936 GLU 115 -1.2936 GLU 116 -1.2936 GLU 117 -1.2936 MET 118 -0.2719 ASP 119 -1.2936 PHE 120 -0.2719 ARG 121 0.7253 SER 122 -0.6994 GLY 123 -0.2719 SER 124 -0.6994 SER 126 -0.6994 ASP 127 -1.2936 ASN 128 -0.2719 SER 129 -0.6994 GLY 130 -0.2719 ALA 131 -0.2719 GLU 132 -1.2936 GLU 133 -1.2936 MET 134 -0.2719 GLU 135 -1.2936 VAL 136 -0.2719 SER 137 -0.6994 LEU 138 -0.2719 ALA 139 -0.2719 LYS 140 0.7253 LYS 142 0.7253 HIS 143 -0.2719 ARG 144 0.7253 VAL 145 -0.2719 THR 146 -0.2719 MET 147 -0.2719 ASN 148 -0.2719 GLU 149 -1.2936 PHE 150 -0.2719 GLU 151 -1.2936 TYR 152 -0.2719 LEU 153 -0.2719 LYS 154 0.7253 LEU 155 -0.2719 LEU 156 -0.2719 GLY 157 -0.2719 LYS 158 0.7253 GLY 159 -0.2719 THR 160 -0.2719 PHE 161 -0.2719 GLY 162 -0.2719 LYS 163 0.7253 VAL 164 -0.2719 ILE 165 -0.2719 LEU 166 -0.2719 VAL 167 -0.2719 LYS 168 0.7253 GLU 169 -1.2936 LYS 170 0.7253 ALA 171 -0.2719 THR 172 -0.2719 GLY 173 -0.2719 ARG 174 0.7253 TYR 175 -0.2719 TYR 176 -0.2719 ALA 177 -0.2719 MET 178 -0.2719 LYS 179 0.7253 ILE 180 -0.2719 LEU 181 -0.2719 LYS 182 0.7253 LYS 183 0.7253 GLU 184 -1.2936 VAL 185 -0.2719 ILE 186 -0.2719 VAL 187 -0.2719 ALA 188 -0.2719 LYS 189 0.7253 ASP 190 -1.2936 GLU 191 -1.2936 VAL 192 -0.2719 ALA 193 -0.2719 HIS 194 -0.2719 THR 195 -0.2719 LEU 196 -0.2719 THR 197 -0.2719 GLU 198 -1.2936 ASN 199 -0.2719 ARG 200 0.7253 VAL 201 -0.2719 LEU 202 -0.2719 GLN 203 -0.2719 ASN 204 -0.2719 SER 205 -0.6994 ARG 206 0.7253 HIS 207 -0.2719 PHE 209 -0.2719 LEU 210 -0.2719 THR 211 -0.2719 ALA 212 -0.2719 LEU 213 -0.2719 LYS 214 0.7253 TYR 215 -0.2719 SER 216 -0.6994 PHE 217 -0.2719 GLN 218 -0.2719 THR 219 -0.2719 HIS 220 -0.2719 ASP 221 -1.2936 ARG 222 0.7253 LEU 223 -0.2719 CYS 224 -1.2719 PHE 225 -0.2719 VAL 226 -0.2719 MET 227 -0.2719 GLU 228 -1.2936 TYR 229 -0.2719 ALA 230 -0.2719 ASN 231 -0.2719 GLY 232 -0.2719 GLY 233 -0.2719 GLU 234 -1.2936 LEU 235 -0.2719 PHE 236 -0.2719 PHE 237 -0.2719 HIS 238 -0.2719 LEU 239 -0.2719 SER 240 -0.6994 ARG 241 0.7253 GLU 242 -1.2936 ARG 243 0.7253 VAL 244 -0.2719 PHE 245 -0.2719 SER 246 -0.6994 GLU 247 -1.2936 ASP 248 -1.2936 ARG 249 0.7253 ALA 250 -0.2719 ARG 251 0.7253 PHE 252 -0.2719 TYR 253 -0.2719 GLY 254 -0.2719 ALA 255 -0.2719 GLU 256 -1.2936 ILE 257 -0.2719 VAL 258 -0.2719 SER 259 -0.6994 ALA 260 -0.2719 LEU 261 -0.2719 ASP 262 -1.2936 TYR 263 -0.2719 LEU 264 -0.2719 HIS 265 -0.2719 SER 266 -0.6994 GLU 267 -1.2936 LYS 268 0.7253 ASN 269 -0.2719 VAL 270 -0.2719 VAL 271 -0.2719 TYR 272 -0.2719 ARG 273 0.7253 ASP 274 -1.2936 LEU 275 -0.2719 LYS 276 0.7253 LEU 277 -0.2719 GLU 278 -1.2936 ASN 279 -0.2719 LEU 280 -0.2719 MET 281 -0.2719 LEU 282 -0.2719 ASP 283 -1.2936 LYS 284 0.7253 ASP 285 -1.2936 GLY 286 -0.2719 HIS 287 -0.2719 ILE 288 -0.2719 LYS 289 0.7253 ILE 290 -0.2719 THR 291 -0.2719 ASP 292 -1.2936 PHE 293 -0.2719 GLY 294 -0.2719 LEU 295 -0.2719 CYS 296 -1.2719 LYS 297 0.7253 GLU 298 -1.2936 GLY 299 -0.2719 ILE 300 -0.2719 LYS 301 0.7253 ASP 302 -1.2936 GLY 303 -0.2719 ALA 304 -0.2719 THR 305 -0.2719 MET 306 -0.2719 LYS 307 0.7253 THR 308 -0.2719 PHE 309 -0.2719 CYS 310 -1.2719 GLY 311 -0.2719 THR 312 -0.2719 GLU 314 -1.2936 TYR 315 -0.2719 LEU 316 -0.2719 ALA 317 -0.2719 GLU 319 -1.2936 VAL 320 -0.2719 LEU 321 -0.2719 GLU 322 -1.2936 ASP 323 -1.2936 ASN 324 -0.2719 ASP 325 -1.2936 TYR 326 -0.2719 GLY 327 -0.2719 ARG 328 0.7253 ALA 329 -0.2719 VAL 330 -0.2719 ASP 331 -1.2936 TRP 332 -0.2719 TRP 333 -0.2719 GLY 334 -0.2719 LEU 335 -0.2719 GLY 336 -0.2719 VAL 337 -0.2719 VAL 338 -0.2719 MET 339 -0.2719 TYR 340 -0.2719 GLU 341 -1.2936 MET 342 -0.2719 MET 343 -0.2719 CYS 344 -1.2719 GLY 345 -0.2719 ARG 346 0.7253 LEU 347 -0.2719 PHE 349 -0.2719 TYR 350 -0.2719 ASN 351 -0.2719 GLN 352 -0.2719 ASP 353 -1.2936 HIS 354 -0.2719 GLU 355 -1.2936 LYS 356 0.7253 LEU 357 -0.2719 PHE 358 -0.2719 GLU 359 -1.2936 LEU 360 -0.2719 ILE 361 -0.2719 LEU 362 -0.2719 MET 363 -0.2719 GLU 364 -1.2936 GLU 365 -1.2936 ILE 366 -0.2719 ARG 367 0.7253 PHE 368 -0.2719 ARG 370 0.7253 THR 371 -0.2719 LEU 372 -0.2719 GLY 373 -0.2719 GLU 375 -1.2936 ALA 376 -0.2719 LYS 377 0.7253 SER 378 -0.6994 LEU 379 -0.2719 LEU 380 -0.2719 SER 381 -0.6994 GLY 382 -0.2719 LEU 383 -0.2719 LEU 384 -0.2719 LYS 385 0.7253 LYS 386 0.7253 ASP 387 -1.2936 LYS 389 0.7253 GLN 390 -0.2719 ARG 391 0.7253 LEU 392 -0.2719 GLY 393 -0.2719 GLY 394 -0.2719 GLY 395 -0.2719 SER 396 -0.6994 GLU 397 -1.2936 ASP 398 -1.2936 ALA 399 -0.2719 LYS 400 0.7253 GLU 401 -1.2936 ILE 402 -0.2719 MET 403 -0.2719 GLN 404 -0.2719 HIS 405 -0.2719 ARG 406 0.7253 PHE 407 -0.2719 PHE 408 -0.2719 ALA 409 -0.2719 GLY 410 -0.2719 ILE 411 -0.2719 VAL 412 -0.2719 TRP 413 -0.2719 GLN 414 -0.2719 HIS 415 -0.2719 VAL 416 -0.2719 TYR 417 -0.2719 GLU 418 -1.2936 LYS 419 0.7253 LYS 420 0.7253 LEU 421 -0.2719 SER 422 -0.6994 PHE 425 -0.2719 LYS 426 0.7253 GLN 428 -0.2719 VAL 429 -0.2719 THR 430 -0.2719 SER 431 -0.6994 GLU 432 -1.2936 THR 433 -0.2719 ASP 434 -1.2936 THR 435 -0.2719 ARG 436 0.7253 TYR 437 -0.2719 PHE 438 -0.2719 ASP 439 -1.2936 GLU 440 -1.2936 GLU 441 -1.2936 PHE 442 -0.2719 THR 443 -0.2719 ALA 444 -0.2719 GLN 445 -0.2719 MET 446 -0.2719 ILE 447 -0.2719 THR 448 -0.2719 ILE 449 -0.2719 THR 450 -0.2719 ASP 453 -1.2936 GLN 454 -0.2719 ASP 455 -1.2936 ASP 456 -1.2936 SER 457 -0.6994 MET 458 -0.2719 GLU 459 -1.2936 CYS 460 -1.2719 VAL 461 -0.2719 ASP 462 -1.2936 SER 463 -0.6994 GLU 464 -1.2936 ARG 465 0.7253 ARG 466 0.7253 HIS 468 -0.2719 PHE 469 -0.2719 GLN 471 -0.2719 PHE 472 -0.2719 SER 473 -0.6994 TYR 474 -0.2719 SER 475 -0.6994 ALA 476 -0.2719 SER 477 -0.6994 GLY 478 -0.2719 THR 479 -0.2719 ALA 480 0.296 Correct charges are unknown for 23 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log The following problems occurred while reading PDB file for frame_747500.pdb warning: Ignored bad PDB record found on line 1 warning: Ignored bad PDB record found on line 3 Model 0 (frame_747500.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. Residues with incomplete side chains: ILE 6 ILE 19 ILE 36 ILE 74 ILE 75 ILE 84 ILE 103 ILE 165 ILE 180 ILE 186 ILE 257 ILE 288 ILE 290 ILE 300 ILE 361 ILE 366 ILE 402 ILE 411 ILE 447 ILE 449 Replacing each by 'swapaa same (residue atom spec) lib Dunbrack preserve True' ILE 6: phi -97.6, psi 123.0 trans Chi angles for ILE 6: -49.2 ILE 19: phi -110.9, psi 157.8 trans Chi angles for ILE 19: 56.5 ILE 36: phi -113.4, psi 132.3 trans Chi angles for ILE 36: -49.8 ILE 74: phi -106.1, psi 127.7 trans Chi angles for ILE 74: -55.6 ILE 75: phi -117.2, psi 133.7 trans Chi angles for ILE 75: -55.8 ILE 84: phi -98.3, psi 121.6 trans Chi angles for ILE 84: -68.6 ILE 103: phi -61.3, psi -46.5 trans Chi angles for ILE 103: -81.6 ILE 165: phi -113.3, psi 146.0 trans Chi angles for ILE 165: 49.5 ILE 180: phi -96.5, psi 127.6 trans Chi angles for ILE 180: -57.0 ILE 186: phi -68.3, psi 152.4 trans Chi angles for ILE 186: 58.6 ILE 257: phi -59.4, psi -43.6 trans Chi angles for ILE 257: -63.7 ILE 288: phi -95.2, psi 104.5 trans Chi angles for ILE 288: -54.8 ILE 290: phi -59.0, psi 103.3 trans Chi angles for ILE 290: -70.7 ILE 300: phi -59.3, psi 153.1 trans Chi angles for ILE 300: 69.1 ILE 361: phi -68.8, psi -24.6 trans Chi angles for ILE 361: 73.7 ILE 366: phi -48.8, psi 148.2 trans Chi angles for ILE 366: -156.2 ILE 402: phi -77.8, psi -45.6 trans Chi angles for ILE 402: -56.6 ILE 411: phi -123.7, psi 143.9 trans Chi angles for ILE 411: -172.2 ILE 447: phi -78.2, psi 130.4 trans Chi angles for ILE 447: -61.5 ILE 449: phi -104.2, psi 10.1 trans Chi angles for ILE 449: 52.1 Applying ILE rotamer (chi angles: 64.6 171.3) to ILE 361 Applying ILE rotamer (chi angles: -55.4 -59.0) to ILE 84 Applying ILE rotamer (chi angles: -65.5 168.9) to ILE 402 Applying ILE rotamer (chi angles: -60.7 170.4) to ILE 75 Applying ILE rotamer (chi angles: -61.2 170.5) to ILE 290 Applying ILE rotamer (chi angles: 60.6 171.1) to ILE 165 Applying ILE rotamer (chi angles: 61.7 170.9) to ILE 19 Applying ILE rotamer (chi angles: -168.6 167.4) to ILE 366 Applying ILE rotamer (chi angles: -68.1 168.5) to ILE 257 Applying ILE rotamer (chi angles: 62.4 170.2) to ILE 186 Applying ILE rotamer (chi angles: 63.8 170.0) to ILE 449 Applying ILE rotamer (chi angles: -61.3 170.0) to ILE 74 Applying ILE rotamer (chi angles: -61.3 170.0) to ILE 36 Applying ILE rotamer (chi angles: 60.9 170.1) to ILE 300 Applying ILE rotamer (chi angles: -67.8 167.9) to ILE 103 Applying ILE rotamer (chi angles: -62.9 169.7) to ILE 447 Applying ILE rotamer (chi angles: -54.1 -58.4) to ILE 288 Applying ILE rotamer (chi angles: -61.6 169.5) to ILE 180 Applying ILE rotamer (chi angles: -175.0 166.3) to ILE 411 Applying ILE rotamer (chi angles: -60.4 170.3) to ILE 6 No SEQRES records for frame_747500.pdb (#0) principal chain; guessing terminii instead Chain-initial residues that are actual N terminii: MET 1 Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: ALA 480 Chain-final residues that are not actual C terminii: 399 hydrogen bonds Hydrogens added Charge model: AMBER ff14SB Non-standard atom names: LEU HN (LEU 12 HN, LEU 28 HN, LEU 29 HN + 38 others) ASN HN (ASN 31 HN, ASN 53 HN, ASN 54 HN + 10 others) GLY HN (GLY 10 HN, GLY 16 HN, GLY 33 HN + 27 others) SER HN (SER 2 HN, SER 56 HN, SER 122 HN + 20 others) SER HG1 (SER 2 HG1, SER 56 HG1, SER 122 HG1 + 20 others) ALA OT1 (ALA 480 OT1) TYR HN (TYR 18 HN, TYR 26 HN, TYR 38 HN + 15 others) ILE HN (ILE 6 HN, ILE 19 HN, ILE 36 HN + 17 others) ARG HN (ARG 15 HN, ARG 23 HN, ARG 25 HN + 27 others) VAL HN (VAL 4 HN, VAL 7 HN, VAL 45 HN + 25 others) TRP HN (TRP 11 HN, TRP 22 HN, TRP 80 HN + 4 others) PHE HN (PHE 27 HN, PHE 35 HN, PHE 55 HN + 24 others) LYS HN (LYS 8 HN, LYS 14 HN, LYS 20 HN + 33 others) ASP HN (ASP 3 HN, ASP 32 HN, ASP 44 HN + 25 others) HIS HN (HIS 13 HN, HIS 89 HN, HIS 143 HN + 10 others) CYS HG1 (CYS 60 HG1, CYS 77 HG1, CYS 224 HG1 + 4 others) ALA HN (ALA 5 HN, ALA 50 HN, ALA 58 HN + 22 others) GLU HN (GLU 9 HN, GLU 17 HN, GLU 40 HN + 46 others) CYS HN (CYS 60 HN, CYS 77 HN, CYS 224 HN + 4 others) MET HN (MET 63 HN, MET 118 HN, MET 134 HN + 12 others) GLN HN (GLN 43 HN, GLN 47 HN, GLN 59 HN + 14 others) THR HN (THR 21 HN, THR 34 HN, THR 65 HN + 27 others) ALA OT2 (ALA 480 OT2) Total charge for #0: -152.379 The following residues had non-integral charges: SER 2 -0.6994 ASP 3 -1.2936 VAL 4 -0.2719 ALA 5 -0.2719 ILE 6 -0.2719 VAL 7 -0.2719 LYS 8 0.7253 GLU 9 -1.2936 GLY 10 -0.2719 TRP 11 -0.2719 LEU 12 -0.2719 HIS 13 -0.2719 LYS 14 0.7253 ARG 15 0.7253 GLY 16 -0.2719 GLU 17 -1.2936 TYR 18 -0.2719 ILE 19 -0.2719 LYS 20 0.7253 THR 21 -0.2719 TRP 22 -0.2719 ARG 23 0.7253 ARG 25 0.7253 TYR 26 -0.2719 PHE 27 -0.2719 LEU 28 -0.2719 LEU 29 -0.2719 LYS 30 0.7253 ASN 31 -0.2719 ASP 32 -1.2936 GLY 33 -0.2719 THR 34 -0.2719 PHE 35 -0.2719 ILE 36 -0.2719 GLY 37 -0.2719 TYR 38 -0.2719 LYS 39 0.7253 GLU 40 -1.2936 ARG 41 0.7253 GLN 43 -0.2719 ASP 44 -1.2936 VAL 45 -0.2719 ASP 46 -1.2936 GLN 47 -0.2719 ARG 48 0.7253 GLU 49 -1.2936 ALA 50 -0.2719 LEU 52 -0.2719 ASN 53 -0.2719 ASN 54 -0.2719 PHE 55 -0.2719 SER 56 -0.6994 VAL 57 -0.2719 ALA 58 -0.2719 GLN 59 -0.2719 CYS 60 -1.2719 GLN 61 -0.2719 LEU 62 -0.2719 MET 63 -0.2719 LYS 64 0.7253 THR 65 -0.2719 GLU 66 -1.2936 ARG 67 0.7253 ARG 69 0.7253 ASN 71 -0.2719 THR 72 -0.2719 PHE 73 -0.2719 ILE 74 -0.2719 ILE 75 -0.2719 ARG 76 0.7253 CYS 77 -1.2719 LEU 78 -0.2719 GLN 79 -0.2719 TRP 80 -0.2719 THR 81 -0.2719 THR 82 -0.2719 VAL 83 -0.2719 ILE 84 -0.2719 GLU 85 -1.2936 ARG 86 0.7253 THR 87 -0.2719 PHE 88 -0.2719 HIS 89 -0.2719 VAL 90 -0.2719 GLU 91 -1.2936 THR 92 -0.2719 GLU 94 -1.2936 GLU 95 -1.2936 ARG 96 0.7253 GLU 97 -1.2936 GLU 98 -1.2936 TRP 99 -0.2719 THR 100 -0.2719 THR 101 -0.2719 ALA 102 -0.2719 ILE 103 -0.2719 GLN 104 -0.2719 THR 105 -0.2719 VAL 106 -0.2719 ALA 107 -0.2719 ASP 108 -1.2936 GLY 109 -0.2719 LEU 110 -0.2719 LYS 111 0.7253 LYS 112 0.7253 GLN 113 -0.2719 GLU 114 -1.2936 GLU 115 -1.2936 GLU 116 -1.2936 GLU 117 -1.2936 MET 118 -0.2719 ASP 119 -1.2936 PHE 120 -0.2719 ARG 121 0.7253 SER 122 -0.6994 GLY 123 -0.2719 SER 124 -0.6994 SER 126 -0.6994 ASP 127 -1.2936 ASN 128 -0.2719 SER 129 -0.6994 GLY 130 -0.2719 ALA 131 -0.2719 GLU 132 -1.2936 GLU 133 -1.2936 MET 134 -0.2719 GLU 135 -1.2936 VAL 136 -0.2719 SER 137 -0.6994 LEU 138 -0.2719 ALA 139 -0.2719 LYS 140 0.7253 LYS 142 0.7253 HIS 143 -0.2719 ARG 144 0.7253 VAL 145 -0.2719 THR 146 -0.2719 MET 147 -0.2719 ASN 148 -0.2719 GLU 149 -1.2936 PHE 150 -0.2719 GLU 151 -1.2936 TYR 152 -0.2719 LEU 153 -0.2719 LYS 154 0.7253 LEU 155 -0.2719 LEU 156 -0.2719 GLY 157 -0.2719 LYS 158 0.7253 GLY 159 -0.2719 THR 160 -0.2719 PHE 161 -0.2719 GLY 162 -0.2719 LYS 163 0.7253 VAL 164 -0.2719 ILE 165 -0.2719 LEU 166 -0.2719 VAL 167 -0.2719 LYS 168 0.7253 GLU 169 -1.2936 LYS 170 0.7253 ALA 171 -0.2719 THR 172 -0.2719 GLY 173 -0.2719 ARG 174 0.7253 TYR 175 -0.2719 TYR 176 -0.2719 ALA 177 -0.2719 MET 178 -0.2719 LYS 179 0.7253 ILE 180 -0.2719 LEU 181 -0.2719 LYS 182 0.7253 LYS 183 0.7253 GLU 184 -1.2936 VAL 185 -0.2719 ILE 186 -0.2719 VAL 187 -0.2719 ALA 188 -0.2719 LYS 189 0.7253 ASP 190 -1.2936 GLU 191 -1.2936 VAL 192 -0.2719 ALA 193 -0.2719 HIS 194 -0.2719 THR 195 -0.2719 LEU 196 -0.2719 THR 197 -0.2719 GLU 198 -1.2936 ASN 199 -0.2719 ARG 200 0.7253 VAL 201 -0.2719 LEU 202 -0.2719 GLN 203 -0.2719 ASN 204 -0.2719 SER 205 -0.6994 ARG 206 0.7253 HIS 207 -0.2719 PHE 209 -0.2719 LEU 210 -0.2719 THR 211 -0.2719 ALA 212 -0.2719 LEU 213 -0.2719 LYS 214 0.7253 TYR 215 -0.2719 SER 216 -0.6994 PHE 217 -0.2719 GLN 218 -0.2719 THR 219 -0.2719 HIS 220 -0.2719 ASP 221 -1.2936 ARG 222 0.7253 LEU 223 -0.2719 CYS 224 -1.2719 PHE 225 -0.2719 VAL 226 -0.2719 MET 227 -0.2719 GLU 228 -1.2936 TYR 229 -0.2719 ALA 230 -0.2719 ASN 231 -0.2719 GLY 232 -0.2719 GLY 233 -0.2719 GLU 234 -1.2936 LEU 235 -0.2719 PHE 236 -0.2719 PHE 237 -0.2719 HIS 238 -0.2719 LEU 239 -0.2719 SER 240 -0.6994 ARG 241 0.7253 GLU 242 -1.2936 ARG 243 0.7253 VAL 244 -0.2719 PHE 245 -0.2719 SER 246 -0.6994 GLU 247 -1.2936 ASP 248 -1.2936 ARG 249 0.7253 ALA 250 -0.2719 ARG 251 0.7253 PHE 252 -0.2719 TYR 253 -0.2719 GLY 254 -0.2719 ALA 255 -0.2719 GLU 256 -1.2936 ILE 257 -0.2719 VAL 258 -0.2719 SER 259 -0.6994 ALA 260 -0.2719 LEU 261 -0.2719 ASP 262 -1.2936 TYR 263 -0.2719 LEU 264 -0.2719 HIS 265 -0.2719 SER 266 -0.6994 GLU 267 -1.2936 LYS 268 0.7253 ASN 269 -0.2719 VAL 270 -0.2719 VAL 271 -0.2719 TYR 272 -0.2719 ARG 273 0.7253 ASP 274 -1.2936 LEU 275 -0.2719 LYS 276 0.7253 LEU 277 -0.2719 GLU 278 -1.2936 ASN 279 -0.2719 LEU 280 -0.2719 MET 281 -0.2719 LEU 282 -0.2719 ASP 283 -1.2936 LYS 284 0.7253 ASP 285 -1.2936 GLY 286 -0.2719 HIS 287 -0.2719 ILE 288 -0.2719 LYS 289 0.7253 ILE 290 -0.2719 THR 291 -0.2719 ASP 292 -1.2936 PHE 293 -0.2719 GLY 294 -0.2719 LEU 295 -0.2719 CYS 296 -1.2719 LYS 297 0.7253 GLU 298 -1.2936 GLY 299 -0.2719 ILE 300 -0.2719 LYS 301 0.7253 ASP 302 -1.2936 GLY 303 -0.2719 ALA 304 -0.2719 THR 305 -0.2719 MET 306 -0.2719 LYS 307 0.7253 THR 308 -0.2719 PHE 309 -0.2719 CYS 310 -1.2719 GLY 311 -0.2719 THR 312 -0.2719 GLU 314 -1.2936 TYR 315 -0.2719 LEU 316 -0.2719 ALA 317 -0.2719 GLU 319 -1.2936 VAL 320 -0.2719 LEU 321 -0.2719 GLU 322 -1.2936 ASP 323 -1.2936 ASN 324 -0.2719 ASP 325 -1.2936 TYR 326 -0.2719 GLY 327 -0.2719 ARG 328 0.7253 ALA 329 -0.2719 VAL 330 -0.2719 ASP 331 -1.2936 TRP 332 -0.2719 TRP 333 -0.2719 GLY 334 -0.2719 LEU 335 -0.2719 GLY 336 -0.2719 VAL 337 -0.2719 VAL 338 -0.2719 MET 339 -0.2719 TYR 340 -0.2719 GLU 341 -1.2936 MET 342 -0.2719 MET 343 -0.2719 CYS 344 -1.2719 GLY 345 -0.2719 ARG 346 0.7253 LEU 347 -0.2719 PHE 349 -0.2719 TYR 350 -0.2719 ASN 351 -0.2719 GLN 352 -0.2719 ASP 353 -1.2936 HIS 354 -0.2719 GLU 355 -1.2936 LYS 356 0.7253 LEU 357 -0.2719 PHE 358 -0.2719 GLU 359 -1.2936 LEU 360 -0.2719 ILE 361 -0.2719 LEU 362 -0.2719 MET 363 -0.2719 GLU 364 -1.2936 GLU 365 -1.2936 ILE 366 -0.2719 ARG 367 0.7253 PHE 368 -0.2719 ARG 370 0.7253 THR 371 -0.2719 LEU 372 -0.2719 GLY 373 -0.2719 GLU 375 -1.2936 ALA 376 -0.2719 LYS 377 0.7253 SER 378 -0.6994 LEU 379 -0.2719 LEU 380 -0.2719 SER 381 -0.6994 GLY 382 -0.2719 LEU 383 -0.2719 LEU 384 -0.2719 LYS 385 0.7253 LYS 386 0.7253 ASP 387 -1.2936 LYS 389 0.7253 GLN 390 -0.2719 ARG 391 0.7253 LEU 392 -0.2719 GLY 393 -0.2719 GLY 394 -0.2719 GLY 395 -0.2719 SER 396 -0.6994 GLU 397 -1.2936 ASP 398 -1.2936 ALA 399 -0.2719 LYS 400 0.7253 GLU 401 -1.2936 ILE 402 -0.2719 MET 403 -0.2719 GLN 404 -0.2719 HIS 405 -0.2719 ARG 406 0.7253 PHE 407 -0.2719 PHE 408 -0.2719 ALA 409 -0.2719 GLY 410 -0.2719 ILE 411 -0.2719 VAL 412 -0.2719 TRP 413 -0.2719 GLN 414 -0.2719 HIS 415 -0.2719 VAL 416 -0.2719 TYR 417 -0.2719 GLU 418 -1.2936 LYS 419 0.7253 LYS 420 0.7253 LEU 421 -0.2719 SER 422 -0.6994 PHE 425 -0.2719 LYS 426 0.7253 GLN 428 -0.2719 VAL 429 -0.2719 THR 430 -0.2719 SER 431 -0.6994 GLU 432 -1.2936 THR 433 -0.2719 ASP 434 -1.2936 THR 435 -0.2719 ARG 436 0.7253 TYR 437 -0.2719 PHE 438 -0.2719 ASP 439 -1.2936 GLU 440 -1.2936 GLU 441 -1.2936 PHE 442 -0.2719 THR 443 -0.2719 ALA 444 -0.2719 GLN 445 -0.2719 MET 446 -0.2719 ILE 447 -0.2719 THR 448 -0.2719 ILE 449 -0.2719 THR 450 -0.2719 ASP 453 -1.2936 GLN 454 -0.2719 ASP 455 -1.2936 ASP 456 -1.2936 SER 457 -0.6994 MET 458 -0.2719 GLU 459 -1.2936 CYS 460 -1.2719 VAL 461 -0.2719 ASP 462 -1.2936 SER 463 -0.6994 GLU 464 -1.2936 ARG 465 0.7253 ARG 466 0.7253 HIS 468 -0.2719 PHE 469 -0.2719 GLN 471 -0.2719 PHE 472 -0.2719 SER 473 -0.6994 TYR 474 -0.2719 SER 475 -0.6994 ALA 476 -0.2719 SER 477 -0.6994 GLY 478 -0.2719 THR 479 -0.2719 ALA 480 0.296 Correct charges are unknown for 23 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log No incomplete side chains No SEQRES records for frame_747500.pdb (#0) principal chain; guessing terminii instead Chain-initial residues that are actual N terminii: MET 1 Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: ALA 480 Chain-final residues that are not actual C terminii: 399 hydrogen bonds Hydrogens added Charge model: AMBER ff14SB Non-standard atom names: LEU HN (LEU 12 HN, LEU 28 HN, LEU 29 HN + 38 others) ASN HN (ASN 31 HN, ASN 53 HN, ASN 54 HN + 10 others) GLY HN (GLY 10 HN, GLY 16 HN, GLY 33 HN + 27 others) SER HN (SER 2 HN, SER 56 HN, SER 122 HN + 20 others) SER HG1 (SER 2 HG1, SER 56 HG1, SER 122 HG1 + 20 others) ALA OT1 (ALA 480 OT1) TYR HN (TYR 18 HN, TYR 26 HN, TYR 38 HN + 15 others) ILE HN (ILE 6 HN, ILE 19 HN, ILE 36 HN + 17 others) ARG HN (ARG 15 HN, ARG 23 HN, ARG 25 HN + 27 others) VAL HN (VAL 4 HN, VAL 7 HN, VAL 45 HN + 25 others) TRP HN (TRP 11 HN, TRP 22 HN, TRP 80 HN + 4 others) PHE HN (PHE 27 HN, PHE 35 HN, PHE 55 HN + 24 others) LYS HN (LYS 8 HN, LYS 14 HN, LYS 20 HN + 33 others) ASP HN (ASP 3 HN, ASP 32 HN, ASP 44 HN + 25 others) HIS HN (HIS 13 HN, HIS 89 HN, HIS 143 HN + 10 others) CYS HG1 (CYS 60 HG1, CYS 77 HG1, CYS 224 HG1 + 4 others) ALA HN (ALA 5 HN, ALA 50 HN, ALA 58 HN + 22 others) GLU HN (GLU 9 HN, GLU 17 HN, GLU 40 HN + 46 others) CYS HN (CYS 60 HN, CYS 77 HN, CYS 224 HN + 4 others) MET HN (MET 63 HN, MET 118 HN, MET 134 HN + 12 others) GLN HN (GLN 43 HN, GLN 47 HN, GLN 59 HN + 14 others) THR HN (THR 21 HN, THR 34 HN, THR 65 HN + 27 others) ALA OT2 (ALA 480 OT2) Total charge for #0: -152.379 The following residues had non-integral charges: SER 2 -0.6994 ASP 3 -1.2936 VAL 4 -0.2719 ALA 5 -0.2719 ILE 6 -0.2719 VAL 7 -0.2719 LYS 8 0.7253 GLU 9 -1.2936 GLY 10 -0.2719 TRP 11 -0.2719 LEU 12 -0.2719 HIS 13 -0.2719 LYS 14 0.7253 ARG 15 0.7253 GLY 16 -0.2719 GLU 17 -1.2936 TYR 18 -0.2719 ILE 19 -0.2719 LYS 20 0.7253 THR 21 -0.2719 TRP 22 -0.2719 ARG 23 0.7253 ARG 25 0.7253 TYR 26 -0.2719 PHE 27 -0.2719 LEU 28 -0.2719 LEU 29 -0.2719 LYS 30 0.7253 ASN 31 -0.2719 ASP 32 -1.2936 GLY 33 -0.2719 THR 34 -0.2719 PHE 35 -0.2719 ILE 36 -0.2719 GLY 37 -0.2719 TYR 38 -0.2719 LYS 39 0.7253 GLU 40 -1.2936 ARG 41 0.7253 GLN 43 -0.2719 ASP 44 -1.2936 VAL 45 -0.2719 ASP 46 -1.2936 GLN 47 -0.2719 ARG 48 0.7253 GLU 49 -1.2936 ALA 50 -0.2719 LEU 52 -0.2719 ASN 53 -0.2719 ASN 54 -0.2719 PHE 55 -0.2719 SER 56 -0.6994 VAL 57 -0.2719 ALA 58 -0.2719 GLN 59 -0.2719 CYS 60 -1.2719 GLN 61 -0.2719 LEU 62 -0.2719 MET 63 -0.2719 LYS 64 0.7253 THR 65 -0.2719 GLU 66 -1.2936 ARG 67 0.7253 ARG 69 0.7253 ASN 71 -0.2719 THR 72 -0.2719 PHE 73 -0.2719 ILE 74 -0.2719 ILE 75 -0.2719 ARG 76 0.7253 CYS 77 -1.2719 LEU 78 -0.2719 GLN 79 -0.2719 TRP 80 -0.2719 THR 81 -0.2719 THR 82 -0.2719 VAL 83 -0.2719 ILE 84 -0.2719 GLU 85 -1.2936 ARG 86 0.7253 THR 87 -0.2719 PHE 88 -0.2719 HIS 89 -0.2719 VAL 90 -0.2719 GLU 91 -1.2936 THR 92 -0.2719 GLU 94 -1.2936 GLU 95 -1.2936 ARG 96 0.7253 GLU 97 -1.2936 GLU 98 -1.2936 TRP 99 -0.2719 THR 100 -0.2719 THR 101 -0.2719 ALA 102 -0.2719 ILE 103 -0.2719 GLN 104 -0.2719 THR 105 -0.2719 VAL 106 -0.2719 ALA 107 -0.2719 ASP 108 -1.2936 GLY 109 -0.2719 LEU 110 -0.2719 LYS 111 0.7253 LYS 112 0.7253 GLN 113 -0.2719 GLU 114 -1.2936 GLU 115 -1.2936 GLU 116 -1.2936 GLU 117 -1.2936 MET 118 -0.2719 ASP 119 -1.2936 PHE 120 -0.2719 ARG 121 0.7253 SER 122 -0.6994 GLY 123 -0.2719 SER 124 -0.6994 SER 126 -0.6994 ASP 127 -1.2936 ASN 128 -0.2719 SER 129 -0.6994 GLY 130 -0.2719 ALA 131 -0.2719 GLU 132 -1.2936 GLU 133 -1.2936 MET 134 -0.2719 GLU 135 -1.2936 VAL 136 -0.2719 SER 137 -0.6994 LEU 138 -0.2719 ALA 139 -0.2719 LYS 140 0.7253 LYS 142 0.7253 HIS 143 -0.2719 ARG 144 0.7253 VAL 145 -0.2719 THR 146 -0.2719 MET 147 -0.2719 ASN 148 -0.2719 GLU 149 -1.2936 PHE 150 -0.2719 GLU 151 -1.2936 TYR 152 -0.2719 LEU 153 -0.2719 LYS 154 0.7253 LEU 155 -0.2719 LEU 156 -0.2719 GLY 157 -0.2719 LYS 158 0.7253 GLY 159 -0.2719 THR 160 -0.2719 PHE 161 -0.2719 GLY 162 -0.2719 LYS 163 0.7253 VAL 164 -0.2719 ILE 165 -0.2719 LEU 166 -0.2719 VAL 167 -0.2719 LYS 168 0.7253 GLU 169 -1.2936 LYS 170 0.7253 ALA 171 -0.2719 THR 172 -0.2719 GLY 173 -0.2719 ARG 174 0.7253 TYR 175 -0.2719 TYR 176 -0.2719 ALA 177 -0.2719 MET 178 -0.2719 LYS 179 0.7253 ILE 180 -0.2719 LEU 181 -0.2719 LYS 182 0.7253 LYS 183 0.7253 GLU 184 -1.2936 VAL 185 -0.2719 ILE 186 -0.2719 VAL 187 -0.2719 ALA 188 -0.2719 LYS 189 0.7253 ASP 190 -1.2936 GLU 191 -1.2936 VAL 192 -0.2719 ALA 193 -0.2719 HIS 194 -0.2719 THR 195 -0.2719 LEU 196 -0.2719 THR 197 -0.2719 GLU 198 -1.2936 ASN 199 -0.2719 ARG 200 0.7253 VAL 201 -0.2719 LEU 202 -0.2719 GLN 203 -0.2719 ASN 204 -0.2719 SER 205 -0.6994 ARG 206 0.7253 HIS 207 -0.2719 PHE 209 -0.2719 LEU 210 -0.2719 THR 211 -0.2719 ALA 212 -0.2719 LEU 213 -0.2719 LYS 214 0.7253 TYR 215 -0.2719 SER 216 -0.6994 PHE 217 -0.2719 GLN 218 -0.2719 THR 219 -0.2719 HIS 220 -0.2719 ASP 221 -1.2936 ARG 222 0.7253 LEU 223 -0.2719 CYS 224 -1.2719 PHE 225 -0.2719 VAL 226 -0.2719 MET 227 -0.2719 GLU 228 -1.2936 TYR 229 -0.2719 ALA 230 -0.2719 ASN 231 -0.2719 GLY 232 -0.2719 GLY 233 -0.2719 GLU 234 -1.2936 LEU 235 -0.2719 PHE 236 -0.2719 PHE 237 -0.2719 HIS 238 -0.2719 LEU 239 -0.2719 SER 240 -0.6994 ARG 241 0.7253 GLU 242 -1.2936 ARG 243 0.7253 VAL 244 -0.2719 PHE 245 -0.2719 SER 246 -0.6994 GLU 247 -1.2936 ASP 248 -1.2936 ARG 249 0.7253 ALA 250 -0.2719 ARG 251 0.7253 PHE 252 -0.2719 TYR 253 -0.2719 GLY 254 -0.2719 ALA 255 -0.2719 GLU 256 -1.2936 ILE 257 -0.2719 VAL 258 -0.2719 SER 259 -0.6994 ALA 260 -0.2719 LEU 261 -0.2719 ASP 262 -1.2936 TYR 263 -0.2719 LEU 264 -0.2719 HIS 265 -0.2719 SER 266 -0.6994 GLU 267 -1.2936 LYS 268 0.7253 ASN 269 -0.2719 VAL 270 -0.2719 VAL 271 -0.2719 TYR 272 -0.2719 ARG 273 0.7253 ASP 274 -1.2936 LEU 275 -0.2719 LYS 276 0.7253 LEU 277 -0.2719 GLU 278 -1.2936 ASN 279 -0.2719 LEU 280 -0.2719 MET 281 -0.2719 LEU 282 -0.2719 ASP 283 -1.2936 LYS 284 0.7253 ASP 285 -1.2936 GLY 286 -0.2719 HIS 287 -0.2719 ILE 288 -0.2719 LYS 289 0.7253 ILE 290 -0.2719 THR 291 -0.2719 ASP 292 -1.2936 PHE 293 -0.2719 GLY 294 -0.2719 LEU 295 -0.2719 CYS 296 -1.2719 LYS 297 0.7253 GLU 298 -1.2936 GLY 299 -0.2719 ILE 300 -0.2719 LYS 301 0.7253 ASP 302 -1.2936 GLY 303 -0.2719 ALA 304 -0.2719 THR 305 -0.2719 MET 306 -0.2719 LYS 307 0.7253 THR 308 -0.2719 PHE 309 -0.2719 CYS 310 -1.2719 GLY 311 -0.2719 THR 312 -0.2719 GLU 314 -1.2936 TYR 315 -0.2719 LEU 316 -0.2719 ALA 317 -0.2719 GLU 319 -1.2936 VAL 320 -0.2719 LEU 321 -0.2719 GLU 322 -1.2936 ASP 323 -1.2936 ASN 324 -0.2719 ASP 325 -1.2936 TYR 326 -0.2719 GLY 327 -0.2719 ARG 328 0.7253 ALA 329 -0.2719 VAL 330 -0.2719 ASP 331 -1.2936 TRP 332 -0.2719 TRP 333 -0.2719 GLY 334 -0.2719 LEU 335 -0.2719 GLY 336 -0.2719 VAL 337 -0.2719 VAL 338 -0.2719 MET 339 -0.2719 TYR 340 -0.2719 GLU 341 -1.2936 MET 342 -0.2719 MET 343 -0.2719 CYS 344 -1.2719 GLY 345 -0.2719 ARG 346 0.7253 LEU 347 -0.2719 PHE 349 -0.2719 TYR 350 -0.2719 ASN 351 -0.2719 GLN 352 -0.2719 ASP 353 -1.2936 HIS 354 -0.2719 GLU 355 -1.2936 LYS 356 0.7253 LEU 357 -0.2719 PHE 358 -0.2719 GLU 359 -1.2936 LEU 360 -0.2719 ILE 361 -0.2719 LEU 362 -0.2719 MET 363 -0.2719 GLU 364 -1.2936 GLU 365 -1.2936 ILE 366 -0.2719 ARG 367 0.7253 PHE 368 -0.2719 ARG 370 0.7253 THR 371 -0.2719 LEU 372 -0.2719 GLY 373 -0.2719 GLU 375 -1.2936 ALA 376 -0.2719 LYS 377 0.7253 SER 378 -0.6994 LEU 379 -0.2719 LEU 380 -0.2719 SER 381 -0.6994 GLY 382 -0.2719 LEU 383 -0.2719 LEU 384 -0.2719 LYS 385 0.7253 LYS 386 0.7253 ASP 387 -1.2936 LYS 389 0.7253 GLN 390 -0.2719 ARG 391 0.7253 LEU 392 -0.2719 GLY 393 -0.2719 GLY 394 -0.2719 GLY 395 -0.2719 SER 396 -0.6994 GLU 397 -1.2936 ASP 398 -1.2936 ALA 399 -0.2719 LYS 400 0.7253 GLU 401 -1.2936 ILE 402 -0.2719 MET 403 -0.2719 GLN 404 -0.2719 HIS 405 -0.2719 ARG 406 0.7253 PHE 407 -0.2719 PHE 408 -0.2719 ALA 409 -0.2719 GLY 410 -0.2719 ILE 411 -0.2719 VAL 412 -0.2719 TRP 413 -0.2719 GLN 414 -0.2719 HIS 415 -0.2719 VAL 416 -0.2719 TYR 417 -0.2719 GLU 418 -1.2936 LYS 419 0.7253 LYS 420 0.7253 LEU 421 -0.2719 SER 422 -0.6994 PHE 425 -0.2719 LYS 426 0.7253 GLN 428 -0.2719 VAL 429 -0.2719 THR 430 -0.2719 SER 431 -0.6994 GLU 432 -1.2936 THR 433 -0.2719 ASP 434 -1.2936 THR 435 -0.2719 ARG 436 0.7253 TYR 437 -0.2719 PHE 438 -0.2719 ASP 439 -1.2936 GLU 440 -1.2936 GLU 441 -1.2936 PHE 442 -0.2719 THR 443 -0.2719 ALA 444 -0.2719 GLN 445 -0.2719 MET 446 -0.2719 ILE 447 -0.2719 THR 448 -0.2719 ILE 449 -0.2719 THR 450 -0.2719 ASP 453 -1.2936 GLN 454 -0.2719 ASP 455 -1.2936 ASP 456 -1.2936 SER 457 -0.6994 MET 458 -0.2719 GLU 459 -1.2936 CYS 460 -1.2719 VAL 461 -0.2719 ASP 462 -1.2936 SER 463 -0.6994 GLU 464 -1.2936 ARG 465 0.7253 ARG 466 0.7253 HIS 468 -0.2719 PHE 469 -0.2719 GLN 471 -0.2719 PHE 472 -0.2719 SER 473 -0.6994 TYR 474 -0.2719 SER 475 -0.6994 ALA 476 -0.2719 SER 477 -0.6994 GLY 478 -0.2719 THR 479 -0.2719 ALA 480 0.296 Correct charges are unknown for 23 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log No incomplete side chains No SEQRES records for frame_747500.pdb (#0) principal chain; guessing terminii instead Chain-initial residues that are actual N terminii: MET 1 Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: ALA 480 Chain-final residues that are not actual C terminii: 399 hydrogen bonds Hydrogens added Charge model: AMBER ff14SB Non-standard atom names: LEU HN (LEU 12 HN, LEU 28 HN, LEU 29 HN + 38 others) ASN HN (ASN 31 HN, ASN 53 HN, ASN 54 HN + 10 others) GLY HN (GLY 10 HN, GLY 16 HN, GLY 33 HN + 27 others) SER HN (SER 2 HN, SER 56 HN, SER 122 HN + 20 others) SER HG1 (SER 2 HG1, SER 56 HG1, SER 122 HG1 + 20 others) ALA OT1 (ALA 480 OT1) TYR HN (TYR 18 HN, TYR 26 HN, TYR 38 HN + 15 others) ILE HN (ILE 6 HN, ILE 19 HN, ILE 36 HN + 17 others) ARG HN (ARG 15 HN, ARG 23 HN, ARG 25 HN + 27 others) VAL HN (VAL 4 HN, VAL 7 HN, VAL 45 HN + 25 others) TRP HN (TRP 11 HN, TRP 22 HN, TRP 80 HN + 4 others) PHE HN (PHE 27 HN, PHE 35 HN, PHE 55 HN + 24 others) LYS HN (LYS 8 HN, LYS 14 HN, LYS 20 HN + 33 others) ASP HN (ASP 3 HN, ASP 32 HN, ASP 44 HN + 25 others) HIS HN (HIS 13 HN, HIS 89 HN, HIS 143 HN + 10 others) CYS HG1 (CYS 60 HG1, CYS 77 HG1, CYS 224 HG1 + 4 others) ALA HN (ALA 5 HN, ALA 50 HN, ALA 58 HN + 22 others) GLU HN (GLU 9 HN, GLU 17 HN, GLU 40 HN + 46 others) CYS HN (CYS 60 HN, CYS 77 HN, CYS 224 HN + 4 others) MET HN (MET 63 HN, MET 118 HN, MET 134 HN + 12 others) GLN HN (GLN 43 HN, GLN 47 HN, GLN 59 HN + 14 others) THR HN (THR 21 HN, THR 34 HN, THR 65 HN + 27 others) ALA OT2 (ALA 480 OT2) Total charge for #0: -152.379 The following residues had non-integral charges: SER 2 -0.6994 ASP 3 -1.2936 VAL 4 -0.2719 ALA 5 -0.2719 ILE 6 -0.2719 VAL 7 -0.2719 LYS 8 0.7253 GLU 9 -1.2936 GLY 10 -0.2719 TRP 11 -0.2719 LEU 12 -0.2719 HIS 13 -0.2719 LYS 14 0.7253 ARG 15 0.7253 GLY 16 -0.2719 GLU 17 -1.2936 TYR 18 -0.2719 ILE 19 -0.2719 LYS 20 0.7253 THR 21 -0.2719 TRP 22 -0.2719 ARG 23 0.7253 ARG 25 0.7253 TYR 26 -0.2719 PHE 27 -0.2719 LEU 28 -0.2719 LEU 29 -0.2719 LYS 30 0.7253 ASN 31 -0.2719 ASP 32 -1.2936 GLY 33 -0.2719 THR 34 -0.2719 PHE 35 -0.2719 ILE 36 -0.2719 GLY 37 -0.2719 TYR 38 -0.2719 LYS 39 0.7253 GLU 40 -1.2936 ARG 41 0.7253 GLN 43 -0.2719 ASP 44 -1.2936 VAL 45 -0.2719 ASP 46 -1.2936 GLN 47 -0.2719 ARG 48 0.7253 GLU 49 -1.2936 ALA 50 -0.2719 LEU 52 -0.2719 ASN 53 -0.2719 ASN 54 -0.2719 PHE 55 -0.2719 SER 56 -0.6994 VAL 57 -0.2719 ALA 58 -0.2719 GLN 59 -0.2719 CYS 60 -1.2719 GLN 61 -0.2719 LEU 62 -0.2719 MET 63 -0.2719 LYS 64 0.7253 THR 65 -0.2719 GLU 66 -1.2936 ARG 67 0.7253 ARG 69 0.7253 ASN 71 -0.2719 THR 72 -0.2719 PHE 73 -0.2719 ILE 74 -0.2719 ILE 75 -0.2719 ARG 76 0.7253 CYS 77 -1.2719 LEU 78 -0.2719 GLN 79 -0.2719 TRP 80 -0.2719 THR 81 -0.2719 THR 82 -0.2719 VAL 83 -0.2719 ILE 84 -0.2719 GLU 85 -1.2936 ARG 86 0.7253 THR 87 -0.2719 PHE 88 -0.2719 HIS 89 -0.2719 VAL 90 -0.2719 GLU 91 -1.2936 THR 92 -0.2719 GLU 94 -1.2936 GLU 95 -1.2936 ARG 96 0.7253 GLU 97 -1.2936 GLU 98 -1.2936 TRP 99 -0.2719 THR 100 -0.2719 THR 101 -0.2719 ALA 102 -0.2719 ILE 103 -0.2719 GLN 104 -0.2719 THR 105 -0.2719 VAL 106 -0.2719 ALA 107 -0.2719 ASP 108 -1.2936 GLY 109 -0.2719 LEU 110 -0.2719 LYS 111 0.7253 LYS 112 0.7253 GLN 113 -0.2719 GLU 114 -1.2936 GLU 115 -1.2936 GLU 116 -1.2936 GLU 117 -1.2936 MET 118 -0.2719 ASP 119 -1.2936 PHE 120 -0.2719 ARG 121 0.7253 SER 122 -0.6994 GLY 123 -0.2719 SER 124 -0.6994 SER 126 -0.6994 ASP 127 -1.2936 ASN 128 -0.2719 SER 129 -0.6994 GLY 130 -0.2719 ALA 131 -0.2719 GLU 132 -1.2936 GLU 133 -1.2936 MET 134 -0.2719 GLU 135 -1.2936 VAL 136 -0.2719 SER 137 -0.6994 LEU 138 -0.2719 ALA 139 -0.2719 LYS 140 0.7253 LYS 142 0.7253 HIS 143 -0.2719 ARG 144 0.7253 VAL 145 -0.2719 THR 146 -0.2719 MET 147 -0.2719 ASN 148 -0.2719 GLU 149 -1.2936 PHE 150 -0.2719 GLU 151 -1.2936 TYR 152 -0.2719 LEU 153 -0.2719 LYS 154 0.7253 LEU 155 -0.2719 LEU 156 -0.2719 GLY 157 -0.2719 LYS 158 0.7253 GLY 159 -0.2719 THR 160 -0.2719 PHE 161 -0.2719 GLY 162 -0.2719 LYS 163 0.7253 VAL 164 -0.2719 ILE 165 -0.2719 LEU 166 -0.2719 VAL 167 -0.2719 LYS 168 0.7253 GLU 169 -1.2936 LYS 170 0.7253 ALA 171 -0.2719 THR 172 -0.2719 GLY 173 -0.2719 ARG 174 0.7253 TYR 175 -0.2719 TYR 176 -0.2719 ALA 177 -0.2719 MET 178 -0.2719 LYS 179 0.7253 ILE 180 -0.2719 LEU 181 -0.2719 LYS 182 0.7253 LYS 183 0.7253 GLU 184 -1.2936 VAL 185 -0.2719 ILE 186 -0.2719 VAL 187 -0.2719 ALA 188 -0.2719 LYS 189 0.7253 ASP 190 -1.2936 GLU 191 -1.2936 VAL 192 -0.2719 ALA 193 -0.2719 HIS 194 -0.2719 THR 195 -0.2719 LEU 196 -0.2719 THR 197 -0.2719 GLU 198 -1.2936 ASN 199 -0.2719 ARG 200 0.7253 VAL 201 -0.2719 LEU 202 -0.2719 GLN 203 -0.2719 ASN 204 -0.2719 SER 205 -0.6994 ARG 206 0.7253 HIS 207 -0.2719 PHE 209 -0.2719 LEU 210 -0.2719 THR 211 -0.2719 ALA 212 -0.2719 LEU 213 -0.2719 LYS 214 0.7253 TYR 215 -0.2719 SER 216 -0.6994 PHE 217 -0.2719 GLN 218 -0.2719 THR 219 -0.2719 HIS 220 -0.2719 ASP 221 -1.2936 ARG 222 0.7253 LEU 223 -0.2719 CYS 224 -1.2719 PHE 225 -0.2719 VAL 226 -0.2719 MET 227 -0.2719 GLU 228 -1.2936 TYR 229 -0.2719 ALA 230 -0.2719 ASN 231 -0.2719 GLY 232 -0.2719 GLY 233 -0.2719 GLU 234 -1.2936 LEU 235 -0.2719 PHE 236 -0.2719 PHE 237 -0.2719 HIS 238 -0.2719 LEU 239 -0.2719 SER 240 -0.6994 ARG 241 0.7253 GLU 242 -1.2936 ARG 243 0.7253 VAL 244 -0.2719 PHE 245 -0.2719 SER 246 -0.6994 GLU 247 -1.2936 ASP 248 -1.2936 ARG 249 0.7253 ALA 250 -0.2719 ARG 251 0.7253 PHE 252 -0.2719 TYR 253 -0.2719 GLY 254 -0.2719 ALA 255 -0.2719 GLU 256 -1.2936 ILE 257 -0.2719 VAL 258 -0.2719 SER 259 -0.6994 ALA 260 -0.2719 LEU 261 -0.2719 ASP 262 -1.2936 TYR 263 -0.2719 LEU 264 -0.2719 HIS 265 -0.2719 SER 266 -0.6994 GLU 267 -1.2936 LYS 268 0.7253 ASN 269 -0.2719 VAL 270 -0.2719 VAL 271 -0.2719 TYR 272 -0.2719 ARG 273 0.7253 ASP 274 -1.2936 LEU 275 -0.2719 LYS 276 0.7253 LEU 277 -0.2719 GLU 278 -1.2936 ASN 279 -0.2719 LEU 280 -0.2719 MET 281 -0.2719 LEU 282 -0.2719 ASP 283 -1.2936 LYS 284 0.7253 ASP 285 -1.2936 GLY 286 -0.2719 HIS 287 -0.2719 ILE 288 -0.2719 LYS 289 0.7253 ILE 290 -0.2719 THR 291 -0.2719 ASP 292 -1.2936 PHE 293 -0.2719 GLY 294 -0.2719 LEU 295 -0.2719 CYS 296 -1.2719 LYS 297 0.7253 GLU 298 -1.2936 GLY 299 -0.2719 ILE 300 -0.2719 LYS 301 0.7253 ASP 302 -1.2936 GLY 303 -0.2719 ALA 304 -0.2719 THR 305 -0.2719 MET 306 -0.2719 LYS 307 0.7253 THR 308 -0.2719 PHE 309 -0.2719 CYS 310 -1.2719 GLY 311 -0.2719 THR 312 -0.2719 GLU 314 -1.2936 TYR 315 -0.2719 LEU 316 -0.2719 ALA 317 -0.2719 GLU 319 -1.2936 VAL 320 -0.2719 LEU 321 -0.2719 GLU 322 -1.2936 ASP 323 -1.2936 ASN 324 -0.2719 ASP 325 -1.2936 TYR 326 -0.2719 GLY 327 -0.2719 ARG 328 0.7253 ALA 329 -0.2719 VAL 330 -0.2719 ASP 331 -1.2936 TRP 332 -0.2719 TRP 333 -0.2719 GLY 334 -0.2719 LEU 335 -0.2719 GLY 336 -0.2719 VAL 337 -0.2719 VAL 338 -0.2719 MET 339 -0.2719 TYR 340 -0.2719 GLU 341 -1.2936 MET 342 -0.2719 MET 343 -0.2719 CYS 344 -1.2719 GLY 345 -0.2719 ARG 346 0.7253 LEU 347 -0.2719 PHE 349 -0.2719 TYR 350 -0.2719 ASN 351 -0.2719 GLN 352 -0.2719 ASP 353 -1.2936 HIS 354 -0.2719 GLU 355 -1.2936 LYS 356 0.7253 LEU 357 -0.2719 PHE 358 -0.2719 GLU 359 -1.2936 LEU 360 -0.2719 ILE 361 -0.2719 LEU 362 -0.2719 MET 363 -0.2719 GLU 364 -1.2936 GLU 365 -1.2936 ILE 366 -0.2719 ARG 367 0.7253 PHE 368 -0.2719 ARG 370 0.7253 THR 371 -0.2719 LEU 372 -0.2719 GLY 373 -0.2719 GLU 375 -1.2936 ALA 376 -0.2719 LYS 377 0.7253 SER 378 -0.6994 LEU 379 -0.2719 LEU 380 -0.2719 SER 381 -0.6994 GLY 382 -0.2719 LEU 383 -0.2719 LEU 384 -0.2719 LYS 385 0.7253 LYS 386 0.7253 ASP 387 -1.2936 LYS 389 0.7253 GLN 390 -0.2719 ARG 391 0.7253 LEU 392 -0.2719 GLY 393 -0.2719 GLY 394 -0.2719 GLY 395 -0.2719 SER 396 -0.6994 GLU 397 -1.2936 ASP 398 -1.2936 ALA 399 -0.2719 LYS 400 0.7253 GLU 401 -1.2936 ILE 402 -0.2719 MET 403 -0.2719 GLN 404 -0.2719 HIS 405 -0.2719 ARG 406 0.7253 PHE 407 -0.2719 PHE 408 -0.2719 ALA 409 -0.2719 GLY 410 -0.2719 ILE 411 -0.2719 VAL 412 -0.2719 TRP 413 -0.2719 GLN 414 -0.2719 HIS 415 -0.2719 VAL 416 -0.2719 TYR 417 -0.2719 GLU 418 -1.2936 LYS 419 0.7253 LYS 420 0.7253 LEU 421 -0.2719 SER 422 -0.6994 PHE 425 -0.2719 LYS 426 0.7253 GLN 428 -0.2719 VAL 429 -0.2719 THR 430 -0.2719 SER 431 -0.6994 GLU 432 -1.2936 THR 433 -0.2719 ASP 434 -1.2936 THR 435 -0.2719 ARG 436 0.7253 TYR 437 -0.2719 PHE 438 -0.2719 ASP 439 -1.2936 GLU 440 -1.2936 GLU 441 -1.2936 PHE 442 -0.2719 THR 443 -0.2719 ALA 444 -0.2719 GLN 445 -0.2719 MET 446 -0.2719 ILE 447 -0.2719 THR 448 -0.2719 ILE 449 -0.2719 THR 450 -0.2719 ASP 453 -1.2936 GLN 454 -0.2719 ASP 455 -1.2936 ASP 456 -1.2936 SER 457 -0.6994 MET 458 -0.2719 GLU 459 -1.2936 CYS 460 -1.2719 VAL 461 -0.2719 ASP 462 -1.2936 SER 463 -0.6994 GLU 464 -1.2936 ARG 465 0.7253 ARG 466 0.7253 HIS 468 -0.2719 PHE 469 -0.2719 GLN 471 -0.2719 PHE 472 -0.2719 SER 473 -0.6994 TYR 474 -0.2719 SER 475 -0.6994 ALA 476 -0.2719 SER 477 -0.6994 GLY 478 -0.2719 THR 479 -0.2719 ALA 480 0.296 Correct charges are unknown for 23 non-standard atom names in otherwise standard residues Charges of 0.0 were assigned to the unknown atoms 1 model(s) had non-integral total charge Details in reply log

3 6

How to subgroup the chains of oligomer pdb
by sktewarybt1993＠gmail.com 26 Jan '25

26 Jan '25

Friends I would like to learn how to subgroup the chains of a oligomer pdb. suppose i have a pdb with chain A to L, in which A,B,C,D,E,F belongs to gp20 and G,H,I,J,K,L belongs to gp20. My question is how to add the descriptions to these groups chains so that when the viewer look the pdb file when he selects the gp20 all the chains to this group are selected A-F. Please give your feedback if chimerax can do it, how to do it?

2 1

Enquiry
by Konstantinos P. Zois 17 Jan '25

17 Jan '25

To whom it may concern, I would like to know if there's a way to automatically setup a default way for visualising orbitals/densities... that is, after opening a .cube file, to present the density by a specific colour, transparency etc. Thanks a lot! KPZ -- _______________________________________________ Konstantinos P. Zois, MSc PhD student Institute of Theoretical Chemistry, Währinger Str. 17, A-1090 Vienna Department of Chemistry, Universität Wien _______________________________________________

2 1

RRDistMaps: plot not corresponding to tabulated distance data?
by Dr. Michael Weber 02 Jan '25

02 Jan '25

Hi, I played around a bit with the nice RRDistMaps tool in Chimera v1.17.3 and I am wondering why the output .png plot's size of a single protein structure analysis doesn't correspond at all to the protein length? For a 659 amino acid long protein I was expecting to find a plot in which the distance matrix data area is sized 659 by 659 pixels (or multiples of this) to allow for placing the corresponding grey-scale value for each calculated distance as indicated in the plot's legend. Instead, it appears that the output image's dimensions are actually dynamically adjusted depending on the RRDistMaps's tool window size at the time of generating the plot. As a result, the core data region in the plot can barely accomodate the full data set with regular screen resolutions - at my end at least, it is always smaller (except maybe for very small proteins; I did not check this in more detail, yet). Playing with the sliders and trying to re-export those manually re-formatted images also doesn't seem to solve the problem. Did I miss something here? I just found out about this accidentally while writing a small Python program analyzing the output plots pixel-wise. ;-) I also noticed that the data area appears bordered by a triple line set (single pixel wide, each: grey-black-grey). Please note that I don't question the numeric distance data as exported in .csv/.tsv format - it's all just about the exported .png file. One additional question: Is it possible to run this tool in batch mode from the command line with parameters specifying (forcing) the (correct) output plot size (data region), the input .pdb structure file and all the options available in the GUI plus export the distance data table in .csv format (and maybe even the alignment data)? And finally, it appears that I encontered a possible bug when trying to process more than two sequences using RRDistMaps: The Muscle-based online alignment seems to fail (tried it for two days now) - here is the log: Traceback from web service request (connection setup): Traceback (most recent call last): File "C:\Program Files\Chimera 1.17.3\share\WebServices\opal_client.py", line 11, in __init__ self._setup(serviceName, opalURL, sessionData) File "C:\Program Files\Chimera 1.17.3\share\WebServices\opal_client.py", line 50, in _setup self.sudsClient = Client(self.serviceURL + "?wsdl", **kw) File "C:\Program Files\Chimera 1.17.3\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\client.py", line 115, in __init__ self.wsdl = reader.open(url) File "C:\Program Files\Chimera 1.17.3\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 150, in open d = self.fn(url, self.options) File "C:\Program Files\Chimera 1.17.3\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\wsdl.py", line 136, in __init__ d = reader.open(url) File "C:\Program Files\Chimera 1.17.3\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 74, in open d = self.download(url) File "C:\Program Files\Chimera 1.17.3\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\reader.py", line 92, in download fp = self.options.transport.open(Request(url)) File "C:\Program Files\Chimera 1.17.3\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\https.py", line 62, in open return HttpTransport.open(self, request) File "C:\Program Files\Chimera 1.17.3\bin\lib\site-packages\suds_jurko-0.6-py2.7.egg\suds\transport\http.py", line 69, in open raise TransportError(str(e), e.code, e.fp) TransportError: HTTP Error 404: Not Found Typically, if you get a TypeError, it's a problem on the remote server and it should be fixed shortly. If you get a different error or get TypeError consistently for more than a day, please report the problem using the Report a Bug... entry in the Help menu. Please include the traceback printed above as part of the problem description. Traceback from web application request: Traceback (most recent call last): File "C:\Program Files\Chimera 1.17.3\share\WebServices\appWebService.py", line 51, in _initApp self.backend = Backend(service, url) File "C:\Program Files\Chimera 1.17.3\share\WebServices\opal_client.py", line 21, in __init__ raise NonChimeraError("Web service appears " NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:MuscleService' is unavailable. See Reply Log for more details. Best regards, Michael. -- Dr. Michael H.W. Weber Rechenkraft.net e.V.

3 5

converting Chimera .py to ChimeraX
by John Price 12 Dec '24

12 Dec '24

Hi, I have looked through the wiki and don't see anything relating to this. Is there a simple way to change the .py or .pyc Chimera to a format that can be used in ChimeraX? Have a great day, JC John C. Price, Ph.D. Professor of Biochemistry Brigham Young University E113 Benson Building 801-422-6040

2 2

Movie from pdb file with 30 models of a conformational change.
by Evan Kantrowitz 02 Dec '24

02 Dec '24

Hi, Can someone give me help with a, I think, simple issue. I have a single pdb file containing 30 MODELS These 30 models correspond to a conformational change. Here is a portion of the Models list When I read it in,I see all 30 models showing in the view. What I want to do is make a movie showing these 30 MODELS one after the other. I have tried coordset and coordset slider but have not got it to work. Thanks Evan PS. This is what the image looks like with the 30 frames.It was generated from the A chain of pdb files 2e2n and 2e2q using the website ViewMotions (viewmotions.bc.edu <http://viewmotions.bc.edu/>). ----------------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu <mailto:evan.kantrowitz@bc.edu> Emeritus Professor of Chemistry Cell: 617-775-9915 Boston College www2.bc.edu/evan-kantrowitz <http://www2.bc.edu/~kantrow> -----------------------------------------------------------------------------

2 1

Issue with Display of Hydrogen Bonds in Find H Bond Tool in Chimera
by GABRIELE SANTOS CEPINHO 12 Nov '24

12 Nov '24

Dear Chimera Support Team, My name is Gabriele Cepinho, and I am using Chimera version 1.17.3 for molecular docking analysis in my research. Recently, I encountered an issue with the Find H Bond tool that I have been unable to resolve, and I hope you may be able to assist me. When I use the Find H Bond tool to display hydrogen bonds between molecules, the generated image also shows polar interactions along with the specific hydrogen bonds. However, in the tool’s output file, I can clearly identify which interactions are true hydrogen bonds. My goal is to display only the hydrogen bonds in the image, excluding the polar interactions, but I have not been able to adjust the tool to achieve this. I have tried modifying the distance and angle parameters to restrict the display, yet polar interactions still appear alongside the hydrogen bonds in the visualization. I appreciate any guidance or recommendations you can provide regarding this matter. If there is any additional option to filter these interactions directly in the image, or if there is an update or specific setting available for the Find H Bond tool, I would be grateful to know about it. Thank you in advance for your attention. Best regards, Gabriele Cepinho -- ---- É obrigatória a utilização do e-mail @unifesp em todas as correspondências oficiais, institucionais e no acesso aos equipamentos e sistemas da Universidade Federal de São Paulo, conforme a portaria Reitoria n. 1182/2022 <https://sti.unifesp.br/documentos/termos-de-uso-do-email> que define a Política de e-mail institucional da Unifesp. <https://sei.unifesp.br/sei/publicacoes/controlador_publicacoes.php?acao=pub…>

2 1

Write out SeqRes entry
by David Bhella 07 Nov '24

07 Nov '24

Dear Chimera/ChimeraX team, I have a model for an asymmetric unit of a virus capsid that has three chains of the same capsid protein – but I am having trouble depositing my model in the PDB because it only has a seqres entry for one of the three chains (B). Whatever I do, chimeraX will only write entries for that chain. Is there a way to force chimeraX (or any other program) to write the seqres card for each chain correctly? Thanks D David Bhella Professor of Structural Virology Director, Scottish Centre for Macromolecular Imaging Associate Director, MRC - University of Glasgow Centre for Virus Research +44 (0)141 330 3685<tel:+441413303685> [signature_1350623625] [Logo, company name Description automatically generated]

3 3

Values at Atom Positions
by jp d 01 Nov '24

01 Nov '24

hi, sorry to bother you again, is it possible to run "Values at Atom Postions" from a script where i specify map,pdb and just the output attribute file ? thanks jpd

2 1

ccp4 map from mtz
by Vitali James 31 Oct '24

31 Oct '24

Dear Greg, I just converted my mtz file in phenix to ccp4 maps. Chimera can open the mFo-DFc.ccp4 and 2mFo-DFc.ccp4 but how to fit pdb into the map?. Somehow the map does not appear as continuous crystals as in coot. Can you please explain how to align the pdb structure wuth the map. best James

3 2

About using Chimera(X) in articles
by Elaheh Kashani-Amin 30 Oct '24

30 Oct '24

Dear Chimera developers, We are a research and education group based in Iran and have been using Chimera(X) to teach our students about homology modeling and molecular docking. Recently, we discovered that our access to your website has been denied. Although we can access it via VPN, we would like to inquire if we can legally use Chimera(X) for academic purposes and cite it in our papers. We would greatly appreciate it if you could provide us with legal access to your products. Thank you for your time and consideration. Best regards Elaheh Kashani-Amin PhD, Molecular Medicine

2 2

which file is the Modeller executable on linux?
by Elaine Meng 30 Oct '24

30 Oct '24

Forwarding to chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> so that somebody who knows the answer can respond. I don't know since I'm not on linux and do not use a local installation, sorry. That is the recommended address for asking questions about Chimera. Note that we do not actively develop Chimera any more. ChimeraX is recmomended instead -- it has essentially the same capabilities to interface with Modeller (local or web service) for loop modeling and for comparative modeling. The comparative modeling tool in ChimeraX is better than in Chimera, because it allows modeling multimers whereas the Chimera tool only allows modeling a single protein chain. Here are the help pages for the two ChimeraX tools, Model Loops and Modeller Comparative: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> Also, there is a different address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> for asking questions about ChimeraX. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: > Date: October 29, 2024 at 3:58:41 PM PDT > To: Yassin Ahmed <yassin.ahmed2200m(a)copharm.uobaghdad.edu.iq> > > On 10/29/24 8:12 AM, Yassin Ahmed wrote: >> Please l have download and installed modeller in my Linux system , >> now I want to run modeller locally by Chimera >> Please where can I find the "Modeller executable file location" and also where can I find the "custom Modeller script file location" ? ,,,, >> Because there are many files named modeller and mod in installation folder,so I am confused. Please guide me > > Hi Yassin, I'm not 100% sure what the Chimera developers mean by "Modeller executable file" so I've cc'd Elaine from the Chimera team, but assuming you're running the latest version of Modeller, they probably mean the mod10.6 script. Where that is depends on how you installed Modeller. If you used the RPM, it is /usr/bin/mod10.6. > > In most cases you would not need to change the Modeller script file, instead using that generated by Chimera, so you can leave that box blank, I think. > > Ben Webb, Modeller Caretaker

2 1

camera view
by Vitali James 29 Oct '24

29 Oct '24

Dear chimera users, My camera window view looks like green and gray lines. I attached the image as well. Can you please suggest why it looks like this? Best J. Vitali

2 1

Request for Example Data for Visualization
by elzaferry9＠gmail.com 28 Oct '24

28 Oct '24

The content of this message was lost. It was probably cross-posted to multiple lists and previously handled on another list.

2 1

Request for Example Data for Visualization
by lilei 26 Oct '24

26 Oct '24

Dear Chimera Development Team, I hope this message finds you well. My name is kevin, and I am currently working on a project that involves the use of UCSF Chimera for molecular visualization. I am reaching out to inquire if you could provide me with example data, particularly the "Example_FCTM" directory that contains the chimera_load.py script and other relevant files. Having access to this data would greatly assist me in understanding and utilizing Chimera more effectively for my work. Thank you for your time and assistance. I look forward to your response. Best regards,

1 0

split local resolution map by color
by jp d 24 Oct '24

24 Oct '24

hi, i have a local resolution map from cryosparc i would like to split it by color (resolution) it seems like Tools -> Color zone may do this ? i can display the local resolution map and it colors correctly, but when i try to split it with color zone, it say the map has no color zone. any pointers or suggestion would be appreciated. thanks jpd

3 2

Inquiry: Covalent bond distances
by Joshua Angelo Mandanas 18 Oct '24

18 Oct '24

Greetings from the Philippines! Hi, I am Assoc. Prof Joshua Angelo, a Lead Researcher. I am currently utilizing Chimera to analyze/visualize the docked structures I processed in ClusPro. In the course of my utilization with Chimera, I came across that majority of hydrogen bonds have closer atomic interactions (e.g. 1.8 Å- 2.5 Å), as opposed to covalent bonds (I usually get atomic distances more than 2.5 or 2 Å). Note, that I based the covalent bonds based on the label from the atomic distance and nature of the residues involved (e.g. S-O, C-O). I humbly would like to know why covalent bonds in UCSF Chimera have further atomic (residue) distances between inter-models? Is it because of torsions from nearby hydrogen bonds? Or torsions from the actual docked structure? Hope for your prompt response. Thank you very much! Best regards, JOSH

2 2

Re: [chimerax-users] Issues accessing your websites
by Elaine Meng 18 Oct '24

18 Oct '24

See previous announcement forwarded below. To the best of my knowledge, we expect the websites etc. to be available again on Oct 21. They may be available earlier than that, but not be reliable (could go back down). Elaine > From: Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> > Subject: [chimerax-users] Oct 14-20 Chimera(X) website downtime > Date: October 10, 2024 at 11:38:29 AM PDT > To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu>, "chimera-users(a)cgl.ucsf.edu List" <chimera-users(a)cgl.ucsf.edu> > Reply-To: Elaine Meng <meng(a)cgl.ucsf.edu> > > Planned downtime for server maintenance: > > The Chimera and ChimeraX websites, Toolshed, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable starting Monday, October 14, 10 AM PDT and continuing for several days, potentially through the following weekend (October 14-20). > > Apologies for the inconvenience, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Resource for Biocomputing, Visualization, and Informatics > Department of Pharmaceutical Chemistry > University of California, San Francisco > On Oct 17, 2024, at 8:10 AM, Karp Mike (External) via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi, > We’ve been trying to install a chimerax plugin over the last few weeks and noticed we were unable to access the webpage the application tries to open (ChimeraX Toolshed). We checked and found this wasn’t accessible from multiple internet connections. > I’ve since noticed we are also unable to access any content on https://cgl.ucsf.edu > Are you aware of an issue with your web sites? > Regards, > Mike.Legal Notice: This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. UCB screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. UCB accepts no liability for any damage caused by any virus transmitted by this electronic mail. (Ref: #*UG1107) [Ref-UG1107] > _______________________________________________ > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

1 0

Question about Ramachandran probability assignment to attributes
by Sergio Garay 18 Oct '24

18 Oct '24

Hi everyone! I have a question regarding the use of probability assignment to attributes: for example, if I take chain A of 1ay7.pdb, open the Ramachandran plot, and ask it to assign the probabilities as an attribute, then select all residues with a probability lower than 0.01, I end up with two selected residues, one in the allowed regions for alpha helices and another in the beta sheet regions. I expected that residues outside the allowed regions or near the edges of the allowed zones would be selected, not in the center of them. Can someone explain what my mistake is? Thanks a lot! Sergio -- *Dr. Sergio Garay* *Profesor Adjunto Càtedra de Práctica Profesional de Bioquímica* *Cátedra de Bioinformática* *Facultad de Bioquimica y Cs. BiológicasUniversidad Nacional del LitoralSanta Fe - ArgentinaC.C. 242 - Ciudad Universitaria - C.P. S3000ZAAArgentinaPh. +54 (342) 4575-213Fax. +54 (342) 4575-221 *

2 3

Assistance required for Chimera software download
by Parnian Soleimani 18 Oct '24

18 Oct '24

I hope this email finds you well. I am having trouble accessing the Chimera software download site. I would greatly appreciate your guidance on how to resolve this matter. Thank you in advance for your help.

1 0

Oct 14-20 Chimera(X) website downtime
by Elaine Meng 10 Oct '24

10 Oct '24

Planned downtime for server maintenance: The Chimera and ChimeraX websites, Toolshed, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable starting Monday, October 14, 10 AM PDT and continuing for several days, potentially through the following weekend (October 14-20). Apologies for the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Center and Orient
by Hernando J Sosa 09 Oct '24

09 Oct '24

Dear Chimera, What would be the equivalent commands to the Center and Orient buttons at the bottom of the Volume Viewer menu tab? Thanks H.

3 3

How will hydrogen bonds be highlighted in the final rendering
by 姜恩誉 09 Oct '24

09 Oct '24

Hello, when chimera software was used to analyze the interaction between small molecular ligands and proteins, the hydrogen bond width was set to 24, but the hydrogen bond in the rendered picture was very thin and difficult to distinguish. How can I solve this problem？ Looking forward to your reply 姜恩誉 2023111025(a)stu.njau.edu.cn

3 4

Request for authorization to use Chimera software
by Stany Tsom 03 Oct '24

03 Oct '24

Dear UCSF Chimera software Coordinator, I am Tsomene Stany Lionel, I have a master's degree in Organic Chemistry obtained at the University of Yaoundé 1, a well known University around central Africa, my studies was focused in isolation, synthesis, characterizations, in vitro and in silico studies, I have worked under the direction of Dr. Messi Angelique Nicolas. Since 2020, during the pandemic there is an increase demand in computerized aided research of bioactive compounds. At the same time, it helps us focus on specific bioactive compounds showing better results. At Yaoundé 1 University, there is a large need in learning and usage of your software for in silico purposes, that is for molecular docking studies, with your permission we will like to organize a series workshops at the University to help masters students, Ph D students and also Professors for the better understanding of molecular docking and help then have better results for their research purposes. We will like at the end of each workshop deliver a certificate for this software learning. Software coordinator, we will really be glad if you accept directing, giving us permission for this use of your software for these workshop Organization and while not coordinating this future. At the end we will with your permission co sign the certificates we will deliver to the participants. References Dr. Messi Angelique Nicolas, Senior Lecturer at University of Yaoundé 1 messiangeliquenicolas(a)gmail.com Dr. Ngomo Orleane , Senior Lecturer at University of Yaoundé 1 orleansn(a)yahoo.fr All the details of my informations are in the attachment -CV/resume - Masters degree (masters 2 and 1 transcripts) -Bachelors degree While waiting for an answer from you UCSF Chimera Software coordinator, receive my distinct greetings. Sincerely Tsomene stany

4 7

Software copyright consulting
by 姜恩誉 27 Sep '24

27 Sep '24

Hello, is the application of your Chimera X software for paper publication a non-commercial use？ Looking forward to your reply。 Thank you 姜恩誉 2023111025(a)stu.njau.edu.cn

2 2

Gaff type for Mn2+ to run antechamber
by Medhanjali Dasgupta 25 Sep '24

25 Sep '24

Dear all, I am trying to generate the electrostatic surface for a protein that contains Mn in the 2+ state in its active site. I've tried to go about it in two ways but keep getting stuck. 1. If I use chimera or Pymol to use the PDB2PQR-APBS plug in, it cannot find GAFF type for Mn2+ so it cannot run anyechamber to allocate the atomic charge to Mn2+. Am i missing an update? Is there any way to get around this? Can I run antechamber myself to recognise my ion of interest, and then determine the charge, input it into the .pqr file and run APBS? 2. I have used the online server hosted at poissonboltzmann.org to run pdb2pqr and apps but run into the problem of not knowing what the atomic charge is for Mn2+. Any help would be appreciated. Thanks!!! Medhanjali

2 5

question about non-standard amino acids
by Jessie Jaynes 23 Sep '24

23 Sep '24

Hi Folks, I have a short peptide (O=ornithine) FEFOGGOFEF Is it possible to construct this peptide in Chimera? Thank you, Jesse

2 1

Generating a single electrostatic potential surface for a protein + ligand complex
by jadeshi88＠gmail.com 22 Sep '24

22 Sep '24

Hi, New user to ChimeraX here, would really appreciate some help! I'm trying to generate an electrostatic potential surface for a protein-ligand complex. Currently, I am using the surface/coulombic, and surface ligand/coulombic ligand commands to generate surfaces separately for the protein and ligand, and then exporting to an .obj file. However, by doing so I'm left with two separate surface meshes, and what I really want is a single surface that encapsulates both entities. Is it possible to do this? Thanks in advance!

2 1

MD on Chimera
by Manon Bulliard 20 Sep '24

20 Sep '24

Good afternoon, I was using chimera to do molecular dynamic simulation. I had to download Chimera on my new computer and now have the 1.18 version. It seems this feature is not anymore present under Tools>MD/Ensemble Analysis>molecular dynamic simulation. Do you know where I can find it to still be able to perform my modeling as previously? Thank you in advance, Manon Manon Bulliard, PhD EPFL | ISREC | Prof. Constam group SV2837 | Station 19 | CH-1015 Lausanne manon.bulliard(a)epfl.ch

3 3

Need help to resolve the architecture
by Farida Aziz 20 Sep '24

20 Sep '24

Dear Sir/Madam, I want to install chimera (chimera-1.18-linux_x86_64.bin) on my ubuntu 24.04 LTS (apple mini mac M2) I am facing so many errors in installtion as shown below •/chimera-1.18-linux_x86_64.bin bash: •/chimera-1.18-linux_x86_64.bin: cannot execute binary file: Exec format error sudo •/chimera-1.16-linux_x86_64.bin [sudo] password for codebind:•/chimera-1.16-linux_x86_64. bin: 1: Syntax error: word unexpected (expecting ")") I used this command ''Uname -m '' to find the archetecture which is ''aarch64'' the binary file is ''x86_64''. Please help me to fix this problem, I this regards. will be very geatful. Thanking in anticipation. Rgards Dr.Farida

2 1

Selecting chain via command line
by Ellen Shrock 19 Sep '24

19 Sep '24

Hello, I am trying to write a script that will iterate through lists of PDB IDs, the relevant antibody chain labels within those PDBs, and antigen chain labels, and annotate the contacts between the antibody and antigen using the command findclash. After opening each PDB file, I am struggling to find a way to select the antibody chains as "sel1" and the antigen chain(s) as "sel2" since the command "select" does not seem to recognize chain labels. Could you please help me find a way to accomplish my goal? Thank you, Ellen

3 8

Python script to add hydrogens to selected carbon atoms
by Mandelli, Davide 18 Sep '24

18 Sep '24

Dear developers, I am trying to automatize a task using the chimera python interface. In the graphical user interface, I can get the result I want by performing the following actions: 1) Select a carbon atom (ctrl+left button) 2) Tools --> Structure Editing --> Build Structure 3) In the "Build Structure" window, select "Modify Structure" 4) Change selected atom to...: "Element C", "Bonds 4", "Geometry Tetrahedral" (basically the default) 5) Apply 6) Save as pdb Is it possible to create a python script to do 1-6 (repeating 1-5 for several carbon atoms identified by residue id and name)? I could then very easily prepare a bash script to apply these changes to hundreds of pdb files. I tried asking chatGPT for a quick answer, but most probably it is using python classes and methods that actually do not exist. Looking at the online documentation was also unsuccesful, but maybe you could point me to the right place. Thanks a lot! Best, Davide Dr Davide Mandelli Institute of Neuroscience and Medicine INM-9 Forschungszentrum Jülich Email: d.mandelli(a)fz-juelich.de<mailto:m.alfonso-prieto@fz-juelich.de> --------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens --------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------

2 2

Error when opening session file cross-platform
by Alexander Lee 17 Sep '24

17 Sep '24

Apologies, I had accidentally sent this email to the ChimeraX platform. Now reposting it to the Chimera mail platform. I created a python session file on ubuntu and tried to open it on windows. Ubuntu was using Chimera 1.18 build 42535 but windows was using 1.18 build 42531. I've tried updating chimera on windows, but it said I was on the latest version already. When I open it on ubuntu on another desktop or from where I created it, it works. My session file is ~ 1.5 GB including smoothed trajectory. What should I do? Here are the outputs after running debug on windows: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics create application loading Pmw creating main window creating menus creating toolbar creating viewer initializing OpenGL initializing preferences initializing dialogs initializing COM initializing extensions Return code: -1073741819 Press return or enter to to exit [cid:0c988132-7bb8-429c-a6c7-f91f6db3b590] [cid:55bba9bf-1168-4782-b772-4d2e36e05e97]

3 3

New Install of Chimera on RHEL 9
by Evan Kantrowitz 12 Sep '24

12 Sep '24

I have been working with my IT department to port a script that uses Chimera from an old linux machine to a new Linux machine running RHEL. I setup my own test node at home with RHEL (same version). I got the script working on my test node. I am now moving the system to the IT node. When I reinstalled the same version of Chimera (Chimera64-2024-04-12) on that machine and run the script when Chimera starts I get Tkinter errors and others (see below). What do I need to do to get this version of Chimera running? Any suggestions would be appreciated. Should I try a more current build? ERRORS: Traceback (most recent call last): File "/opt/viewmotions/chimera64/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/opt/viewmotions/chimera64/share/chimeraInit.py", line 680, in init import chimera File "/opt/viewmotions/chimera64/share/chimera/__init__.py", line 2782, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/opt/viewmotions/chimera64/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/opt/viewmotions/chimera64/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/opt/viewmotions/chimera64/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/opt/viewmotions/chimera64/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: libXss.so <http://libxss.so/>.1: cannot open shared object file: No such file or directory Thanks Evan ----------------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu <mailto:evan.kantrowitz@bc.edu> Emeritus Professor of Chemistry Cell: 617-775-9915 Boston College www2.bc.edu/evan-kantrowitz <http://www2.bc.edu/~kantrow> -----------------------------------------------------------------------------

2 1

Announcement: Release of DOCK 6.12
by Scott Brozell 12 Sep '24

12 Sep '24

We are pleased to announce the release of DOCK 6.12. DOCK is a suite of programs for molecular docking. The source code for DOCK 6.12 is available for download and free for academic users at https://dock.compbio.ucsf.edu/DOCK_6/index.htm This release includes several major new features: A new implementation of the hierarchical database search method of DOCK 3 which samples ligand degrees of freedom from precomputed conformations, a new covalent docking algorithm called attach-and-grow which aligns covalent residues and dummy atoms on ligands to grow conformations, a new receptor desolvation scoring function based on GIST, and updates to the chemgrid scoring function to match DOCK 3.7. For full information on what is new in DOCK 6.12, please visit: https://dock.compbio.ucsf.edu/DOCK_6/new_in_6.12.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. https://dock.compbio.ucsf.edu

1 0

How to move ions along with protein structure
by Amir Mehdi 10 Sep '24

10 Sep '24

Hi, I am MEHDI I am trying to make a fusion between two proteins but when I am joining them by using build structure->joint structure (C-N peptide bonds) it will only move the protein structure but not the ions attached with the structure, can you suggest me something what to do in this case? Thank you

2 2

morph command in chimerax
by Hansen, Bryan (NIH/NIAID) [E] 09 Sep '24

09 Sep '24

Hi, I'm using ChimeraX v 1.8 (2024-06-10) and I'm having a problem with the morph command. No matter how I format the command I'm getting the same error message of "Require at least 2 structures for morph" I've tried morph #3,4 core 0.1 frames 75 wrap t and morph #3#4 core 0.1 frames 75 wrap t These are 2 electron density maps so there's no sequence info docked in yet. Thanks for any tips or advice on what I'm doing wrong. Bryan Hansen Computational Biologist / Electron Microscopist NIH/NIAID/RTB/RML/EMU Rocky Mountain Laboratories 903 S. 4th St Hamilton, MT 59840 406.363.9202 *********************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ***********************************************************

2 1

Chimera interface to Modeller
by Vonderviszt Ferenc 03 Sep '24

03 Sep '24

Hello, I have been using the Chimera interface to Modeller via a web service. This service has been down for a few days. It always stops with the following error message: Service 'opal:Modeller9v8Service' is unavailable What should I do? Please help me. Thanks, Feri

4 4

Finding SASA for individual residues
by Prathvi Singh 29 Aug '24

29 Aug '24

Hi Elaine, Can I use chimera or chimeraX to know the solvent accessible surface area (SASA) for selected residues? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

3 6

display cartoon and H-bonds
by Bryan Sutton 27 Aug '24

27 Aug '24

I can't for the life of me figure out how to display ONLY a cartoon representation of my protein and backbone H-bonds. ChimeraX keeps forcing side-chain:backbone bonds.. I don't want that. I can do it if I show the backbone atoms, but I don't want to do that either. I only want it to show ONLY backbone H-bonds.

2 1

Problem of starting Chimera
by 郭家瑞 24 Aug '24

24 Aug '24

Hello, This is the first time I am stalling Chimera, but I meet the problem of starting the software. According to the Debug command, I have tried update my graphic driver, installed Gzip and tried different Chimera releases including 1.18, 1.17 and 1.14. However, the software still cannot be started. The content of debug log is copied as following: D:\Chimera 1.14\share\chimeraInit.py:99: UnicodeWarning: Unicode equal comparison failed to convert both arguments to Unicode - interpreting them as being unequal if chimera_env.get(e) == _original_environ.get(e): initializing general preferences loading Tix initializing graphics Return code: -1073741819 I am looking forward to any guidance or help for solving the problem. My graphic is NVIDIA Geforce 3050Ti and the opperation system is Windows 10. If necessary, more details can be supplied. Sincerely Appreciated, Jiarui Guo from China

2 1

Mac Version
by Gonzalo de Prat Gay 22 Aug '24

22 Aug '24

Hello I have downloaded Chimaera 1.18 for Mac I am running Ventura 13.4.1, and it tells me the file is corrupted when I try to open de dmg Is there any compatibility issue or should it run on this OS X? Thanks Gonzalo

3 5

chimera
by 2719354821＠qq.com 13 Aug '24

13 Aug '24

After installing and opening the UCSF Chimera software, pythonw.exe keeps popping up new windows, causing the software to malfunction. I have tried downloading various versions of the UCSF Chimera software, but after installation, when I double-click to open it, various interfaces keep popping up. At the same time, Microsoft Edge also continuously opens web pages, rendering both the software and the computer unusable. I found that a few years ago, someone in the community had the same experience. How can this be resolved? Most concerning is that, like them, I am also using a Honor laptop.

2 1

Chimera
by Kotin, Robert 13 Aug '24

13 Aug '24

Good afternoon – I’d appreciate advise for virus capsid viewing. Adeno-associated viruse structures, e.g., 1lp3, consist of the asymmetric unit repeated 60x to form the icosahedral capsid (T=1). I’d like to highlight the equivalent residue in each of the 60 subunits but haven’t figured out how to do that (except by manually going through each of the 60 chains). Please let me know if there are commands that can specify the residue in chains 1, 2, 3,…60. Thank you Robert Kotin

2 2

.crd file not opening
by safi ch 05 Aug '24

05 Aug '24

Greetings, hope you are doing well. I want your guidance on how can I open a .crd file on UCSF Chimera. I am working on a protein and its mutants and performed their docking via Swiss Dock, it gave results in form of .crd file that I cannot open. My supervisor also has no idea how to open it, so please help me in this regard, I need to open it to work further on my research. Waiting for your kind response please.

2 8

August 1 Chimera(X) website downtime
by Elaine Meng 01 Aug '24

01 Aug '24

Planned downtime for server maintenance: The Chimera and ChimeraX websites, Toolshed, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable August 1, 3-6 pm PDT. Apologies for any inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

1 1

column selection: chimera vs chimeraX
by 7mkf 22 Jul '24

22 Jul '24

Hi there, I'm an avid user of chimera and have begun transitioning to chimeraX. A feature I find very useful in chimera is expand selection to columns within the multialignviewer. Is there a way to do this in ucsf chimeraX? Many thanks, Mike

2 1

molmap onGrid option
by Hernando J Sosa 18 Jul '24

18 Jul '24

Dear Chimera I am using the molmap command with the option onGrid but the results are not what I would have expected. With a loaded map (#0) and an atomic model(#1) The command: molmap #1 6.0 onGrid #0 generates a map with a voxel size of 6.768 even though the loaded map #0 has a voxel size of 0.846 Trying to force the voxel size with molmap #1 6.0 onGrid #0 gridSpacing 0.846 produces the same result as the onGrid option overrides the gridSpacing option. How can I produce a map using molmap that has exactly the same dimensions and voxel size of map #0? Thanks H. _

2 1

Internal Server Error. Can Not Download chimera 1.18
by Setyanto Md 17 Jul '24

17 Jul '24

Dear Chimera User and Development Team, I tried to download ucsf-chimera version 1.18. However, the message 500 Internal Server Error appears. Is this error from our internet network, or is it from the chimera server? Thank you ------- Setyanto Tri Wahyudi ------- Computational Biophysics Group, Department of Physics, IPB University - Indonesia Gedung Fisika Wing-S Lt.2 Jl. Meranti Kampus IPB Darmaga Bogor - 16680 Indonesia

2 1

Docking with auto dock fails for a ligand containing a Boron atom
by Patrone Marco 15 Jul '24

15 Jul '24

Dear All, I’m trying to dock a ligand containing a boronate substituent using Auto Dock Vina within Chimera v. 1.13.1 The process fails as the B in the pdb instance is not recognized for Boron and the following syntax error is printed “Parse error on line 27 in file "ligand.pdbqt": ATOM syntax incorrect: "B" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive” Is there any way to overcome this? Are there newer/different libraries that inlcude also Boron element I can update my ADV with? Many thanks for your time and best regards, marco -- Marco Patrone – PhD Biocrystallography Unit Division of Immunology, Transplantation, and Infectious Disease (DITID) DIBIT – San Raffaele Scientific Institute Via Olgettina, 58 20132 Milano Italy phone: +39 0226434921 fax: +39 0226434153 http://www.hsr.it/research/organzation/massimo-degano [https://p.hsr.it/5xmille/b2024.jpg]<https://www.5xmille.org/?utm_source=firmamail&utm_medium=email&utm_campaign…> CODICE FISCALE 07636600962 Scopri di più su www.5xmille.org<https://www.5xmille.org/?utm_source=firmamail&utm_medium=email&utm_campaign…> Rispetta l’ambiente: non stampare questa mail se non è necessario. Respect the environment: print this email only if necessary.

2 1

Covalent substrate modeling and minimization
by wh-kelvin.chung＠polyu.edu.hk 14 Jul '24

14 Jul '24

Good day I am a researcher studying antibiotic interaction and trying to make a model with a substrate covalently bound to the active site. There is a homolog with a crystal structure (PDB: 4KQO), and I am going to add the bound substrate in this pdb file to my target protein where the mode was generated by alphafold server. Although the workflow shall be simple, I still have some problems, could you kindly help? 1. Firstly, I would like to check whether the model of 4KQO is good enough for modeling, by examining the electron density map (open 4KQO, open 4KQO from eds). However, I found that it is a bit different from the tutorial (https://www.cgl.ucsf.edu/chimerax/docs/quickstart/index.html, pdb:1a0m) that the electron density of 4KQO did not cover the substrate molecule. I am totally ignorant in crystallography, so, how could I visualize the electron density of the substrate? by any symmetry operation / command so that I could check whether there is "electron density in the substrate" ? 2. I aligned 4KQO with the alphafold generated model, and I deleted the protein from 4KQO, and combined the two model, make a bond between the active residue with the substrate, however, I am not sure how to (1) check the bond length and angle is appropriately assigned, and (2) do energy minimization to reorientate side change to eliminate the crash with the substrate. Thank you very much for your help in advance Have a nice weekend

4 3

Capturing output of measure center command
by ldreher＠smith.edu 12 Jul '24

12 Jul '24

Hello, I am trying to write a python script to prepare proteins for molecular docking, and as part of that I want to be able to identify and save the center coordinates of each protein. using runCommand('measure center #0') works fine, but I am at a loss as to how to capture the output of that command. Ideally I would like to save the output as a string in python. Any advice on how to go about this would be appreciated! Thanks! Laura

2 1

Difference between command line and menus
by edith.gincel＠u-paris.fr 09 Jul '24

09 Jul '24

Dear all I am trying to check contacts between ligands and protein. I tried to use the command line, to be able to do it semi-automatically, but I don't find any contact. When I use the command line, I find contacts. Has someone experienced such problems? Thank you for your help

2 7

Stereo in ChimeraX
by Engelhardt, Peter 01 Jul '24

01 Jul '24

Hi chimera team, We can’t get any stereo to work in ChimeraX though several trials. In the earlier Chimera all worked perfectly. We are especially interested in red-cyan stereo as it’s most suitable for a large public and easy to use even with colors. Could you please let us know how to install e.g. red-cyan stereo for ChimeraX. We thank you in advance Cheers Peter __________________________ Peter Engelhardt PhD., Docent Adjunct Professor in Molecular Genetics Unit of Molecular Electron Tomography and Nanoscopy Nanomicroscopy Center (NMC), Otanano Aalto University, School of Science and Technology, Puumiehenkuja 2, FI02150 Espoo Finland Mobil Phone: +358 400193342 Email: Peter.Engelhardt(a)Helsinki.Fi<https://webmail.helsinki.fi/horde/imp/dynamic.php?page=message&buid=2535&ma…> Email: Peter.Engelhardt(a)Aalto.Fi<mailto:Peter.Engelhardt@Aalto.Fi> Sent from my iPhone

2 1

script for comparing surfaces bits
by chiarini＠takisbiotech.it 24 Jun '24

24 Jun '24

Dear all, I'm trying to come up with some method to compare surfaces of the same protein area over some trajectory. A simple RMSF doesn't cover the analysis as a roto-traslation of some parts might retain the surface form and shape, whereas a residue might have a complete rearrangement of its surrounding without undergoing large RMSF changes. Some software based on Masif are available, tough they do not confront between trj frames. Are there any turnarounds in chimera to do this? A function similar to RMSD but for surfaces that maybe could be emplyed in this specific case? Thank you all, Valerio Chiarini -- Dr. Valerio Chiarini _Senior Scientist_ Proteins & Monoclona Antibodies Department b Takis Biotech c/o Tecnopolo Via di Castel Romano, 100 00128 Rome, Italy Tel.: +39 06-50576077 Fax: +39 06-50576710 Email: chiarini(a)takisbiotech.it Web: http://www.takisbiotech.it 196/03_ _Le informazioni contenute in questa comunicazione e gli eventuali documenti allegati hanno carattere confidenziale, sono tutelate dal segreto professionale e sono ad uso esclusivo del destinatario. Nel caso questa comunicazione Vi sia pervenuta per errore, Vi informiamo che la sua diffusione e riproduzione C( contraria alla legge e preghiamo di darci prontamente avviso e di cancellare quanto ricevuto. __Grazie._ _This e-mail message and any files transmitted with it are subject to attorney-client privilege and contain confidential information intended only for the person(s) to whom it is addressed. If you are not the intended recipient, you are hereby notified that any use or distribution of this e-mail is strictly prohibited: please notify the sender and delete the original message. __Thank you._

2 1

(no subject)
by furkan calapoğlu 20 Jun '24

20 Jun '24

How can i do organometalic ligand and protein docking ?

2 1

Score decimals question
by VALERIA MARIA CARRILLO RAMIREZ 19 Jun '24

19 Jun '24

Hi, I'm doing a work for college and my professor is asking for an analysis via Autodock Vina. However I have to calculate scores and the program is giving them with only one decimal and I need to report the values with 3 decimals. How can I change that? Thanks a lot :)

2 1

Aligning small molecules in Chimera
by Prathvi Singh 19 Jun '24

19 Jun '24

Hi Elaine, Is it possible to superimpose/align small molecules in chimera/chimeraX? I have isolated a very small part of a polypeptide chain from a PDB file (it contains a CO and NH group engaged in peptide bond formation and both the groups are flanked by C-alpha atoms such that the structure's formula becomes CH3-CO-NH-CH3). I have 10 such PDB files. I want to extract this fragment from each PDB file and superimpose them to know the differences. Thank you Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 1

RBVI downtime
by Eric Pettersen 13 Jun '24

13 Jun '24

Hi all, The RBVI compute cluster will be down for scheduled maintenance Monday and Tuesday of next week (June 17/18) which means that the Chimera and ChimeraX web sites (including the ChimeraX toolshed) and mailing lists will be down during that time. This also means that web services from Chimera/ChimeraX that access our compute cluster will not work (Blast Protein, Modeller tools, sequence realignment). We are sorry for any inconvenience. --Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

ChimeraX_InfoRequest
by Altan KARA (MAM-GMBE) 09 Jun '24

09 Jun '24

To whom it may concern, How we can create high resolution images with ChimeraX? No matter what I tried still the outputted images are not in high resolution. Thanks Dr. Altan KARA Kd. Uzman Araştırmacı TÜBİTAK MAM Gen Mühendisliği ve Biyoteknoloji Enstitüsü Barış Mah. Dr. Zeki Acar Cad. No.1 P.K. 21 41470 GEBZE / KOCAELİ T +90 262 677 3371 F +90 262 641 2309 www.mam.gov.tr altan.kara(a)tubitak.gov.tr

2 2

Converting a carbonyl group to carboxylic acid group
by Prathvi Singh 06 Jun '24

06 Jun '24

Hi Elaine, I have a SER residue which is in the middle of a polypeptide chain. Is there a way in chimera/chimeraX to specifically extract this residue such that the carbonyl group bonded to its N-terminal NH group also gets extracted but is converted to carboxylic acid group (-COOH group) before extracting? Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 3

Help saving models as .pdb file
by Jacek Jagodzinski 03 Jun '24

03 Jun '24

I have constructed model of pentameric protein by exchanging one of the chains with a very closely related chain from other variant of such pentameric protein. Chimera recognizes that my model consists of parts of two proteins. I would like to save it as a single protein file. When I attempt to save model as a single file (option in save dialog) a PDB file is produced. However, when I open this file in other application (such as Cresset Flare) to explore molecular dynamics or docking in this newly constructed hybrid system - it opens as two different proteins. Is it possible to “merge” the parts to become a single pentameric protein, that would behave as single entity during docking or MD computations? Jacek Jagodzinski PS. I am not computational chemist, I am medicinal chemist by training and long career.

2 2

Using Chimera/AutoDock Vina for oligomers
by Ballanah Torbett 24 May '24

24 May '24

Hello, I hope this email finds you well! I had a question about using the Chimera and its AutoDock Vina interface, as I'm relatively new to using these programs. I've been able to dock substrate onto one binding site of my protein of interest, but I'd like to apply it to the other three binding sites of the tetramer as well. I wouldn't be able to work with the monomer since the active sites are formed from the interactions between the N and C termini. I have also tried saving the session as a new PDB file and docking a new substrate, but it bound to the already-occupied site. Is there a way to dock substrate onto the other sites while "ignoring" the occupied site? Thank you! Sincerely, Ballanah Torbett 3rd Year PhD Student Gaucher Group Georgia State University

2 1

Saving symmetry model in pdb format
by Kailash Singh Bisht 17 May '24

17 May '24

Hello ChimeraX team I am trying to export the symmetry structure of the protomer virus protein as a pdb file but whenever I am saving that model it only saves the same protomer instead of the whole symmetry structure. Can you please help? How to export those symmetry models as PDB files -- With Regards Thanking You Kailash Singh Bisht Ph.D. Student

2 1

Displaying angles in chimera
by Prathvi Singh 16 May '24

16 May '24

Hi Elaine, Is it possible in chimera/chimeraX to display angles between two covalent bonds like in pymol? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 2

Difficulty with Ribbon Visualization in Chimera Software
by 罗舒月 15 May '24

15 May '24

Dear Chimera Software Team,     I hope this email finds you well. I am writing to seek assistance regarding a challenge I am facing while using the Chimera software. Specifically, I am experiencing difficulties in visualizing my protein structure in ribbon mode.     When I load my PDB file and choose the ribbon representation, the resulting visualization appears as linear segments rather than the desired helical structure. I am unsure whether this issue is related to my file or if there is a specific step or setting I am overlooking.    I would greatly appreciate it if you could provide me with guidance on how to achieve the desired helical ribbon model in Chimera or any insights on potential issues with my file. To assist you in troubleshooting, I have attached the PDB file in question, as well as an image showing the current ribbon visualization.    Thank you in advance for your time and support. I look forward to your prompt response.  Best regards, Shuyue Luo the result of my file the effect I want 发自我的企业微信

3 2

Difficulty with Ribbon Visualization in Chimera Software
by 罗舒月 14 May '24

14 May '24

Dear Chimera Software Team,      I hope this email finds you well. I am writing to seek assistance regarding a challenge I am facing while using the Chimera software. Specifically, I am experiencing difficulties in visualizing my protein structure in ribbon mode.      When I load my PDB file and choose the ribbon representation, the resulting visualization appears as linear segments rather than the desired helical structure. I am unsure whether this issue is related to my file or if there is a specific step or setting I am overlooking.    I would greatly appreciate it if you could provide me with guidance on how to achieve the desired helical ribbon model in Chimera or any insights on potential issues with my file. To assist you in troubleshooting, I have attached the PDB file in question, as well as an image showing the current ribbon visualization.     Thank you in advance for your time and support. I look forward to your prompt response.   Best regards, Shuyue Luo the result of my file the effect I want 发自我的企业微信

1 0

Preparing molecular structures for panel of figures
by Prathvi Singh 10 May '24

10 May '24

Hi Elaine, I want to create a panel containing 4 figures. Each figure in the panel will be a ball and sticks representation of an amino acid residue. I have tried using the "Tile Structures" feature in UCSF chimera to create the panel. Although it does ease the job a lot, I find it difficult in aligning residue labels or 2D labels. Is there a grid based feature which can display a grid on the chimera workspace so that I can use its lines as a guide to better align my labels? Thanks in advance Prathvi, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 1

Chimera scripting
by Flip Jansen 06 May '24

06 May '24

Hello Chimera dev team, I am a junior specialist from across the hall working at the Fraser Lab and I have some questions about using chimera scripting for omitting densities and generating reference maps. One of the issues I have been having has been that using the molMap function in Chimera generates a non-cubic output and I am aware that I can use onGrid with a pre-existing map with the desired dimensions. However, in the workflow, I am setting up I do not yet have a reference map and I am in most scenarios starting with just a PDB or an adapted from PDB map. Is there a way to let Chimera(X) generate a cubic output map from PDB without requiring another map from an external program like cryoSPARC? Another question I have is regarding the loss of secondary structural information when saving a map in Chimera. Is there a way to save a map while maintaining that information? Any help is highly appreciated, I would also be happy to come by an talk in person. Best, Flip Jansen

2 1

Issues installing chimera on linux
by Conor Bonal 02 May '24

02 May '24

Hello, I tried to follow the tutorial to install Chimera on Linux. I'm using a computer with Ubuntu 18.04.5 and it is 64-bit. I followed the tutorial word for word then substituted "chimera-installer.bin" with the file name "chimera-1.17.3-linux_x86_64.bin" and I continued to get the same error message telling me the file or directory does not exist, although I can clearly see it in my downloads folder. Can you provide any assistance with installing the software? Thank you! Conor Bonal

2 1

Question about save images
by Chang, Jufang 29 Apr '24

29 Apr '24

Hi, there, I used Chimera for a very short period of time. When I just started using Chimera I was able to save image by going to "file" and "save image" to save the image on the display window. For some reason, this stopped working. Now, after I did the same thing, the image I saved has complete blackness (attached). I wonder whether I might get be able to get help from you. I also tried using command line to save image. The result is the same. The exact procedure I used are: Go to "Presets", choose "publication 1" , then go to "File" and "save image" I used window system. Thank you J ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

3 4

Ligand has no chain ID after saving docked complex
by kalabamelisa＠yahoo.com 24 Apr '24

24 Apr '24

Hello. I want to use PRODIGY web server to predict the binding affinity of my docked complexes, and the server requires a single PDB file containing both the docked ligand and the protein. I open the .pdbqt file containing the docking results using ViewDock and then I open my receptor file in .pdb format. I combine the two (receptor and the best ligand) and then save the complex as a PDB file. The server requires the ligand's name and what chain it's on, but when I open the complex in Chimera the ligand has no chain ID, it just shows up as "het". How do I assign a chain ID to my ligand in this situation?

2 2

Problem in Docking Output
by Mrs Kumud Pant 22 Apr '24

22 Apr '24

Dear Developers, I am facing problem of incomplete docking. The error statement is pasted below. Also attaching receptor and ligand file for your perusal. Since I am new to this software therefore, detailed explanation is requested in eliminating the problem. #0, chain A: prostaglandin G/H synthase 1 Model 0 (oxidoreductase.pdb) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. No incomplete side chains Terminii for oxidoreductase.pdb (#0) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: LEU 599.A Chain-final residues that are not actual C terminii: 595 hydrogen bonds Hydrogens added Charge model: AMBER ff14SB Total charge for #0: -2.000 No incomplete side chains Terminii for oxidoreductase.pdb (#0) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: LEU 599.A Chain-final residues that are not actual C terminii: 566 hydrogen bonds Hydrogens added Charge model: AMBER ff14SB Total charge for #0: -2.000 Wrote C:\Users\GEU\Downloads\new dock\oxidoreductase.pdb #1, chain A: prostaglandin G/H synthase 1 Terminii for oxidoreductase.pdb (#1) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: #1 MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #1 LEU 599.A Chain-final residues that are not actual C terminii: 566 hydrogen bonds Hydrogens added Wrote oxidoaspirin.receptor.pdb into C:\ProgramData\Chimera adding gasteiger charges to peptide Wrote oxidoaspirin.ligand.pdb into C:\ProgramData\Chimera Autodock Vina ligand docking initiated for oxidoreductase.pdb Status file contents: 1639 1713445280.81 1713445293.84 Terminii for oxidoreductase.pdb (#1) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: #1 MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #1 LEU 599.A Chain-final residues that are not actual C terminii: 566 hydrogen bonds Hydrogens added Wrote oxidoaspirin.receptor.pdb into C:\ProgramData\Chimera adding gasteiger charges to peptide Wrote oxidoaspirin.ligand.pdb into C:\ProgramData\Chimera Autodock Vina ligand docking initiated for oxidoreductase.pdb Running AutoDock Vina for oxidoreductase.pdb failed; see Reply Log for more information Application stderr ----- [no output] ----- Application stdout ----- [no output] ----- Status file contents: 1639 1713445301.94 1713445303.83 Running AutoDock Vina for oxidoreductase.pdb failed; see Reply Log for more information Application stderr ----- [no output] ----- Application stdout ----- [no output] ----- Search error: couldn't compile regular expression pattern: invalid escape \ sequence Probably an error in regular expression. Search error: couldn't compile regular expression pattern: invalid escape \ sequence Probably an error in regular expression. #1, chain A: prostaglandin G/H synthase 1 Terminii for oxidoreductase.pdb (#1) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: #1 MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #1 LEU 599.A Chain-final residues that are not actual C terminii: 566 hydrogen bonds Hydrogens added Wrote oxidoaspirin.receptor.pdb into C:\ProgramData\Chimera adding gasteiger charges to peptide Wrote oxidoaspirin.ligand.pdb into C:\ProgramData\Chimera Autodock Vina ligand docking initiated for oxidoreductase.pdb Status file contents: 1639 1713447116.49 1713447119.45 Running AutoDock Vina for oxidoreductase.pdb failed; see Reply Log for more information Application stderr ----- [no output] ----- Application stdout ----- [no output] ----- Terminii for oxidoreductase.pdb (#1) chain A determined from SEQRES records Chain-initial residues that are actual N terminii: #1 MET 1.A Chain-initial residues that are not actual N terminii: Chain-final residues that are actual C terminii: #1 LEU 599.A Chain-final residues that are not actual C terminii: 566 hydrogen bonds Hydrogens added Wrote oxidoaspirin.receptor.pdb into C:\ProgramData\Chimera adding gasteiger charges to peptide Wrote oxidoaspirin.ligand.pdb into C:\ProgramData\Chimera Autodock Vina ligand docking initiated for oxidoreductase.pdb Status file contents: 1639 1713447148.99 1713447151.35 Running AutoDock Vina for oxidoreductase.pdb failed; see Reply Log for more information Application stderr ----- [no output] ----- Application stdout ----- [no output] ----- Thank you in advance Dr. Kumud Pant Associate Professor Department of Biotechnology Graphic Era (Deemed to be) University Dehradun

2 1

i can´t installate chimera.
by Suilma Ivette Pérez Pineda 14 Apr '24

14 Apr '24

hi! i cannot installate chimera, when i acept "terms and conditions", the windows says tht "i dessagree", when im agree. Suilma Ivette Pérez Pineda

2 1

AutoDockVina: Merge charges
by limbuingso2112＠gmail.com 12 Apr '24

12 Apr '24

Hi all, Beginner to molecular docking. I tried to find answers to my question but to no avail and was hoping this site would help me in some ways. When conducting autodockVina after DockPrep, Tools > Surface/Binding Analysis > AutoDockVina. In the receptor/ligand options, there are two sections where you can merge charges Straight from the documentation: Merge charges and remove non-polar hydrogens (true/false) - note AutoDock Vina does not use charges or nonpolar hydrogens, so this setting is not expected to affect results except for the presence or absence of nonpolar hydrogens in the processed receptor Merge charges and remove lone pairs (true/false) - note AutoDock Vina does not use charges or lone pairs, so this setting is not expected to affect results except for the presence or absence of lone pairs in the processed receptor (and there may not have been any lone pairs to start with) While there is a caveat that it might affect results in some ways. I have been trying to dig deeper into this merge charges aspect of docking and could not find much explanation or documentation on it. My question stems from the fact that im docking a protein [5A8K] with 1 ligand. When i put false for the merge charges for both ligand and receptor, i get a negative score but with a absurd binding pose but when i put true for the merge charges [default] for both ligand and receptor, i get a negative score with a good binding pose which has matched literature. I initially placed false because i got the idea that merging charges was an approximation/simplification and i wanted to model the system better without merging charges. If autodock does not use charges at all, why does my result differ so much when i change those settings. Any insights into this matter is highly appreciated. TIA

2 1

AutoDockVina: Merge charges
by limbuingso2112＠gmail.com 11 Apr '24

11 Apr '24

Hi all, Beginner to molecular docking. I tried to find answers to my question but to no avail and was hoping this site would help me in some ways. When conducting autodockVina after DockPrep, Tools > Surface/Binding Analysis > AutoDockVina. In the receptor/ligand options, there are two sections where you can merge charges Straight from the documentation: Merge charges and remove non-polar hydrogens (true/false) - note AutoDock Vina does not use charges or nonpolar hydrogens, so this setting is not expected to affect results except for the presence or absence of nonpolar hydrogens in the processed receptor Merge charges and remove lone pairs (true/false) - note AutoDock Vina does not use charges or lone pairs, so this setting is not expected to affect results except for the presence or absence of lone pairs in the processed receptor (and there may not have been any lone pairs to start with) While there is a caveat that it might affect results in some ways. I have been trying to dig deeper into this merge charges aspect of docking and could not find much explanation or documentation on it. My question stems from the fact that im docking a protein [5A8K] with 1 ligand. When i put false for the merge charges for both ligand and receptor, i get a negative score but with a absurd binding pose but when i put true for the merge charges [default] for both ligand and receptor, i get a negative score with a good binding pose which has matched literature. I initially placed false because i got the idea that merging charges was an approximation/simplification and i wanted to model the system better without merging charges. If autodock does not use charges at all, why does my result differ so much when i change those settings. Any insights into this matter is highly appreciated. TIA

1 0

Protein Modeling with Model/Refine Loops Tool
by Ecem Güngör 09 Apr '24

09 Apr '24

Hello all, I have encountered an issue while working with a protein in complex with ligands. There are some missing regions in the protein structure, and I attempted to model these regions using the "Model/Refine Loops" tool in UCSF Chimera (version 1.17.3). However, I observed that when I saved the modeled structures as PDB files, the ligands were not included in the file. Additionally, in some models, the modeled C-terminal extended into the binding pocket in an unusual manner. I am curious whether this tool takes into account the presence of ligands or molecules in the structure while modeling missing regions. How can I prevent such issues from occurring? How can I model the missing long C-terminal in Chimera while ensuring that the presence of other ligands or molecules is also considered? Thanks in advance. Ece.

2 1

Bug
by Anoop B S 09 Apr '24

09 Apr '24

Sometimes its not responsive.How to resolve that

2 1

Opening chimera within MS powerpoint
by Prathvi Singh 08 Apr '24

08 Apr '24

Hi Elaine, I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)? This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation. Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

4 4

Fw: Chimera numpy error
by Garrett Scapellato 01 Apr '24

01 Apr '24

Garrett Scapellato Research Technician II Edwards Lab DHVI Duke University [cid:133a3af9-3314-4e94-9c72-9d0bc6ffe6cc] ________________________________ From: Garrett Scapellato <garrett.scapellato(a)duke.edu> Sent: Friday, March 29, 2024 2:24 PM To: pett(a)cgl.ucsf.edu <pett(a)cgl.ucsf.edu> Subject: Re: Chimera numpy error Eric, Apologies for sending so many emails. I was able to delete all numpy modules from Chimera. Now when I try to open Chimera I get this error. Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 680, in init import chimera File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 2782, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/Applications/Chimera.app/Contents/Resources/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/Applications/Chimera.app/Contents/Resources/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/Applications/Chimera.app/Contents/Resources/share/chimera/selection/__init__.py", line 1033, in <module> from chimera import oslParser File "/Applications/Chimera.app/Contents/Resources/share/chimera/oslParser.py", line 690, in <module> import numpy ImportError: No module named numpy I tried reinstalling numpy the same way I installed pandas, but I get the same error as above. How can I fix this issue? Thanks, Garrett Scapellato Research Technician II Edwards Lab DHVI Duke University [cid:5a4e481b-169d-4789-87e0-4c616c5183fc] ________________________________ From: Garrett Scapellato Sent: Friday, March 29, 2024 2:11 PM To: pett(a)cgl.ucsf.edu <pett(a)cgl.ucsf.edu> Subject: Chimera numpy error Eric, I get the following error whenever I try to open chimera. I tried uninstalling numpy with a pip installer, and that didn't work, I assume because it doesn't uninstall the module from chimera specifically. DHVI-F5KJC04Q:~ edwardslab$ chimera Traceback (most recent call last): File "/Applications/Chimera.app/Contents/Resources/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", line 680, in init import chimera File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 2782, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/Applications/Chimera.app/Contents/Resources/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/Applications/Chimera.app/Contents/Resources/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/Applications/Chimera.app/Contents/Resources/share/chimera/selection/__init__.py", line 1033, in <module> from chimera import oslParser File "/Applications/Chimera.app/Contents/Resources/share/chimera/oslParser.py", line 690, in <module> import numpy File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/numpy/__init__.py", line 142, in <module> from . import core File "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/numpy/core/__init__.py", line 91, in <module> raise ImportError(msg.format(path)) ImportError: Something is wrong with the numpy installation. While importing we detected an older version of numpy in ['/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/numpy']. One method of fixing this is to repeatedly uninstall numpy until none is found, then reinstall this version. I also tried rm -rf ~/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/numpy/ repeatedly, but that didn't work. I couldn't use Finder to navigate to the python2.7 folder to delete the files manually, either. Any help would be appreciated. Thanks, Garrett Scapellato Research Technician II Edwards Lab DHVI Duke University [cid:570bb78a-e702-4643-995c-11d5cdaf82fd]

2 1

Importing Modules into Chimera
by Garrett Scapellato 28 Mar '24

28 Mar '24

Chimera Help, Hello, I hope you are doing well. I am attempting to use the "pandas" module while using Chimera to read python code. I receive this error any time I do. I am able to use pandas while using other python interpreters on my computer. I am also able to use other modules, such as NumPy when using Chimera to run python code. Any help in this issue would be greatly appreciated. Thank you for your time, Garrett Scapellato Research Technician II Edwards Lab DHVI Duke University [cid:d20c0851-a63b-49a0-a3e5-efa576c4dc55]

2 9

Problems installing Chimera for command line use on Centos
by Evan Kantrowitz 25 Mar '24

25 Mar '24

Hi All, I am trying to move our viewmotions.bc.edu <http://viewmotions.bc.edu/> server to a new server running Centos 9. I downloaded the most recent chimera (chimera-1.17.3-linux_x86_64.bin <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=linux_x…>). Followed the install procedure with no issues. When I ran chimera I got these errors, both in commandline mode or regular. Any help would be appreciated. Thanks kantrow@localhost ~/vm_test]$ chimera --preferences /data/viewmotions/lib/chimeraVMPreferences --script chimera_script.py Traceback (most recent call last): File "/progs/share/__main__.py", line 73, in <module> value = chimeraInit.init(sys.argv) File "/progs/share/chimeraInit.py", line 680, in init import chimera File "/progs/share/chimera/__init__.py", line 2782, in <module> from SimpleSession import BEGIN_RESTORE_SESSION, END_RESTORE_SESSION File "/progs/share/SimpleSession/__init__.py", line 14, in <module> from save import saveSession, sessionID, noAutoRestore, autoRestorable, \ File "/progs/share/SimpleSession/save.py", line 13, in <module> from chimera import replyobj, selection, SessionPDBio, version File "/progs/share/chimera/replyobj.py", line 24, in <module> import Tkinter File "/progs/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module> import _tkinter # If this fails your Python may not be configured for Tk ImportError: libXss.so.1: cannot open shared object file: No such file or directory ----------------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu <mailto:evan.kantrowitz@bc.edu> Emeritus Professor of Chemistry Cell: 617-775-9915 Boston College www2.bc.edu/evan-kantrowitz <http://www2.bc.edu/~kantrow> -----------------------------------------------------------------------------

2 1

cannot access Chimera website
by lbmccusker＠retired.ethz.ch 19 Mar '24

19 Mar '24

I am an enthusiastic user of Chimera for non-protein applications (in particular zeolites), and would like to use it in an upcoming workshop on charge flipping. However, when I tried to check the website (https://www.cgl.ucsf.edu/chimera/ to give students instructions for downloading, I got the message Secure Connection Failed An error occurred during a connection to http://www.cgl.ucsf.edu PR_END_OF_FILE_ERROR Error code: PR_END_OF_FILE_ERROR The page you are trying to view cannot be shown because the authenticity of the received data could not be verified. Please contact the website owners to inform them of this problem. Can you check into this? I tried Safari, Firefox and Edge, and all have the same problem. Thanks! Lynne McCusker

2 2

Can I import the molecule Cellulose in Chimera?
by Mazin Nasralla 18 Mar '24

18 Mar '24

Hello, I would like to open a molecule of cellulose https://en.wikipedia.org/wiki/Cellulose in Chimera. I go to Open Fetch ID and open the Pubchem option and input the id and I get this error. [cid:image001.png@01DA7784.1097E770] I can import cellobiose which is a two monomer β-Glucose. If I could import something with say 6 monomers that would be fine. Is there a way to do it? Thanks, Mazin

2 1

APBS OpenDX file conversion to XYZ
by Scott Bembenek 05 Mar '24

05 Mar '24

Is it possible to use Chimera to convert an APBS OpenDX grid to coordinates: x,y,x, grid point value?

3 4

volume image intensity 1 vs 0.99
by Tyler Luchko (Lists) 05 Mar '24

05 Mar '24

Hello, I’m trying to fine tune the intensity of my volume image, but there is a large discontinuity between an intensity of 0.99 and 1 that is causing me problems. Using the following script, I get volume #1 style image volume #1 colormapongpu true volume #1 level 0,1 color black level 1,.55 color white level 2,.6 color blue level 4,0.99 color orange Changing the last list to volume #1 level 0,1 color black level 1,.55 color white level 2,.6 color blue level 4,1 color orange I get The last level goes from barely visible to completely opaque. I don’t know if this is the intended behavior or not, but I would like to have a smooth transition to full intensity. Is this possible? I notice that for levels between 0 and 1, the intensity seems to work as I expected. It is only for levels greater than 1 that I notice this behavior. I am on a Mac using version 1.7.1. The MRC file is 59 MB, so I have not included it. If it helps, the visualization is trying to show the water density around methanol (not shown) relative to bulk. Black (0) is zero density, white (1) is bulk density, blue (2) is 2 times bulk density, and orange (4) is 4 time bulk density. Thank you, Tyler

2 1

Rview in UCSF Chimera
by Richardson, Cory 04 Mar '24

04 Mar '24

Hi, I am new to chimera and would like to use 'rview' in UCSF Chimera. I have UCSF Chimera version 1.17.3 installed and would like to use 'rview' as it is not currently listed under Tools as an option to select. May you please provide guidance on how I may get UCSF Chimera to recognize and integrate 'rview'? Respectfully, Cory Richardson Sr., Systems Engineer Developing Brain Institute Diagnostic Imaging and Radiology Children’s National Hospital O: (202) 476-3866 F: (202) 476-6833 S: DevelopingBrainReserachLab [Description: cnmc_logo_sig2] “Scientists study the world as it is, engineers create the world that never has been.” Theodore von Kármán 1962 National Medal of Science Recipient Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

2 1

how to select atoms without substituents?
by Sara Luz Gomez Maya 04 Mar '24

04 Mar '24

Hi all, Is there any way to select (or directly remove) atoms without substituents? The situation is that I have to cut a region of a system. So, after selecting by zone *without* including the entire residues, I save the selection and I get some single atoms that I would like to get rid of. For example, in the attached file I got H atoms, C atoms, and also C2 chains that do not have any sense even if I complete their valences by adding H. Notice that in such a way they will become H2, CH4 and CH3CH3, respectively, which are very strange molecules for my system that actually contains phospholipids, ibuprofen, and water. I would like to know if there is any automatic tool to do it, for example defining an attribute or using the command line. Any help is appreciated. Regards, Sara

2 1

Dock problem selenium atom
by turgut şekerler 11 Feb '24

11 Feb '24

Dear Chimera Team, I hope this message finds you well. I am writing to inquire about an issue I encountered while attempting to perform docking with a selenium atom using the Dock Prep module in Chimera. My goal is docking selenium atom and my target protein. But ı always get a error message : cant prepare ligand. I have been utilizing Chimera's Dock Prep module to prepare ligands for docking with proteins, and it has been an effective tool thus far. However, I have encountered difficulties when attempting to prepare a ligand containing a selenium atom. It seems that the Dock Prep module is unable to handle the selenium atom properly, resulting in errors during ligand preparation. I have attempted to troubleshoot this issue by researching error codes and exploring potential solutions, but I have been unable to find a resolution. As such, I am reaching out to inquire if there are any specific recommendations or alternative approaches that could be used to successfully prepare a ligand containing a selenium atom for docking in Chimera. I understand that Chimera utilizes standard force field parameters for ligand preparation, but given the unique properties of selenium, it may be necessary to consider additional or specialized parameters to ensure accurate docking results. Any guidance or assistance you could provide on this matter would be greatly appreciated. I am eager to resolve this issue and continue utilizing Chimera for my docking studies. Thank you for your attention to this matter. I look forward to your response. Sincerely,

2 1

Trouble in Creating Peptide bond
by Vignesh Nandhagopal 06 Feb '24

06 Feb '24

Dear Chimera Help Team, I want to create a peptide bond. I followed this manuscript which I have attached along with this mail. I followed the steps of the manual I have used and I have seen a slight change in build structure. Kindly help me with this I am getting an error in the unrecognized protein code. Kindly help me with the steps.

2 3

polymer formation
by Kainaat Mahzaib 02 Feb '24

02 Feb '24

Respected sir, I've been using Chimera software for quite some time now, but I'm unable to create a hexamer from a monomer. Is there any feature available to do so? and if present can you guide me on how to do it... please attach some tutorials too if possible. I'll be grateful to you, as these will be added in my research thesis. Regards, Kainaat Mahzaib John

2 1

polymer formation
by Kainaat Mahzaib John 02 Feb '24

02 Feb '24

Respected sir, I've been using Chimera software for quite some time now, but I'm unable to create a hexamer from a monomer. Is there any feature available to do so? and if present can you guide me on how to do it... please attach some tutorials too if possible. I'll be grateful to you, as these will be added in my research thesis. Regards, Kainaat Mahzaib John

1 0

CHIMERA scripting
by chiarini＠takisbiotech.it 31 Jan '24

31 Jan '24

Dear Responsible, I am trying to acquaint myself with "chimera --nogui --script" mode in order to automatize some pdb processing for a pipeline. I manage to search for pdb, to open the file, to select residues and to calculate COM for the selection. On the shell, I get the COM coordinates but I would like to print or store them to write them elsewhere. So the question is how can I print the replylog from shell to a text file, under the --nogui mode? I have tried with saveReplyLog but it doesn't seem to work...Any suggestions are appreciated. This is an excerpt from what I'm writing so far: import os from chimera import runCommand as rc from chimera import replyobj from chimera import saveReplyLog #change to the folder containing the pdb files os.chdir("xxx/yyy/zzz/ABC.pdb") def find_string_with_substring(string, substring): for s in strings: if substring in s: return s return None # list_files contain only the .pdb files list_pdb_files = [fn for fn in os.listdir(".") if fn.endswith(".pdb")] # specify the characters 'HLA' you want the filenames contain HLA_characters = HLA file_pdb_HLA = fins_string_with_substring(list_pdb_files, HLA_characters) print(list_pdb_files) print(file_pdb_HLA) nome = file_pdb_HLA replyobj.status(Processing " + nome) rc ("open " + nome) rc ("select :1.232") rc("measure center sel") saveReplyLog("~/reply-log.txt") Thank you so much -- Dr. Valerio Chiarini _Senior Scientist_ Proteins & Monoclona Antibodies Department b Takis Biotech c/o Tecnopolo Via di Castel Romano, 100 00128 Rome, Italy Tel.: +39 06-50576077 Fax: +39 06-50576710 Email: chiarini(a)takisbiotech.it Web: http://www.takisbiotech.it 196/03_ _Le informazioni contenute in questa comunicazione e gli eventuali documenti allegati hanno carattere confidenziale, sono tutelate dal segreto professionale e sono ad uso esclusivo del destinatario. Nel caso questa comunicazione Vi sia pervenuta per errore, Vi informiamo che la sua diffusione e riproduzione C( contraria alla legge e preghiamo di darci prontamente avviso e di cancellare quanto ricevuto. __Grazie._ _This e-mail message and any files transmitted with it are subject to attorney-client privilege and contain confidential information intended only for the person(s) to whom it is addressed. If you are not the intended recipient, you are hereby notified that any use or distribution of this e-mail is strictly prohibited: please notify the sender and delete the original message. __Thank you._

2 3

Intune Deployment
by CLIFFORD RAYMOND 31 Jan '24

31 Jan '24

Hi, My name is Clifford Raymond and I'm a manager in the tech department at East Brunswick Public Schools in New Jersey. I would like to know if you have the Chimera software in a MSI format for ease of installation? I'm currently trying to push the software out to my teachers through Microsoft Intune and the installer fails for unknown reasons. If you can assist I would greatly appreciate it. Clifford Raymond Senior Manager of Desktop Support Admin Building 760 Route 18N 732-613-6735 clifford.raymond(a)ebnet.org<mailto:clifford.raymond@ebnet.org> ________________________________ CONFIDENTIALITY NOTICE: The contents of this email message and any attachments are intended solely for the addressee(s) and may contain confidential and/or privileged information. If you are not the intended recipient of this message or their agent, or if this message has been addressed to you in error, please immediately alert the sender by reply email and then delete this message and any attachments. If you are not the intended recipient, you are hereby notified that any use, dissemination, copying, or storage of this message or its attachments is strictly prohibited. Email received by or sent to school district officials/employees is subject to the Open Public Records Act [OPRA]. Consider alternate avenues of communication should you have concerns about the contents of your email being read by someone other than the person(s) you are contacting. ________________________________

3 5

Nucleic acid "mutation"
by Samo Lešnik 30 Jan '24

30 Jan '24

Dear Madam/Sir, I was wondering if it possible to "mutate" a base pair in nucleic acid (e..g A-->C), in the same way as can very elegantly be done for proteins with the rotamere function. Thank you and best regards, Samo

2 2

PDB file breaking down
by NCdt In Gue Chang 30 Jan '24

30 Jan '24

Good Afternoon, I'm currently a master's student using chimera but I have a problem and I was wondering if you guys have a solution for it. When the original PDB file is loaded onto chimera, I can see different alpha and beta chains however, when I run optimization using gaussian program and load the fchk file or pdb file converted from chk file, the chains are gone and I'm left with just atoms. When I convert the chk file to pdb file in gaussian, it does the same and I was wondering if you guys know a solution or tips to bypass this. If you could help me out, it would be great! Thank you ASLt / Ens 2 In Gue Chang Royal Military College of Canada Canadian Armed Forces s29459(a)rmc-cmr.ca / Tel: 778-828-1252 Collège militaire royal du Canada Forces armées canadiennes s29459(a)rmc-cmr.ca / Tél: 778-828-1252

2 1

CHIMERA scripting
by chiarini＠takisbiotech.it 30 Jan '24

30 Jan '24

Dear Responsible, I am trying to acq -- Dr. Valerio Chiarini _Senior Scientist_ Proteins & Monoclona Antibodies Department b Takis Biotech c/o Tecnopolo Via di Castel Romano, 100 00128 Rome, Italy Tel.: +39 06-50576077 Fax: +39 06-50576710 Email: chiarini(a)takisbiotech.it Web: http://www.takisbiotech.it 196/03_ _Le informazioni contenute in questa comunicazione e gli eventuali documenti allegati hanno carattere confidenziale, sono tutelate dal segreto professionale e sono ad uso esclusivo del destinatario. Nel caso questa comunicazione Vi sia pervenuta per errore, Vi informiamo che la sua diffusione e riproduzione C( contraria alla legge e preghiamo di darci prontamente avviso e di cancellare quanto ricevuto. __Grazie._ _This e-mail message and any files transmitted with it are subject to attorney-client privilege and contain confidential information intended only for the person(s) to whom it is addressed. If you are not the intended recipient, you are hereby notified that any use or distribution of this e-mail is strictly prohibited: please notify the sender and delete the original message. __Thank you._

1 0

Inquiry regarding file opening issue
by LEE JIA QI . 26 Jan '24

26 Jan '24

Dear Ms/Mr, I hope this email finds you well. I am writing to bring to your attention an issue I am experiencing with your software. I have been attempting to open my protein file using Chimera, but unfortunately I have encountered difficulties. The file opened with nothing, but I can open it last time I will send my file here, and I would appreciate it if you could provide guidance for me as soon as possible. I look forward to your assistance in resolving this issue. Best regards Jia Qi -- *PENAFIAN*: E-mel ini dan apa-apa fail yang dikepilkan bersamanya ("Mesej") adalah ditujukan hanya untuk kegunaan penerima(-penerima) yang termaklum di atas dan mungkin mengandungi maklumat sulit. Anda dengan ini dimaklumkan bahawa mengambil apa jua tindakan bersandarkan kepada, membuat penilaian, mengulang hantar, menghebah, mengedar, mencetak, atau menyalin Mesej ini atau sebahagian daripadanya oleh sesiapa selain daripada penerima(-penerima) yang termaklum di atas adalah dilarang. Jika anda telah menerima Mesej ini kerana kesilapan, anda mesti menghapuskan Mesej ini dengan segera dan memaklumkan kepada penghantar Mesej ini menerusi balasan e-mel. Pendapat, rumusan, dan sebarang maklumat lain di dalam Mesej ini yang tidak berkait dengan urusan rasmi Universiti Kebangsaan Malaysia (UKM) adalah difahami sebagai bukan dikeluar atau diperakui oleh mana-mana pihak yang disebut. _*DISCLAIMER *: This e-mail and any files transmitted with it ("Message") is intended only for the use of the recipient(s) named above and may contain confidential information. You are hereby notified that the taking of any action in reliance upon, or any review, retransmission, dissemination, distribution, printing or copying of this Message or any part thereof by anyone other than the intended recipient(s) is strictly prohibited. If you have received this Message in error, you should delete this Message immediately and advise the sender by return e-mail. Opinions, conclusions and other information in this Message that do not relate to the official business of The National University of Malaysia (UKM) shall be understood as neither given nor endorsed by any of the aforementioned._

2 1

RMSD related query
by Dhindwal, Poonam 16 Jan '24

16 Jan '24

Hello, I was wondering if there is a way in Chimera to generate RMSD values for individual C alpha after structure alignment. I want to plot a graph of RMSD vs individual Amino acids. I performed 'Matchmaker' to generate the structure alignment and in the output tab, I can see rmsd bars on top of aligned sequences but I am unable to get the exact values of RMSD. Any help would be greatly appreciated. Thank you, Poonam Dhindwal, Ph.D. Post-doctoral fellow Department of Veterinary Microbiology Western College of Veterinary Medicine University of Saskatchewan 52 Campus drive Saskatoon SK S7N5B4 Phone: 639-317-4702 Email: pod898(a)usask.ca

2 2

CAN NOT RECORD VIDEO
by akmalyati sulong 16 Jan '24

16 Jan '24

Dear Sir or Madam, I am trying to record a movie in Chimera 1.17.2, but I consistently get the following error without a proper error message: "An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: ". Please help me to solve the problem Regards, Akmalyati email : nays5098(a)gmail.com

2 1

Query on the force field for energy minimization
by Prabuddha Bhattacharya 15 Jan '24

15 Jan '24

Dear Sir I would be grateful if you kindly let me know what force field is used by Chimera to optimize the geometry of a small organic molecule (not peptide) if I minimize the structure using the parameters as shared in the attached file. Thank you Kind regards *Prabuddha Bhattacharya * [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> 13/01/24, 15:02:51

2 2

LIGAND ENERGY MINIMIZATION
by DR. SHAZIA DAWOOD 12 Jan '24

12 Jan '24

Dear Sir , I want to minimize ligand and protein energy (pre docking step) . which chimera should be downloaded. I have an ucsf chimera for windows but currently it is not working. mention me chimera for my laptop windows 10. Thanking You -- *Dr. Shazia Dawood* Assistant Professor Pharmacy And Allied Health Sciences M.Phil. PhD. Biochemistry (UOK) North Karachi Campus, Plot No. 204-205 Sector 7B/1, North Karachi, Karachi, Pakistan. 7580 03319764733 +9221-36723221-6/111-11-IQRA shazia.dawood(a)iqra.edu.pk <saad.saleem(a)iqra.edu.pk> --

2 3

how to play trajectory frames ?
by Mitch Murphy 11 Jan '24

11 Jan '24

i tried "open 3ft6.psf coordsets true coords 3ft6.xtc" but i get "*'coordsets' has no suffix*" error message. and with "open 3ft6.psf coords 3ft6.xtc coordsets true" i get "*Expected a keyword*". how do i play frames of a trajectory. i have the psf and xtc or dcd trajectory files available.

2 1

Chimera export morph animation to 3D software
by Rebekah Moore 09 Jan '24

09 Jan '24

Hi, I was wondering if it's possible to export a morph animation to a 3D software like C4D, Maya, or Blender? I don't wish to render a "movie" in Chimera, as I would like to add the protein morph to a 3D scene in C4D with other animated objects and render it using Redshift. Is this possible? I've tried exporting in vrml xmd and glb formats, which in theory can have animation data, but when I import the files into C4D or Blender the protein has no keyframes and is static. Thanks for your help! Best, Rebekah

2 1

Finding interacting residues between receptor and ligand
by Prathvi Singh 04 Jan '24

04 Jan '24

Hi Elaine, I used the HPEPDOCK server (http:// huanglab.phys.hust.edu.cn/hpepdock /) to dock a ligand onto a receptor and downloaded the conformation (pose) of the ligand with lowest energy. Next I opened the receptor and ligand structure in UCSF chimera. The ligand fitted perfectly in the binding site. Now is it possible to know which residues of the ligand are interacting with the receptor and what is the type of non-covalent interaction between them? Thanks in advance, Prathvi

4 4

Need help using AutoDock Vina with Chimera on Mac
by Kush Unadkat 04 Jan '24

04 Jan '24

Greetings I am a student and I just got a new Mac and I am having a difficult time using AutoDock Vina in Chimera on my Mac. When working with two proteins (.mol2) format, I use AutoDock Vina in tools, input the required values and describe the path to “vina” using the browse button but instead of getting a pop up with the docking possibilities, I get an error like this: [Errno 30] Read-only file system: ‘docking.receptor.pdb’ I tried to look into the problem and if I can understand this correctly, I has something to do with Mac not allowing users to Write on the disk but I’m not sure. Can you please tell me what I’m doing wrong or how I can solve this issue? I am currently working on a project and I have a deadline so it is really important that I find a solution soon. Thank you. Your assistance is really valuable to me.

2 2

Unrecognized command: "hide"
by Gourav Das 03 Jan '24

03 Jan '24

Greetings everyone! I am trying to hide the hydrogen atoms of a molecule using the command line in Chimera. But the software does not recognize the "hide" command. In addition, it could not recognize the "undo" command. Please help me regarding this issue. With regards, Gourav Das Research Scholar Department of Chemistry IIT Kharagpur India

2 3

Unrecognized command: "hide"
by Gourav Das 03 Jan '24

03 Jan '24

Greetings everyone! I am trying to hide the hydrogen atoms of a molecule using the command line in Chimera. But the software does not recognize the "hide" command. In addition, it could not recognize the "undo" command. Please help me regarding this issue. With regards, Gourav Das Research Scholar Department of Chemistry IIT Kharagpur India

1 0

Highlighting residues
by Henen, Morkos 18 Dec '23

18 Dec '23

Hello, I'm running into an issue with using Chimera. When I move with the cursor over a protein residue or particular atom, it is used to show the name/number of this residue or atom. Now, for some reason, this option doesn't work. It has to be something I disabled by mistake, but I can't find that. Could you kindly guide me on what I can do to fix that? Thanks a lot Morkos Morkos Henen, Ph.D. Assistant Professor - Research University of Colorado-Anschutz Medical Campus Denver, USA

2 1

Distance between centroids
by Francesco Pietra 17 Dec '23

17 Dec '23

Hello with candidate version 1.15, linux64, X11 I want to measure the distance between the centroids of two aromatic stacking rings. The usual way of measuring distances does not work (clicking as needed has no effect), contrary to what the manual says. And I should have done successfully that measurement in the past. Also between one of the centroids and a regular atom: same issue. Distance between regular atoms works correctly. thanks for advice francesco pietra

2 2

A Software bug
by yongsheng_zhao 12 Dec '23

12 Dec '23

Hello, I installed the latest version of UCSF CHIMERA 1.17.3 on my win11 computer. After the installation, a window of related Settings kept coming up, and the EDGE browser was automatically opened to go to the CHIMERA help website. May I ask why? Now as long as you use this software, it keeps popping up small Windows, and the EDGE browser has been playing websites, like a virus, and it can't be used at all. | | yongsheng_zhao | | yongsheng_zhao2023(a)163.com |

3 3

[chimera] modeller.SequenceMismatchError
by Yang, Li-Yen 29 Nov '23

29 Nov '23

Hello, I am trying to use the modeler comparative tool in Chimera to model the structure of a protein (in fasta format) by another similar protein’s structure (in pdb format). I first associated this sequence (in fasta) with the corresponding chain in the pdb, and I used the modeller comparative tool to model the structure (I selected the fasta file as the target sequence and selected the corresponding chain in the pdb. ) However, I’m getting this error: _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb : From the log window, I didn’t get any other details beyond the above error. Does anyone know how I can figure out what is going wrong? Thank you! I really appreciate it! Best, Zoey

3 8

Changing threshold value of attributes
by Abril Gijsbers 28 Nov '23

28 Nov '23

Dear community, I want to render my model by attribute and change the thresholds (up and bottom limits). I want to change the 0.3 to 0.1 and the 2.6 to 2.7 (see the figure), this way I can compare the colour intensity with other conditions. [image: image.png] When I do that, I get the following error. My ignorance in command use limits my understanding. Could someone help me out to understand this? I have a colleague that changes the up and bottom limit with no problem. Why? :( ui tool show "Render By Attribute" Traceback (most recent call last): File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 759, in _set_value_cb self._redraw_cb() File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 646, in _redraw_cb self._bins = left + filled_bins + right ValueError: operands could not be broadcast together with shapes (0,) (157,) ValueError: operands could not be broadcast together with shapes (0,) (157,) File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 646, in _redraw_cb self._bins = left + filled_bins + right *See log for complete Python traceback.* Traceback (most recent call last): File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 760, in _set_value_cb self._move_cur_marker(v) File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 570, in _move_cur_marker self._active_markers._update_plot() File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 1222, in _update_plot self._update_marker_coordinates() File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 1207, in _update_marker_coordinates x, y = self._scene_xy(m.xy) File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 1090, in _scene_xy return self.histogram._scene_xy(abs_xy) File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 512, in _scene_xy num_bins = len(self._bins) TypeError: object of type 'function' has no len() TypeError: object of type 'function' has no len() File "/Applications/ ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/histogram.py", line 512, in _scene_xy num_bins = len(self._bins) *See log for complete Python traceback.*

2 1

saving selected residues
by Dieter Blaas 27 Nov '23

27 Nov '23

Hi, I selected several residues in an icosahedral viral capsid and want to save the corresponding pdb. However, whatever name I try to give this selection I receive the error "You must provide a file name that contains either $name or $number, which will be changed to the model name or model number (respectively) in the final saved file name". Can you please give me an example of a valid name! The viral subunits are 6sk5.pdb1 (#0.1), 6sk5.pdb1 (#0.2), and so on. I have no clue what I should call this selection for it being accepted. Thanks a lot, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas(a)meduniwien.ac.at ------------------------------------------------------------------------

2 4

recording a movie as series of PNGs with a transparent background
by Eugene Valkov 20 Nov '23

20 Nov '23

Hi folks, Per instructions ( https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html) I'm trying to make a movie with a series of PNGs with a transparent background to make into a GIF afterward. However, I get an error below. Any help would be appreciated! Thanks, Eugene Eugene Valkov Stadtman Investigator RNA Biology Laboratory National Cancer Institute This works: movie record size 1000,1000 format PNG supersample 4 directory ~/chimera_images; wobble y 120 aspect 2 model #1; wait 50; stop; movie stop This doesn't work: movie record size 1000,1000 format PNG supersample 4 transparentBackground true directory ~/chimera_images; wobble y 120 aspect 2 model #1; wait 50; stop; movie stop and I get this error: "Expected a keyword". Saving individual PNGs with a transparent background works fine. My version is 1.6.1 (2023-05-09).

2 2

Announcement: Release of DOCK 6.11
by Scott Brozell 16 Nov '23

16 Nov '23

We are pleased to announce the release of DOCK 6.11. DOCK is a suite of programs for molecular docking. The source code for DOCK 6.11 is available for download and free for academic users at http://dock.compbio.ucsf.edu/DOCK_6/index.htm This is a release of the new descriptor-driven de novo design method DOCK_D3N which takes advantage of the integration of the open source toolkit RDKit into DOCK6. DOCK_D3N tailors ligand growth towards desirable regions of chemical space by calculating cheminformatic descriptors at each stage of ligand construction. For full information on what is new in DOCK 6.11, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.11.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu

1 0

Unable run Modeller: [Errno 13] Permission denied
by naghmehn85＠gmail.com 27 Oct '23

27 Oct '23

Hello, I was trying to use the Modeller (run it locally) on Chimera UCSF but I encountered this error: Unable run Modeller: [Errno 13] Permission denied. I, as well, received this error when I wanted to load PDB files from my local MacOs. Would you mind please telling me what the issue is? Thank you so much.

3 2

Chimera(X) website and web services down Oct 30-31
by Elaine Meng 26 Oct '23

26 Oct '23

Dear users, Due to system upgrades, the Chimera and ChimeraX websites, associated web services hosted by the UCSF RBVI (Modeller, Blast Protein, etc.), and the ChimeraX Toolshed will be unavailable -- the estimated downtime is from Monday, Oct 30 8:00 am PDT through Tuesday, Oct 31 11:59 pm PDT. Please pardon the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Error on Chimera
by Giovanni Stelitano 23 Oct '23

23 Oct '23

Dear developers, first of all thank you for your work, the program is quite useful and interesting. I'm using it to perform molecular dynamics for small organic molecules but I have quite a few troubles. I was able to perform a MD in void, but I got this error when I try to analyze the energies, for both kinetic and potential. File "C:\Program Files\Chimera 1.17.3\share\md\mdMovie.py", line 22, in <lambda> name, lambda i, values=values: values[i-1]) Moreover, when I try to run a MD in water (I followed a tutorial on youtube to set up the system and balancing), it stops at the first step of minimization (after 2 days of running it didn't go further according to the log file). I used the Amber preparation (since Gestgeiger seems to not work for my molecules) integrated with AmberFF18SB or 99 that are the one that mostly worked out. I don't think the problem is the calculation power of my machine since I've an Intel i5 processor with a GeForce MX230 and in the options I set up 4 processors. Probably the troubles are just related to the fact that I'm working with small organic molecules instead of proteins? Hoping to find some help/hint in your kind reply, whish a good day and good work, Giovanni. -- *Giovanni Stelitano, PhD in Biomedical Science - Biochemistry* *Department of Biology and Biotechnology "L. Spallanzani"* *University of Pavia* *via Ferrata 9, Pavia, Italy*

2 1

How to obtain transformation matrix between protein structures
by 夏前程 22 Oct '23

22 Oct '23

Hi, I want to use chimera to obtain the transformation matrix between two protein structures. I know that matchmaker can superimpose them together, but I still want to obtain the transformation matrix. I've noticed that matchmaker in chimerax (https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html) offer a keyword "reportMatrix" to do that. But when I use that keyword in chimerax, "Expected a keyword" will be returned without match or a matrix. With Regards, Qiancheng Xia National Institute of Biological Sciences Beijing, China 2023/10/20

2 3

Questions about phosphorylating residues on proteins
by Hoang-Long Bui 16 Oct '23

16 Oct '23

Hello, My name is Andy and I am a student researcher at San Jose State University with the Grazioli Research Group. I am trying to research a section of a protein using your software and was wondering if I could phosphorylate certain residues of the protein, and how. Thank you! Andy Bui

2 2

ChimeraX Redistribution Policy Question
by Patrick Rynkiewicz (RIT Student) 09 Oct '23

09 Oct '23

Hello! I am a co-developer on a molecular dynamics software package that relies on UCSF ChimeraX, and am looking to package this software in a docker container. It's unclear to me from the licensing process what the policy is for ChimeraX redistribution, such as including the .deb package in a docker build. Can you please clarify if I would be able to cite and redistribute ChimeraX 1.6, Ubuntu 22.04 to* non-commercial users* in my software package, or does each individual user need to accept the non-commercial license agreement separately? Thanks! Pat Rynkiewicz

2 1

Circular DNA Construction and DNA Origami in Chimera 1.17.3
by fatemeh F 29 Sep '23

29 Sep '23

I am writing to inquire about the capabilities of Chimera 1.17.3 for constructing circular DNA and DNA origami, and to seek guidance on saving PDB output files for future use in GROMACS with the AMBER force field. Firstly, I am interested in constructing circular DNA using Chimera 1.17.3. Could you please provide information or guidance on whether this version of Chimera supports circular DNA construction? If so, I would appreciate any instructions or resources that can help me achieve this. Additionally, I would like to explore the possibility of building DNA origami structures using Chimera 1.17.3. Could you please inform me if this version of Chimera has the functionality to create DNA origami structures? If it does, any pointers or documentation on how to get started with DNA origami in Chimera would be highly valuable. Lastly, my goal is to save the PDB output files generated in Chimera for subsequent use in GROMACS with the AMBER force field. Could you provide guidance on the best practices for saving PDB files from Chimera for compatibility with GROMACS and the AMBER force field? Any specific settings or considerations to ensure seamless integration would be greatly appreciated.

2 4

Disulfide bond recognition in Chimera
by wangyizhen＠nibs.ac.cn 28 Sep '23

28 Sep '23

Dear developers of UCSF chimera, I am interested in the reason why chimera recognize the disulfide bond only by the CONNECT record in PDB files. Why not use the bond identification algorithm as used on other heavy atoms (sum of the covalent bond radii and tolerance 0.4A) to show the bond? Is there any special considerations for this? Thanks in advance for any help. Yizhen

2 1

Re: Question about Selecting Structure Parts in Chimera
by Tom Goddard 25 Sep '23

25 Sep '23

Hi Maytha, The most basic way to select parts of an atomic model within a map is to ctrl-click with the left mouse button on an atom or ribbon residue. Then the up-arrow key on the keyboard will expand the selection to the containing helix or strand, and pressed again to the whole chain. Maybe you don't have an atomic model -- hard to tell from your question. Tom > On Sep 24, 2023, at 1:05 PM, MAYTHA ALSHAMMARI <malsh009(a)odu.edu> wrote: > > Dear Goddard, > > I hope you're well. I have a quick query about selecting parts of a structure within a boxed map in Chimera. Can you provide some guidance or instructions on how to do this effectively? Your help is much appreciated. > > Best regards, > Maytha

1 0

Chimera X menu "View" vs. "Focus"
by C. Klein 25 Sep '23

25 Sep '23

Dear Chimera Team first of all, thank you very much for your important and good work on the Chimera software. Two comments: I did some recent work with Chimera X. The menu item "Focus" was changed to "View", which I find less suitable. The term "View" is often applied in other contexts, in particular if a certain residue should be shown vs. not shown. In contrast, "Focus" is not ambiguous, it is not related to showing vs. hiding certain parts of the molecular representation but exactly indicates what is done by the command. The direct pdb download from rcsb or whatever repository is a highly useful tool which is more difficult to access than it used to be. Ok I know it is there, I type "open xxxx" and I use the command line quite a lot anyway, but for others who start with the menus it does not appear to be accessible. Perhaps I also missed something, but then others may not find it as well. Thank you and best wishes Christian Klein

2 1

Cannot Minimize the Water Molecules
by Gourav Das 13 Sep '23

13 Sep '23

Dear all, I am trying to minimize the crystal structure of a protein using Chimera. But the program could not minimize the water molecules of the protein. I added hydrogen atoms to the whole structure. But during the minimization, it is showing the following error: No MMTK name for atom "H" in standard residue "HOH" It would be very helpful for me if you can suggest what changes I should make. Thank you! Sincerely Gourav Das Research Scholar Department of Chemistry IIT Kharagpur India

2 2

Any plan to support sdf as 3D molecules output format?
by Francois Berenger 11 Sep '23

11 Sep '23

Dear Chimera hackers, This might be nice, because mol2 is not supported by rdkit while sdf is. It would ensure that molecules saved from chimera can be properly read in by rdkit (hopefully). Regards, F.

2 2

inquire about the capabilities of the UCSF Chimera software in visualizing bond atoms in a spring mode
by Wee Zhang 11 Sep '23

11 Sep '23

Dear RBVI Team, I hope you are doing well. I am writing to inquire about the capabilities of the UCSF Chimera software in visualizing bond atoms in a spring mode, similar to the exemplary images I have enclosed for reference. I have been using UCSF Chimera for various molecular visualization and analysis tasks, and I am particularly interested in exploring this feature for my research and projects. The visualizations I am referring to are those that effectively represent covalent bonds as springs connecting atoms in a molecular structure. These spring-like representations can provide valuable insights into the flexibility and dynamics of molecules, which are crucial aspects of my research in materials science. I have attached images that illustrate the visualizations I want to achieve with UCSF Chimera for your reference. These images serve as excellent examples of dynamic and informative representations that I believe could greatly enhance my research. I would appreciate it if you could provide information on whether UCSF Chimera can generate bond atom visualizations in a spring mode, and if so, any guidance on how to achieve this would be beneficial. Additionally, if any specific plugins or settings are required to create such visualizations, please let me know. Furthermore, if any workshops, tutorials, or resources can assist me in mastering this feature, I would be eager to participate in or access them. Thank you in advance for your time and assistance. I look forward to hearing from you regarding the feasibility of incorporating the spring mode bond atom visualization into UCSF Chimera and any guidance you can provide on achieving this. Please feel free to contact me via email at [your email address] or by phone at [your phone number] if you require additional information or clarification. Sincerely,

2 1

Chimera will not start
by Secor, Maxim 06 Sep '23

06 Sep '23

Hello, I am a postdoc in the Lin lab at Tufts. We use Chimera for everything. Thank you for such wonderful software. Last week Chimera stopped working on my machine. I tried (1) restarting my machine (2) Updating my OS (3) reinstalling Chimera (4) Installing the daily release of Chimera. Nothing works… Thankfully ChimeraX is a good substitute. However, (A) I cannot seem to find all the features that I want in ChimeraX that I loved in Chimers, for example minimization tools, and (B) would really like the Chimera GUI to work. Any thoughts? Maybe there is a corrupted hidden cache file that I need to delete somewhere. Best Max

2 3

Very big THANKS FOR SENT ME ACCESS to ;st version by CHIMERA X.IT IS FANTASTIC!!!Boris
by Boris Atanasov 02 Sep '23

02 Sep '23

-- Prof. BORIS ATANASOV <borisatanasov2(a)gmail.com> Institute of Organic Chemistry, Bulgarian Academy of Sciences, SOFIA 1113, Bulgaria

1 0

Unable to run UCSF chimera using
by Prathvi Singh 30 Aug '23

30 Aug '23

Hi, Is it possible to use python to execute commands on the command line of UCSF chimera without actually opening its GUI on the Windows platform? If not, then how to use python to open its GUI and execute the commands? I tried the "subprocess.Popen()" and "os.system()" methods to run its GUI by passing the path of chimera executable (version 1.17.1) to them but chimera is displaying an error with exit code 1 (snapshot attached). However, I am able to launch chimeraX (version 1.6.1) via these methods. -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

3 6

Display of double/tripe bonds
by Ghislain Deslongchamps 29 Aug '23

29 Aug '23

Hi all, I wish to use Chimera for my students to view organic models that I created in MOE. How can Chimera display double/triple bonds? They appear as single bonds in .pdb, .mol, .mol2 formats. Thanks. Cheers, Ghislain GHISLAIN DESLONGCHAMPS Professor Department of Chemistry • Faculty of Science T 506 470-9976 F 506 453-3570 WWW https://www.deslongchamps<https://www.deslongchamps.ca/>.ca<https://www.deslongchamps.ca/> UNB campuses are open with strict adherence to New Brunswick Public Health requirements. Our priority continues to be providing high quality education while ensuring the health and safety of our community. [attachment.jpeg] [attachment.jpeg] /uofnb<https://www.facebook.com/uofnb> [attachment.jpeg] @unb<https://twitter.com/UNB> [attachment.jpeg] @discoverunb<https://instagram.com/discoverunb/> UNB.ca<http://www.unb.ca/> Confidentiality Note: This email and the information contained in it is confidential, may be privileged and is intended for the exclusive use of the addressee(s). Any other person is strictly prohibited from using, disclosing, distributing, or reproducing it. If you have received this communication in error, please reply by email to the sender and delete or destroy all copies of this message.

2 1

How to show certain hydrogen bonds and hide others
by Karjalainen, Mikael 29 Aug '23

29 Aug '23

Hi! I am having problems to show certain hydrogen bonds and hide others. For example, I would like to hide some completely. Then others should be shown always. Even when atoms are not shown and only ribbon is. I couldn't find how to do this by googling or for example reading how to use hbonds command. I am using Chimera 1.16. I know that there is ChimeraX, but now I need to modify old project. Regards, Mikael

2 1

Atlocs
by Hernando J Sosa 28 Aug '23

28 Aug '23

Dear ChimeraX, I have an atomic model with several chains that have residues with alternate locations A and B. I noticed that while Chimera by default displays alternate locations A. ChimeraX for some chains display alternate locations A and for other chains alternate locations B. Why is this behavior different in Chimera and ChimeraX? Is this a novel feature of ChimeraX? I this is the case how ChimeraX decides which of the two alternate locations A or B to display? Thanks Hernando ___________________________________ Hernando Sosa, PhD. Dept. of Biochemistry Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 emai: hernando.sosa@einsteinmed.<mailto:hernando.sosa@einsteinmed.org>edu ___________________________________

2 1

Saving the resolution of structure to a file
by Prathvi Singh 22 Aug '23

22 Aug '23

Hi Elaine, Is there a way to save the resolution of a protein structure to a file using command line, either in chimeraX or chimera? Thanks -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 1

dms from command line
by Guido Leoni 21 Aug '23

21 Aug '23

Dear list Is there an option to write dms from command line? I' m able to launch the command line interface with a pdb loaded within . Then I estimate the surface with this command surface #0 now I would write a dms ... Please do you have any tips that can help me? Thank you Guido

2 1

non-integral charge warning
by Chris Ellis 21 Aug '23

21 Aug '23

Hi, After running the dock prep, I get the following warning in the reply log. Charges for residue MHS determined Total charge for #0: -79.622 The following residues had non-integral charges: VAL 124.A -0.2719 LYS 38.F 0.66 1 model(s) had non-integral total charge Details in reply log How can I fix this warning? Do I need to fix this? Thank you for any help you can provide. I truly appreciate it. Chris

2 6

San Jacinto College Software Intake Form Chimera
by Yates, Michael 18 Aug '23

18 Aug '23

Greetings. I am the Supervisor of Desktop Support Services for San Jacinto College. Information Technology Services (ITS) has been asked to evaluate Chimera to ensure that the San Jacinto College computing environment meets the requirements for the service as well as to ensure that the service offering complies with our requirements. As part of our standard process we reach out to software vendors to request the completion of the attached form after the requestor has completed section 1. At this time we request that you complete section 2 or 3 of the attached form and return it to us by August 21st so that we may complete our evaluations and grant purchase eligibility if the service qualifies. Additional questions may follow. In addition to what is in the form, please include (if applicable) any information / documentation that you have available regarding the options below and please indicate if there are any additional charges for the implementation of such: * Azure AD Single Sign On capability * Office 365 Integration features * Ellucian Banner Integration features [Description: Description: cid:image001.png@01CEC8EF.F2E97C50] Michael Yates San Jacinto College Supervisor of Desktop Support Services 4624 Fairmont Pkwy, Pasadena, TX 77504 Direct: (281) 998-6150 X7325 | Technical Support: (281) 998-6137 Web<http://blogs.sanjac.edu/its> | Facebook<http://www.facebook.com/sanjacits> | ITS Twitter<http://www.twitter.com/sanjacits>

2 3

Moving atoms of a protein
by Abril Gijsbers 18 Aug '23

18 Aug '23

Hi Elaine, I have this alphafold structure (see picture) that is basically a huge string/thread and then a folded domain. I wanted to stretch the string to make its length more obvious. Is it possible to pull the residues without messing with the connections (peptide bond)? I am using chimeraX and I saw that you can "move atoms" but when you pull one you don't pull the others. If chimera cannot do this, do you know if another program will allow me to do it? Thank you in advance for your help, Best regards, Abril Gijsbers [image: image.png]

2 2

Re: ChimeraX license and download
by Elaine Meng 17 Aug '23

17 Aug '23

Please disregard and delete the previous message. I messed up and accidentally CC'd the chimera users list instead of the licensing address. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 17, 2023, at 12:56 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > [...] > Thank you for licensing the commercial version of ChimeraX, the next-generation molecular visualization and analysis program from our research lab. ChimeraX is under active development, with version 1.6.1 released in May 2023. As new features are added, daily development builds are also available for download. Daily builds are not tested as thoroughly as production releases, but in practice are highly usable. > [...]

1 0

Requesting protocol to find protein configuration units
by Panapakam, Jyotheeswaran 17 Aug '23

17 Aug '23

Dear Officail, This is Jyo writing from UNT biological sciences at Denton, TX, USA. I have been using your software for my research project for about an year. I was looking for a help/instructions about how to find out the configuration change in the protein after docking with a ligand. I have heard about RMSD docking value, that will be given in Amstrong units, could you kindly instruct me the process to perform it. It would be more glad if you are able to answer me withing a week from now : ) Sincerely, Jyotheeswaran Panapakam, PhD Candidate &Teaching Assistant, Department of Biological Sciences, University of North Texas. Jyotheeswaran Panapakam, PhD Candidate &Teaching Assistant, Department of Biological Sciences, University of North Texas.

2 1

Re: [chimerax-users] re error with Movie recorder utility
by Elaine Meng 16 Aug '23

16 Aug '23

Hi Anna, This chimerax-users email address is for questions about ChimeraX, but it sounds like you are using the Chimera program instead, since only Chimera has a Movie Recorder tool. So I am CC-ing the chimera-users email address on this reply, and you do not need to re-send your question. There is no separate "freeware version" -- Chimera is free for academic use and the download is the same for academically or commercially licensed users. (This is also the case for ChimeraX). The Command Line is always for entering one command at a time, i.e. that is the normal situation, not a problem or bug. If you have just a few commands you can enter them as one line with semicolons between them. However, if you mean that you have a script that contains many Chimera commands, you do not enter them one at a time into the command line. Instead you use some text-editing program (outside of Chimera) to create a plain text command file containing those commands, then you open that file using either the Chimera menu File... Open, or the Chimera "open" command. Normally command files are named with the filename extension ".com" or ".cmd" so that Chimera knows what kind of file you are trying to open. See Chimera help pages and tutorials on making movies, namely: Making movies: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html> Movie Recorder help page (you can just click the Help button on the tool, or see the copy of the same thing at our website here): <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorde…> Chimera movie-making tutorials: <https://www.rbvi.ucsf.edu/chimera/data/tutorials/movies09/moviemaking.html> <https://www.rbvi.ucsf.edu/chimera/data/tutorials/movies08/moviemaking.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 16, 2023, at 6:31 PM, Anna Lohning via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi > I have the freeware version installed and trying to make a movie using the Tools/Utilities/Movie recorder window. > At this stage, I seem to only have the command line available for commands one at a time. > Anyway, under the Tools/Utilities, the only options there currently are > Register > Updates > > Be grateful for some clarification as I cant seem to find anyone having this issue. > Many thanks > Kind regards > > Anna > Dr Anna Elizabeth Lohning > Associate Professor - Biochemistry > Faculty of Health Science & Medicine > Bond University > ROBINA 4229 > (07) 5595 4779 > alohning(a)bond.edu.au >

2 1

.msi chimera
by Yanni Goudetsidis (Staff) 11 Aug '23

11 Aug '23

Good morning Is there a .msi installer for chimera I could download, please? Thank you

2 2

making composite map using vop maximum command
by ytakagi＠iu.edu 10 Aug '23

10 Aug '23

Hi I want to make a composite map using two locally refined maps. I tried Phenix but did not work well. So, I like to do it by Chimera. Apparently, a composite map can be made using Chimera's vop maximum command. But I could not find the instruction of how to do it. Can you tell me how to do it? Thanks

3 4

San Jacinto College Security Evaluation
by Melendez, Aaron 09 Aug '23

09 Aug '23

Good afternoon, San Jacinto College, as part of its new application/vendor procurement process, is evaluating the security posture of Chimera and would like to ask for your help in procuring documentation that proves the security controls in place for the company. If you have any Information Security documentation you can share with us, it would be greatly appreciated. If an NDA needs to be signed, we would be happy to provide that to you. Documents that help: * HECVAT (one will be attached that can be filled out) * SJC Vendor Questionnaire (one will be attached that can be filled out) * Information security policies and procedures * Datacenters or Hosting Providers used. * Incident response plan * Disaster recovery plan * Business continuity plan * System and network architecture diagrams * Penetration testing reports * Vulnerability scan reports If you can provide the Data Centers that are used and the Hosting Providers, it will also help our evaluation process. Thank you in advance for your help. Please reach out if you have any questions. Regards, e Aaron C. Melendez Third-Party Risk Analyst The Office of Cybersecurity Cell: (281) 635-2940 (Please call x 2 or Text) San Jacinto Community College 4624 Fairmont Pkwy, Pasadena, TX 77504 Technical Support: Get help at SanJac ITS<https://www.sanjacits.org/> | call (281) 998-6137 www.sanjac.edu<https://www.sanjac.edu/> | www.facebook.com/sanjacintocollege<http://www.facebook.com/sanjacintocollege> | @SanJacCollege [2z5cr1lnO9iMtMLfMHSAYwzcMySsBwfq8SYpRxc6xBeRPF2c+m+YTgIc8IdrhL4f1IjMkJpGrM5AAAAAElFTkSuQmCC] “Under pressure, you don’t rise to the occasion, you sink to the level of your training.”

3 4

Secondary structure editing of molecules
by GABRIELLE LUPETI DE CENA 08 Aug '23

08 Aug '23

Good morning! I have doubts about how to turn the peptide structures of the four images below (A), (B), (C), and (D) into a cartoon model like figure (E). I've tried, but I'm not succeeding. Thank you very much. -- ---- É obrigatória a utilização do e-mail @unifesp em todas as correspondências oficiais, institucionais e no acesso aos equipamentos e sistemas da Universidade Federal de São Paulo, conforme a portaria Reitoria n. 1182/2022 <https://sti.unifesp.br/documentos/termos-de-uso-do-email> que define a Política de e-mail institucional da Unifesp. <https://sei.unifesp.br/sei/publicacoes/controlador_publicacoes.php?acao=pub…>

2 2

Saving phi psi values to a text file
by Prathvi Singh 06 Aug '23

06 Aug '23

Hi Elaine, Is there a command to save the phi and psi angle values of each residue of a PDB file in a text file using UCSF chimera? I know we can do this in chimeraX using the command: save C:\myphi.defattr attrName phi format defattr model #1 Also, can we use chimeraX to save the phi and psi values in a single file? Thanks in advance -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 1

Query regarding selection
by Prathvi Singh 04 Aug '23

04 Aug '23

Hi Elaine, I want to select all the atoms except the backbone oxygen and nitrogen atom of residues 100.A to 120.A . Is there a command to do this in either chimera or chimeraX? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 1

Re: [EXTERNAL] Chimera-users Digest, Vol 243, Issue 22
by Reza Khayat 01 Aug '23

01 Aug '23

Hi Elaine, Thanks for the help. This will speed things up quite a bit. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 ________________________________________ From: chimera-users-request(a)cgl.ucsf.edu <chimera-users-request(a)cgl.ucsf.edu> Sent: Tuesday, August 1, 2023 3:00 PM To: chimera-users(a)cgl.ucsf.edu Subject: [EXTERNAL] Chimera-users Digest, Vol 243, Issue 22 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Measure rotation without writing PDB (Reza Khayat) 2. Re: Measure rotation without writing PDB (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Tue, 1 Aug 2023 18:23:19 +0000 From: Reza Khayat <rkhayat(a)ccny.cuny.edu> Subject: [Chimera-users] Measure rotation without writing PDB To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> Message-ID: <1690914198332.72284(a)ccny.cuny.edu> Content-Type: multipart/alternative; boundary="_000_169091419833272284ccnycunyedu_" Hi, I'm trying to measure the movement of a domain between two structures of the same protein. Here are the conditions: 1. There are two domains in each structure 2. I want to overlay the first domain and measure the rotation of the second domain 3. There are lots of structures, so I want to minimise the number of steps 4. I'd like to do this with a script and the --no_gui option on headless Chimera Here is my current script for the routine: open pdb1 open pdb2 match #1:1-50 #0:1-50 write format pdb relative #1 #0 t.pdb delete #1 open t.pdb match #1:55-80 #0:55-80 measure rotation #1 #0 delete #1 open pdb3 ... Is it possible to not have to write, delete, and open #1 after the first match step? If I don't do this, then the measure rotation #1 #0 will measure rotation of the initial match rather than the second match. Thanks for the help. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

1 0

Measure rotation without writing PDB
by Reza Khayat 01 Aug '23

01 Aug '23

Hi, I'm trying to measure the movement of a domain between two structures of the same protein. Here are the conditions: 1. There are two domains in each structure 2. I want to overlay the first domain and measure the rotation of the second domain 3. There are lots of structures, so I want to minimise the number of steps 4. I'd like to do this with a script and the --no_gui option on headless Chimera Here is my current script for the routine: open pdb1 open pdb2 match #1:1-50 #0:1-50 write format pdb relative #1 #0 t.pdb delete #1 open t.pdb match #1:55-80 #0:55-80 measure rotation #1 #0 delete #1 open pdb3 ... Is it possible to not have to write, delete, and open #1 after the first match step? If I don't do this, then the measure rotation #1 #0 will measure rotation of the initial match rather than the second match. Thanks for the help. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

3 2

Silent install?
by Jim Richard 27 Jul '23

27 Jul '23

Hello, We are using MECM (SCCM) to install Chimera and need to suppress ALL windows. I have tried the /verysilent flag but a command prompt still pops up with what looks to be the compiling portion. Is there a way to have ALL windows silent? -- *Jim Richard* Pronouns: he/him/his Client Systems Administrator

2 1

Saving Animations on Mac OS
by Natalie Walsh 25 Jul '23

25 Jul '23

Hello, I am having troubles saving my animations on my Mac OS. I get this error when I record and save my animation: An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: -1 Error message: Could not find ffmpeg executable —————————————— I googled some solutions regarding “ffmpeg” and I believe I successfully installed it to my terminal, but I am still receiving the same error. Thank you, Natalie Walsh

2 6

Unable to dock
by Panapakam, Jyotheeswaran 20 Jul '23

20 Jul '23

[cid:9962344b-5095-47ba-a1c2-1c6fef113ef2] Dear Official, I was unable to move the green grid, thus, I am unable to dock a compound on the protein target. Could you please help me with this? Jyotheeswaran Panapakam, PhD Candidate &Teaching Assistant, Department of Biological Sciences, University of North Texas.

2 4

How do I colour all my hydrogen atoms grey?
by Mazin Nasralla 17 Jul '23

17 Jul '23

Hello, I imported an x,y,z model of water molecules into Chimera. I want to create an image of my water structure so I am setting the background to grey. That works. But I would prefer to set the hydrogen atom colour to light grey. I can't work out how to do that. I can select each individual atom, and then colour edit it but that will take ages. Is there a simple command line solution? Thanks Mazin

2 2

hiding a model slowly
by Sen, Anindito 14 Jul '23

14 Jul '23

Dear Chimera X team, Is there a way I can hide one of the models in a ChimeraX session slowly (like fading it off) while making a movie. typically I use hide #7 model Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu<http://microscopy.tamu.edu/>

2 1

Chimera-X inteprhase of the AlphaFold
by Enrico Martinez 13 Jul '23

13 Jul '23

Dear Chimera-X users! In parallel to the modeller, I am trying to use the Alpha fold interface with the aim to full model starting from the sequence using template. The problem is that I can not define manually which template I would like to use for each prediction so the interphase takes its automatically based on the input sequence and the final prediction is not very precise. Would it be possible rather to specify a specific pdb ID additionally to a given sequence ? Many thanks in advance Enrico

2 1

Modeler interphase in Chimera
by Enrico Martinez 13 Jul '23

13 Jul '23

Dear Chimera Users! I would like to try MODELLER interphase implemented in the Chimera for prediction of the segments missed in input PDB structure having as the input: the pdb structure with missed N and C terminal fragments (everything in one chain), as well as the full sequence of the protein in FASTA. Could you please provide me with a link to the tutorial (or just explain a very basic workflow here .. ), which simply explains how I could predict the model based on the data and save the predicted solutions in pdb format ? Many thanks in advance Cheers Enrico

2 4

Remove me from mailing list
by Saima Sam 10 Jul '23

10 Jul '23

Hi, I am no longer a user of Chimera so please opt me out of these emails. I would truly appreciate it.

1 0

Placing of a hame-ion centre into an AlfaFold structure
by George Tzotzos 10 Jul '23

10 Jul '23

I’d be grateful for any suggestions regarding the following problem/question. Problem Placing of the haem-iron centre in mosquito P450 structure(s) obtained by means of AlfaFold. This is required for follow up docking simulations. There no insect P450 structures deposited in PDB. However, there are numerous mammalian P450 crystal structures some of which are homologous to the mosquito structures I’m dealing with. A distinctive feature of these structures is a haem-iron centre tethered to the protein via a cysteine thiolate ligand. Six regions have been designated as substrate recognition sites (SRS 1-6) based on comparative sequence analysis methods. These SRS are conserved and are thought to participate in the formation of the substrate access channel, and form part of the catalytic site surrounding the haem iron center. My initial approach would be to use Chimera to align the AlfaFold structure against its mammalian homologue PDB structure and assume that the haem-iron centre would be located in the same place. Is there a better way to achieve the same objective?. Your help will be greatly appreciated. Best regards George

2 5

Chimera?
by Emma 05 Jul '23

05 Jul '23

Chimera, this is me again

1 0

Opening MTZ files on Mac OS
by Natalie Walsh 03 Jul '23

03 Jul '23

Hello, I am having troubles opening MTZ maps from PDB on ChimeraX 17.1. on Mac OS. I read somewhere that you need to download the Clipper plug-in. I went ahead and installed that (although I am not sure that I was successful) and am still struggling to open these files. Thank you, Natalie Walsh

2 1

Removing lonbond links from pipes-and-planks representation
by philip.robinson＠bbk.ac.uk 02 Jul '23

02 Jul '23

Hi, I'm trying to generate a pipes-and-planks representation of an atomic model that contains gaps. Before generating the pipes-and-planks representation I hid the long bonds to remove the links in the gap regions. However, the gaps are connected again in the pipes-and-planks representation and I cannot find the command to hide them. Any help would be appreciated. Phil

3 2

ChimeraX Question
by Bani Kaur 30 Jun '23

30 Jun '23

Hi, I hope you are doing well! My name is Bani Kaur and I am an active user of ChimeraX for a research project concerning protein modeling, specifically with the CFTR protein. I have been running into issues with showing atoms on my residue, specifically after I change the romater. I am not sure what to do about this as I have downloaded the latest version of ChimeraX. Additionally, I am not able to see clashes for some very reason and am only able to see it when limit by selection is unchecked, but for my research project, we require that it is checked in the clashes settings. Thank you so much for your help! Best, Bani Kaur

2 1

Questions regarding reply log
by Prathvi Singh 28 Jun '23

28 Jun '23

Hi Elaine, Is there a way to clear the Reply Log using the command line? Is there a way to write the contents of the Reply log to a text file? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 3

Supoort for automating superimposition process of multiple pairs of structures using command line
by Vaibhav Anand 27 Jun '23

27 Jun '23

Hello Chimera team, I am seeking your assistance in automating the process of superimposing multiple pairs of structures using the command line. I've performed the MD simulation of the UBA domain (PDB ID - 1OQY), and for analyzing the structural changes, I've extracted the 11 structures from the trajectory at 500ns to 1000ns with steps of 50ns. In total, I've 12 structures [1 reference structure (em.gro - energy minimized structure) and 11 extracted structures]. Now I want to superimpose each extracted structure w.r.t. em.gro and save the image of superimposition with the image name to be (time + rmsd_value). For the RMSD value, I'll have to save the reply log file (or the last 10-15 lines of the reply log) and then copy the rmsd value and save my image file with it. Could you please give me an outline or references on how I can do this task? Thank you for your attention Regards, Vaibhav

2 2

downloading and saving multiple PDB's
by Dmitry Semchonok 26 Jun '23

26 Jun '23

Dear colleagues, Is there a way to 1. download the multiple pdb/mmcif using Chimerax knowing their ID entry? 2. save multiple opened pdbs using their corresponding original names in Chimerax? Thank you in advance. Kind regards, Dmitry

2 1

Regarding issue detected while running chimera
by Suman Dhungel 26 Jun '23

26 Jun '23

Dear concerned one, I have been using UCSF Chimera from another device for the past 10 years. Recently I tried to operate chimera-1.17.1 on my computer. I have been facing a repeated issue that has been reported below. I tried to reinstall however, the issue persisted. I even tried with the new version (Chimera alpha ), similar issue with that as well. [image: chimera error.JPG] [image: my device.JPG] Would you please help... Regards Suman...

2 1