- Chimera-users - RBVI Mailing Lists

Occupancy clusters
by Yasser Almeida 16 Mar '21

16 Mar '21

Hello, I want to do an occupancy analysis of a rigid ligand in a MD trajectory. I used the MD Movie > Analysis > Calculate occupancy tool, and obtained the volume maps of each heavy atom of the ligand. To check, I also used the gmx spatial tool from GROMACS and the VolMap from VMD, to obtain the grids for the whole ligand, which have basically the same shape. This grid has a characteristic shape showing that particular orientations are stable through the MD run. I want to extract representative structures of these orientations, something like an "occupancy clustering". Note that I say orientations and not conformations. Since the ligand is rigid, there is no point to calculate the RMSD. So, what I want is to calculate clusters of orientations of the ligand in the binding site. Is this possible with Chimera? Thanks in advance, -Yasser

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Problem with nucleotide objects settings for 1d86
by svle＠tiscali.it 16 Mar '21

16 Mar '21

Hi, I have a visualization that seems not a correct one for 1d86 for DT 20.b when using Actions -> Atoms/Bonds -> nucleotide objects -> settings... . Settings: Show backbone as: Ribbon Show sides( .... ) as ladder Ladder Options: Ignore non-base H-bonds: false Shows stubs: false Rung radius: 0.45 Using existing H-bonds: true In the png file the problem. Where I'm wrong? Thanks Saverio Con Tiscali Mobile Smart 30 4G hai minuti illimitati, 100 SMS e 30 Giga in 4G a soli 8,99€ al mese. http://tisca.li/smart30

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render by attribute displacement of a NMA
by Giorgio Giardina 15 Mar '21

15 Mar '21

Hy, I have a pdb file containing the models (only CA atoms) describing the lowest mode from a NMA. I can easily generate a movie using the morphing tool, but I would like to visualize the mode as an image, using the render by attribute tool and with the displacement of each CA as value of the worm radius. How can I generate this attribute? Thanks in advance for you rhelp! Giorgio -- ------------------------------- Giorgio Giardina, Ph.D. Dep. of Biochemical Sciences (CU027) - Room T2 SAPIENZA - University of Rome Tel. +39.06.49910713 | Lab: http://www.macinmec.it/giorgio-giardina/ | Art: http://www.giorgio-giardina.com/ Art. 33 della Costituzione: *L’arte e la scienza sono libere e libero ne è l’insegnamento* -- ________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono strettamente riservate e indirizzate esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non si è il legittimo destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per errore, si prega di restituirlo al mittente e di cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential and intended for the use of the addressee only. If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you have received the message in error, please forward it back to the sender and delete it permanently from your computer system.

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Failure Running ANTECHAMBER
by Mailyn Terrado 12 Mar '21

12 Mar '21

To whom it may concern: I am trying to use Chimera for protein Energy Minimization. I encountered a problem in running the program. Please find the attached screenshots of the error details. The problem seemed to be with the ligand BEF (beryllium trifluoride). Any help would be greatly appreciated. Many thanks, Mailyn

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ORCA XYZ FILES
by Rade Jibawi Rivera 10 Mar '21

10 Mar '21

Hello, I am a student from Nova Southeastern University, and I am conducting research where I am interested in utilizing your software "Chimera" for visualization of molecular dynamics. My concern is if your software will be able to create a movie of bond interactions with multiple time frames using ORCA XYZ output files. I would greatly appreciate it if you can give in some input. I hope to hear from you. Thank you for your time and consideration. Best regards, Rade Jibawi Rivera

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Regarding Chimera vina executable file
by Heshani Mudalige 10 Mar '21

10 Mar '21

Dear Elaine, Hi, hope you are doing well. I used Chimera for protein docking. But I got stuck in the last step when setting the local path. I downloaded the windows version and that installed to C drive program files and like this C:\Program Files(86)\The Scripps Research Institute But even after browse even it doesn't show any vina.exe file when setting the local path.Can you please tell me where I can find that? Or how to check whether that properly installed or not? Inside the Vina folder there are 3 files which two were applications files.But no exe file is visible I went many tutorials and heard after 2020 we need to install Auto dock vina to support Chimera. I did that as well.But still I can't properly debug this. Different you tube videos they mentioned inside Vina folder can fine vina.exe or inside bin can find vina.exe. Apperciate your help on this and your earliest reply.Thank you Kind regards Heshani

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Sidechain selection in Python
by achatz 10 Mar '21

10 Mar '21

Hello, I want to select a sidechain without CA in Python. The working command line select #0:30 & without CA/C1' is recreated in Python like this: chimera.selection.OSLSelection("#0:30 & without CA/C1'") But the lexer complains about an "illegal symbol in identifier" which is the apostrophe after C1. How do I solve this issue? Thanks Stefan

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Problem trying to download Chimera
by Elaine Meng 10 Mar '21

10 Mar '21

> From: Austine Gozie <austinegozieaustine(a)gmail.com> > Date: March 8, 2021 at 11:47:40 PM PST > > Good day sir/madam, > > I am trying to download the ucsf Chimera software for my ongoing project but its not responding. When i try to proceed to download icon, the next page displays "cant open page or refresh page, connection failed" I need your assistance in helping me with the download methodology or right website to enable me download the software. Thanks in anticipation for your kindest help. Hello Austine, I don't know what you mean by "proceed to download icon". In the download page, you would click on the link for the installer that you want: <https://www.rbvi.ucsf.edu/chimera/download.html> Then it shows the license, and if you agree, then click the "Accept" button at the bottom of the page to start the download. Occasionally the website is down, but as far as I can tell it is fine right now. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Scene transition is delayed in chimera animation
by Shanti Pal Gangwar 10 Mar '21

10 Mar '21

Hi All, I am trying to make scene based animation in chimera where every scene is rotated 360 by using action Roll 360. What I observe is that the scene transitions from 1 scene to another is extremely slow and not continuous also. For some scenes it is fast as well. How can I keep this transition minimum and fixed to all scenes to make a continuous animation. Thank you very much Shanti Pal

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Fwd: error code -1073741819
by Tom Goddard 09 Mar '21

09 Mar '21

Beni's problem with Chimera not starting was a graphics problem related to supersampling / super-resolution / multisampling. Not clear whether the fix was to change a graphics driver setting or the Chimera multisampling setting. Beni's email below. Tom > Begin forwarded message: > > From: Beni Sued <benisued(a)gmail.com> > Subject: Re: [Chimera-users] error code -1073741819 > Date: March 9, 2021 at 1:50:10 PM PST > To: Tom Goddard <goddard(a)sonic.net> > > > That's impressive knowledge! I was indeed using supersampling and superresolution (not sure if They are the same as multisampling but it worked) > Thanks so much! > solved > > On Tue, 9 Mar 2021 at 20:54, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Beni, > > The gzip message is just misleading. It is not an error and is explained here > > https://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-July/011199.html <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-July/011199.html> > > The real problem is almost surely that your graphics driver is broken since it gets to "Initializing graphics" and then dies. Updating the graphics driver was the right thing to try. > > One other remote possibility is that some Chimera preference setting is causing startup to fail -- like maybe you enabled multisampling in the past and the new graphics driver wipes out whenever you try to use it. The location of preferences is > > C:\Users\username\AppData\Roaming\.chimera\ > > (from documentation here https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html>). You might rename that .chimera folder so Chimera starts with factory default preferences and try to start. > > Tom > >> On Mar 7, 2021, at 1:18 PM, Beni Sued <benisued(a)gmail.com <mailto:benisued@gmail.com>> wrote: >> >> Hey there >> I've been using UCSF chimera for some time with no problems but it is having trouble starting up, this is the error message: >> >> Cannot execute 'gzip': no automatic decompression of .Z files >> >> initializing general preferences >> loading Tix >> initializing graphics >> Return code: -1073741819 >> Press return or enter to to exit >> >> precisely like this gentleman: >> https://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-April/015675.html <https://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-April/015675.html> >> and this >> https://www.cgl.ucsf.edu/pipermail/chimera-users/2011-December/007021.html <https://www.cgl.ucsf.edu/pipermail/chimera-users/2011-December/007021.html> >> >> my dxdiag info is attached, nothing wrong jumps to me. >> >> What I've tried: >> - uninstalling and reinstalling Chimera >> - manually installing GZIP for windows ( https://sourceforge.net/projects/gzip-for-windows/ <https://sourceforge.net/projects/gzip-for-windows/> ) >> - updating drivers (graphics drivers and chipset drivers) >> - getting the alpha version of the program >> - going to and fro compute mode in the the graphical settings >> >> I'm using Chimera 1.15 and this is my hardware >> chipset b550m >> ryzen 5600x >> RX 590 >> >> in trying to fix it I learned about ChimeraX, I'm learning to use it, but I would still like to keep chimera until i can properly stop and change my workflow >> >> thanks so much, let me know if I missed any info >> <DxDiag.txt>_______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >

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error code -1073741819
by Beni Sued 09 Mar '21

09 Mar '21

Hey there I've been using UCSF chimera for some time with no problems but it is having trouble starting up, this is the error message: *Cannot execute 'gzip': no automatic decompression of .Z filesinitializing general preferencesloading Tixinitializing graphicsReturn code: -1073741819Press return or enter to to exit* precisely like this gentleman: https://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-April/015675.html and this https://www.cgl.ucsf.edu/pipermail/chimera-users/2011-December/007021.html my dxdiag info is attached, nothing wrong jumps to me. What I've tried: - uninstalling and reinstalling Chimera - manually installing GZIP for windows ( https://sourceforge.net/projects/gzip-for-windows/ ) - updating drivers (graphics drivers and chipset drivers) - getting the alpha version of the program - going to and fro compute mode in the the graphical settings I'm using Chimera 1.15 and this is my hardware chipset b550m ryzen 5600x RX 590 in trying to fix it I learned about ChimeraX, I'm learning to use it, but I would still like to keep chimera until i can properly stop and change my workflow thanks so much, let me know if I missed any info

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renseignements
by Camelia Hamadouche 09 Mar '21

09 Mar '21

je n'arrive pas a télecharger votre logiciel meme si je clique sur accepter on me dirige vers une fenetre disant quelle partie vous ne voulez pas accepter? alors que j'ai bien cliqué sur accepter

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each rotation of the molecule in chimera will unexpectedly add an extra "c" at command line
by xiaoyu liu 03 Mar '21

03 Mar '21

Hello, I'm Xiaoyu Liu, a chimera user. Thank you for developing and sharing this powerful software. I have a problem now and bothered me for a while when using chimera. I'm wondering if you know how to solve it. I downloaded chimera-1.15-mac64.dmg <https://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=mac64/c…> from "https://www.cgl.ucsf.edu/chimera/download.html" for my Mac OS Catalina(10.15.5). When I rotate the molecule with left mouse button, an extra character "c" will be automatically added in command line. Each rotation will result in adding one "c". Here I have some screen shot to show more clearly. [image: image.png] [image: image.png] [image: image.png] I tried to restart my computer. It is helpful within the first 10 minutes after the restart, but later it has the problem again. Please let me know if you know how to solve it. Many thanks! Best, Xiaoyu

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problem with pdb file saved from chimera-autodock vina analysis
by Amol Ghodke 03 Mar '21

03 Mar '21

Hi, First of all thank you so much for making such a wonderful tool and sharing it freely with scientific community. I have been using chimera for sometime now and performed docking analysis using autodock vina. I recently come across a problem. After exporting pdb file with desired docking pose, I tried to run protein ligand interaction analysis on PLIP<https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index> server. But ligand in my file does not get recognised for analysis. I opened pdb file in a text editor and upon looking care fully I see chimera saves receptor and ligand as separate model like this ATOM 7453 HD2 PRO A 462 15.986 11.983 20.450 1.00 0.00 H ATOM 7454 HD3 PRO A 462 16.532 10.334 20.885 1.00 0.00 H ENDMDL MODEL 2 HETATM 1 S1 CGT A 1 9.051 5.106 43.099 1.00 0.00 S HETATM 2 C6 CGT A 1 8.150 3.680 42.370 1.00 0.00 C After comparing it with the pdb file from pbd database I removed “ENDMDL” and “MODEL 2” and re-ran the PLIP analysis. This time it works but PLIP also mentions that – [cid:image001.png@01D7103D.5D0AB030] Analysis went well but the .pse file that I get from PLIP server does not allow me to show ligand in stick format in Pymol software. I suspect this is due to the original pdb file format. I also noticed that pdb file when opened in pymol shows ligand and receptor as different states which is not correct (if I am right). I have attached both original pdb file that I saved from Chimera-autodock vina and pse file from PLIP analysis. May I request to help me resolve this issue? Please let me know if you need any further information or clarification. Thanks for your time and support Amol --------------------------------------------------------------------------------------------------------------------------------------------------------- Dr Amol Bharat Ghodke | Post-Doctoral Research Fellow Queensland Alliance for Agriculture and Food Innovation Level 3, Queensland Bioscience Precinct [#80] Room 3.318, 306 Carmody Rd, St Lucia The University of Queensland St Lucia, Brisbane Qld 4072, AU E. a.ghodke(a)uq.edu.au<mailto:a.ghodke@uq.edu.au>

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active/non active
by Ana Andreea ARTENI 03 Mar '21

03 Mar '21

Dear all, I want to fit a pdb structure into a cryoem map. Accordingly to the youtube tutorials I open both, place the correct pixel size, centre, and then I want to zoom only on the pdb file, but inactivating the cryoem map doesn't work: both maps zoom together. What am I doing wrong? Best regards, -- Ana Andreea ARTENI, PhD ******************************** UMR 9198 Institut de Biologie Intégrative de la Cellule Platforme de cryo-microscopie électronique Bâtiment 14B (RDC. pièce 111) 1 avenue de la Terrasse 91198 Gif-sur-Yvette Cedex, FRANCE Phone: + 33 (0)1 69 82 38 56 Fax: +33 (0)1 69 82 43 08 E-mail : ana-andreea.arteni(a)i2bc.paris-saclay.fr Site web: http://www.i2bc.paris-saclay.fr/spip.php?article277

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editing session file
by Olivier Bignucolo 02 Mar '21

02 Mar '21

Dear Chimera-users, I am new to Chimera. I saved a session.py file that manages the appearance of, say, folder1/proteinA.pdb. I would like to apply exactly the same formats, colors, etc... to proteinB.pdb located in folder2. I edited session.py but was unable to find out how to do it. It seems that the python script does not contain any line like: "open("filename","r") or anything similar. How can I reuse session.py for a new pdb file? Thanks Olivier

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Hydrophobicity extensions
by Sam Hopgood 26 Feb '21

26 Feb '21

Hello, I'm currently studying at Imperial to complete my final year project for my MSci in Chemistry, but due to remote working I have to take on more of a computational project rather than something lab based and I'm not too experienced in the area and neither is my group. I have been told to use chimera to model the hydrophobic surface of proteins and determine a value for the surface hydrophobicity that can be later linked to data collected from HIC studies. I've been told to use chimera to model this but even basic visualisation of the hydrophobic surface does not work for proteins as large as rubisco. I know this is a big ask and an open ended question but are you aware of any extensions available to use to mitigate this issue? Or are you aware of any techniques I could use utilising the software to calculate an actual value for the surface hydrophobicity? I hope you are all keeping safe and well, and thank you for any insight! Best, Sam

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Re: [Chimera-users] Chimera-users Digest, Vol 214, Issue 8
by Khurram Shahzad 26 Feb '21

26 Feb '21

My username and password incorrect plese help me On Thu, Feb 25, 2021, 7:11 PM <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, 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. Re: (no subject) (Thomas Cheatham) > 2. MD analysis of ion position (Elaine Meng) > 3. Re: Chimera Visualization Tool (Ela Ka) > 4. Chimera help submission (David Leeming) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 24 Feb 2021 21:06:55 +0000 > From: Thomas Cheatham <tec3(a)utah.edu> > To: K Jan <10dunajkr(a)gmail.com>, "chimera-users(a)cgl.ucsf.edu" > <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] (no subject) > Message-ID: <6bbb12c3268847adbbf93577d9f4313a(a)utah.edu> > Content-Type: text/plain; charset="us-ascii" > > > The program CPPTRAJ can bin ion densities on a grid which can be > visualized with chimera... > > See: > https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-s… > > CPPTRAJ is available in AmberTools or via GitHub - > https://github.com/Amber-MD/ > > Also AmberHub may have a tutorial related - > https://amberhub.chpc.utah.edu/making-a-3d-histogram/ > > --tec3 > > ________________________________________ > From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of K > Jan <10dunajkr(a)gmail.com> > Sent: Wednesday, February 24, 2021 1:53:36 PM > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] (no subject) > > Hello, > > I`ve just finished a simulation on DNA with K+ ions and I would like to > get images of the average ion location at different points in the > simulation. > > I was wondering how I could find the average location of K+ ions ( because > right now they`re scattered around the DNA) at different points of the > simulation.? > > Thanks > > > > ------------------------------ > > Message: 2 > Date: Wed, 24 Feb 2021 13:22:02 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: K Jan <10dunajkr(a)gmail.com> > Cc: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Subject: [Chimera-users] MD analysis of ion position > Message-ID: <870D7C13-E4ED-49DB-8AA0-5E503A94DCA9(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=us-ascii > > Thanks, I agree that CPPTRAJ is a great solution for analyzing > trajectories. Looks like it can read several formats: > <https://amberhub.chpc.utah.edu/cpptraj/trajectory-file-commands/> > > Alternatively: > In Chimera, if you can view your trajectory in the MD Movie tool, you can > also use that tool to calculate and display an occupancy map. I think > that's essentially the same thing that Tom mentioned, a density map on a > grid that can be viewed as isosurfaces. > > MD Movie help, click "Occupancy Analysis" in the left hand links: > < > https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie… > > > > Occupancy analysis is also covered in the last section of this Chimera > tutorial: > < > https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.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 Feb 24, 2021, at 1:06 PM, Thomas Cheatham <tec3(a)utah.edu> wrote: > > > > > > The program CPPTRAJ can bin ion densities on a grid which can be > visualized with chimera... > > > > See: > https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-s… > > > > CPPTRAJ is available in AmberTools or via GitHub - > https://github.com/Amber-MD/ > > > > Also AmberHub may have a tutorial related - > https://amberhub.chpc.utah.edu/making-a-3d-histogram/ > > > > --tec3 > > > > ________________________________________ > > From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of K > Jan <10dunajkr(a)gmail.com> > > Sent: Wednesday, February 24, 2021 1:53:36 PM > > To: chimera-users(a)cgl.ucsf.edu > > Subject: [Chimera-users] (no subject) > > > > Hello, > > > > I`ve just finished a simulation on DNA with K+ ions and I would like to > get images of the average ion location at different points in the > simulation. > > > > I was wondering how I could find the average location of K+ ions ( > because right now they`re scattered around the DNA) at different points of > the simulation.? > > > > Thanks > > > > > > > ------------------------------ > > Message: 3 > Date: Wed, 24 Feb 2021 22:18:45 +0330 > From: Ela Ka <e.kashani.a(a)gmail.com> > To: Chimera User Help <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Chimera Visualization Tool > Message-ID: > < > CAFiNxG3Ca3WthCUCR3Oad2bt+i6mmMSTsCAkOTvG3oez7s1dzQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Elaine, > > Thank you very much. I appreciate your consideration. Sure, we'll take care > of the credit and other considerations. > > Best Regards > Elaheh Kashani-Amin > > On Wed, Feb 24, 2021, 10:13 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > Dear Elaheh Kashani-Amin, > > Thanks for asking. Yes, it would be acceptable to use Chimera (free > > version) to create images for your slides, providing that Chimera is > > credited for the images in these materials. > > > > However, if you were going to use Chimera interactively as part of the > > paid educational sessions, your group would need to license the software > as > > described here: > > <https://www.rbvi.ucsf.edu/chimera/commercial_license.html> > > > > Best regards, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Feb 24, 2021, at 2:40 AM, Ela Ka <e.kashani.a(a)gmail.com> wrote: > > > > > > Dear Madam/Sir, > > > > > > We are a group of researchers who try to prepare educational contents > in > > different aspects of protein molecular modeling for the students. Access > to > > these educational content is not free. We need to prepare some pictures > of > > proteins, ligand-receptor interaction, etc. for the slides. Can we use > the > > Chimera software (free version) to prepare some pictures for the slides? > > Though, we won't use the tool, itself, for those educational sessions. > > > > > > Thank you for your consideration > > > > > > Best Regards > > > Elaheh Kashani-Amin > > > PhD, Bioscience > > > > >

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Chimera help submission
by David Leeming 25 Feb '21

25 Feb '21

Dear Chimera users, I'm attempting to write a chimera script to automate the process of calculating the relative exposure of residues as per this tutorial: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html The script I have is as follows: rc('surface') # defines areaSES of residues rc('defattr C:/Users/Admin/Downloads/areaSESgxg.txt log 0') # define attribute using areaSESgxg.txt for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): for r in m.residues: r.relSESA = r.areaSES/ r.areaSESgxg However, when I run this script, I am receiving this error: [cid:39cc50d4-a627-494c-b0f5-411a7785a9a2] When I run the process using the UI I can successfully calculate relSESA By using the command: "surface" Then using the assign attribute function to assign areaSESgxg.txt Followed by using the calculate attribute function to calculate per residue: residue.areaSES/ residue.areaSESgxg Could you advise on any methods I could use to fix this script to produce the output I am receiving from the UI. Kind regards, David

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(no subject)
by K Jan 24 Feb '21

24 Feb '21

Hello, I`ve just finished a simulation on DNA with K+ ions and I would like to get images of the average ion location at different points in the simulation. I was wondering how I could find the average location of K+ ions ( because right now they`re scattered around the DNA) at different points of the simulation.? Thanks

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Chimera Visualization Tool
by Ela Ka 24 Feb '21

24 Feb '21

Dear Madam/Sir, We are a group of researchers who try to prepare educational contents in different aspects of protein molecular modeling for the students. Access to these educational content is not free. We need to prepare some pictures of proteins, ligand-receptor interaction, etc. for the slides. Can we use the Chimera software (free version) to prepare some pictures for the slides? Though, we won't use the tool, itself, for those educational sessions. Thank you for your consideration Best Regards Elaheh Kashani-Amin PhD, Bioscience

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No mmcif module in ChimeraX 1.0?
by Yangqi Gu 23 Feb '21

23 Feb '21

Dear Chimera Developer, I am trying to use an external python script to run some calculations. I am using ChimeraX 1.0 and the script requires the import of mmcif module but apparently it is not installed in ChimeraX 1.0? How should I install this module? I also downloaded a newer version 1.1, but it is a precompiled version. Do I need to remove ChimeraX 1.0? Because the older version was installed in /usr/bin with an executable file, but for the newer version, I assume I need to add the path for the executables? I also need to run some ISODLE refinement with my gpu, will ChimeraX configure gpu automatically? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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volume position/placement question
by Chen Mu 23 Feb '21

23 Feb '21

Hi Dear List, I am new to Chimera and I have a question using the volume viewer: I have three volumes (reconstructions from different tomographic reconstruction algorithms) to compare. They are in the same size and structure as saved in the .mrc files. I will rotate one volume and adjust the volume viewer and view it. And I then will create an animation video by adding 'roll' in timeline. But the question is, how can I make sure that when I open the other volumes, all of them are in the same starting position/placement, in order to compare and each frame in the animation video to make it possible to compare, because they should start at exactly the same volume position/placement. How can I set up this placement of the volumes to be the same? Thanks very much in advance! Best, Chen

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On pdb structure match or align
by Smith Lee 23 Feb '21

23 Feb '21

Dear All, With chimera I open A.pdb abd B.pdb. A.pdb contains domain a and doain b, B.pdb contains domain b and domain c, which is to say, the 2 structures share a common domain b. Will you please tell me the chimera specific command to align or match the 2 structures based fully on the common domain b in each structure, without consideration of the domain a and domain c for calculation of the alignment? Best wishes, Smith

2 1

on chimera mask
by Smith Lee 22 Feb '21

22 Feb '21

Dear All, When I use command "mask ones #0" to get the mask for #0 image and use the mask.mrc for further processing by other program, it says the mask.mrc got was not in the "cube volume" format. Will you please explain what is the "cube volume" format mrc, and is any way to convert the above mentioned 'non-cube volume" format mask.mrc to "cube volume" format mask.mrc? Best wishes, Smith

4 3

Green bars in side view on new install
by Rochelin Dalangin 21 Feb '21

21 Feb '21

Hello, I installed Chimera 1.15 on a Windows 10 Pro laptop running i5-10300H and Intel UHD 630. When I try to open side view to clip the protein, I end up with green bars on the side view window (as shown). I've tried reinstalling to see if that fixes the issue, but it didn't work. Would you have any idea what's causing this? Thanks, Rochelin [image: image.png] -- ------------- Rochelin Dalangin Department of Chemistry 4-135 Centennial Centre for Interdisciplinary Science University of Alberta Edmonton, AB T6G 2G2

2 1

saving several pdb files in one
by Dieter Blaas 18 Feb '21

18 Feb '21

Dear Elaine and all, I have a large number of aligned pdb files and want to mask a volume including density near all these atoms. Is there an easy way of doing so? Usually I would load map and pdb, position the pdb model accordingly, activate all atoms and use 'zone' to mask everything further away from all atoms than a given distance. But this seams to be difficult with more than 100 coordinate files, each containing about 1000 coorinates! I also tried to combine all coordinates in a single file omitting everything else but chimera tries desperately to find secondary structure elements, which is difficult with this mess.... Is there an easy way of doing so? Thanks, best, 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@meduniwien.ac.at ------------------------------------------------------------------------

4 7

Installing chimerax linux
by Francesco Pietra 18 Feb '21

18 Feb '21

Hello I would like to change to chimerax, installing it on Debian (10 Buster) Regrettably, it has become practice to refer to ubuntu when .deb packages are concerned. I would appreciate being informed which u. version, if any, is suitable for Debian 10 thanks francesco pietra

2 1

Hide (pseudo-)bond between neighboring residues
by Konstantin Richter 18 Feb '21

18 Feb '21

Dear Chimera Community, I currently experience some trouble hiding certain bonds that Chimera automatically displays. But first things first: I want to design a figure of the active site of two very similar protein structures (models #0 and #1; let's assume they are mutants of the same molecule differing in only a few amino acid residues). I therefore display the ribbon as well as certain residues of model #0. Additionally, I align #1 on #0 and display the same residues in #1, but without the ribbon. So, the side chains of #1 should end in the ribbon of #0 (which is basically identical to ribbon #1). Since Chimera automatically displays all atoms of the residues when the respective ribbon is hidden, I also hide C,O,N of #1 residues. Now this looks fine expect for one thing. Chimera creates long (pseudo?)bonds between the CA atoms of residues that follow one another in sequence, e.g. res 64 and 65. This very long 'bond' messes up my figure, and I haven't yet figured out how to delete or hide it. I already tried the ~bond #1:64-65@CA command, but this one hides ALL bonds in residue 64 (but not the one between 64-Ca and 65-Ca) and other variations of the atom specifier. Is something wrong with my atom specification, or is this command not suitable for what I want to do? I also tried the bonddisplay command without succes, since it deletes all bonds in one residue. In the end, I want the residues of #1 to contain all atoms except for C,N,O including bonds between all atoms, but not the elongated connection between Ca atoms. best regards Konstantin Richter -- P. Konstantin Richter - M.Sc. Biochemistry Department of Structure Analysis of Biopolymers - Institute of Bioanalytical Chemistry Center for Biotechnology and Biomedicine (BBZ) - Leipzig University Deutscher Platz 5 D-04103 Leipzig Tel.: +49 341 9731316

2 2

Writing each rotamers to individual PDB file
by Chemmama, Ilan 17 Feb '21

17 Feb '21

Dear Developers, I am trying to write a PDB for each rotamer in Chimera. I run the command: `swapaa RES :RESNUM lib Dunbrack criteria manual` I get the enumeration for each rotamers from SCRWL library. I was wondering if there was a way to write each of those rotamers into separate PDB file using a script. Some residues have large number of possible rotamers and manually selecting the rotamer and saving the PDB file is not tractable. Thank you very much ! Ilan

2 3

fill solvent accessible channels
by Dieter Blaas 16 Feb '21

16 Feb '21

Hi, I am wondering whether chimera can fill/colour channels accessible from outside of a cryo-EM density map at a given level! If so, how? I'd like to check for size selectivity. Thanks, best, 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 1

Homology modelling with Chimera/Modeller
by StaidsonBio 16 Feb '21

16 Feb '21

Hi: I am trying to do homology modelling with Chimera/Modeler for a Fc fusion protein, which contains three domains, one is Fc, one is receptor and the 3rd is ligand. Fc has many PBD structures in PDB database and the receptor has couple of 3D structures with the ligand as well. I used the fusion protein sequence to do blast in Chimera and it gave matched sequence files to Fc domain only, no sequence files for the receptor-ligand complex, even it already has couple of solved 3D crystal structure files in PDB database. Is there any suggestion about this issue? Can I do separately, use Fc domain alone as search sequence for its template and use receptor-ligand sequences as search sequence for its template? If it is ok, there are two template files. How to make them into one template file for modelling late? Thanks very much for your suggestion. Sincerely TW Sent from Mail for Windows 10

3 4

Cutoff for clustering
by Yasser Almeida 15 Feb '21

15 Feb '21

Hello, I have a question regarding the clustering in the MD Movie tool (MD Movie/Analysis/Cluster). What's the RMSD cutoff value to make the clustering? I don't see any mention of this in the documentation. Thanks in advance, -Yasser

2 1

fitting open conformation (map)
by Neha Gandhi 13 Feb '21

13 Feb '21

Hi Elaine, There is a cryo-EM structure of the spike trimer in closed conformation. I have downloaded pdb file and map files for the locked conformation. I am interested in aligning or mapping map of the open conformation (fitting pdb from closed conformation pdb on the map). Could you please advise how this can be achieved? Many thanks, Neha -- Regards, Dr. Neha S. Gandhi, Vice Chancellor's Research Fellow, Queensland University of Technology, 2 George Street, Brisbane, QLD 4000 Australia LinkedIn Research Gate <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 1

on chimera vop threshold
by Smith Lee 13 Feb '21

13 Feb '21

Dear All, I have a map (A.mrc). When I open it in chimera (the map should be #0), the Volume Viewer shows the Range is -0.618 to 1.63, the default Level is 0.175. With command "vop threshold #0 minimum 0.18 set 0" I got another map (let us call it B.mrc, should be #1), the Volume Viewer shows the Range is 0 to 1.63 (understandable, the maximum value is still 1.63 as in A.mrc, the minimum value is 0 as for all values not higher than 0.18 has been set to 0), the default Level is still 0.175. Immediately I run the command "vop threshold #1 maximum 0.17 set 1". Before I running the command, I guess all the density value should be either "0" or "1", because all the value lower than 0.18 has been set to "0", and all value higher than 0.17 has been set to "1". However after I run the command "vop threshold #1 maximum 0.17 set 1", I got another map (let us call it C.mrc, should be #2),the Volume Viewer shows the Range is 0 to 0.17 rather than 0 to 1, and wen I change the Level, the image of #2 changes correspondingly with the Level from 0 to 0.17. Here I would ask, why the command "vop threshold #1 maximum 0.17 set 1" did not lead to a map with all values greater than 0,17 as 1? How to get a map based on A.mrc so that all values less than 0.18 as 0 and all values greater than 0.17 as 1 (please tell me the specific method)? Is any significance for the obtained C.mrc with range from 0 to 0.17? I am looking forward to getting your reply. Smith

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Apple M1 chip
by 163 11 Feb '21

11 Feb '21

Hi There, Is there a version that is suitable for Apple M1 Mac? I found the old version is quite on M1 Mac. Thanks! ML

3 5

Re: [Chimera-users] Creating new models from existing crystal structures
by Elaine Meng 08 Feb '21

08 Feb '21

You're welcome, I'm glad you figured it out! Elaine > On Feb 8, 2021, at 2:40 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > > Hi Elaine > Nevermind, I found my error. I tested the Join Model tool with 1AV1 which has four chains and I was able to correctly pick the correct C and N atoms to join residue segments from each chain. The select command that I had written originally wasn't right so it was picking the correct atoms to join. > Thanks for your help. > Best > Tiglath > > > On Feb 8, 2021, at 2:27 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > > If the residue is already in a peptide bond, you can't add another peptide bond. You would have to delete the rest of the chain after 130 in one copy of the model and the rest of the chain before 131 in the other copy for it to make sense. > > > > Also, make sure that your "select" command is selecting exactly two atoms, 1 from each model. > > > > Elaine > > > >> On Feb 8, 2021, at 1:53 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > >> > >> Hi Elaine > >> > >> I've been using the biological assembly of 3R2P and I'm thinking that the reason why it's not working is because both chains are labeled A. I'm just following a paper where they're building a monomeric structure using the residue fragments but in their case the biological assembly of 3R2P is labeled as chain A and chain B. > >> From: Elaine Meng <meng(a)cgl.ucsf.edu> > >> Sent: Monday, February 8, 2021 1:01 PM > >> To: Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> > >> Cc: chimera-users(a)cgl.ucsf.edu <chimera-users(a)cgl.ucsf.edu> > >> Subject: Re: [Chimera-users] Creating new models from existing crystal structures > >> > >> Hi Tiglath, > >> If you just opened 3r2p one time, you only have one model. Join works on bonding two separate models. Also it contains only chain A (there is no chain B in this structure) and residue 130 in chain A is already bonded to residue 131 in chain A. So I do not understand what you already did to modify the structure(s) before joining, or what you are trying to do now, sorry. > >> > >> You could send a session file if you want. > >> Elaine > >> ----- > >> Elaine C. Meng, Ph.D. > >> UCSF Chimera(X) team > >> Department of Pharmaceutical Chemistry > >> University of California, San Francisco > >> > >>> On Feb 8, 2021, at 12:35 PM, Moradkhan, Tiglath A <tmoradkhan(a)csus.edu> wrote: > >>> > >>> Hi > >>> > >>> I'm trying to join two models together using the Build Structure tool but I'm having problems. Here is my process. > >>> > >>> • Using the 3R2P crystal structure I select residues 3-130 from chain A and 131-182 from chain B > >>> • Then using the following command in Chimera I select the N atom of residue 130 that will form a bond with the C atom of residue 131: sel #0:130@N#1:131@C (#0 is the name of the 3-130 segment and #1 is the name of the 131-182 segment) > >>> • Then using the Build Structure tool I select Form C-N peptide bond, but the Apply button doesn't activate. > >>> I don't understand what the issue is. Is the command that I've written wrong? > >>> > >>> I would be very glad for your help. I can provide the pdb files of the residue segments if necessary. > >>> Thanks > >>> > >>> Tiglath > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

1 0

Creating new models from existing crystal structures
by Moradkhan, Tiglath A 08 Feb '21

08 Feb '21

Hi I'm trying to join two models together using the Build Structure tool but I'm having problems. Here is my process. 1. Using the 3R2P crystal structure I select residues 3-130 from chain A and 131-182 from chain B 2. Then using the following command in Chimera I select the N atom of residue 130 that will form a bond with the C atom of residue 131: sel #0:130@N#1:131@C (#0 is the name of the 3-130 segment and #1 is the name of the 131-182 segment) 3. Then using the Build Structure tool I select Form C-N peptide bond, but the Apply button doesn't activate. I don't understand what the issue is. Is the command that I've written wrong? I would be very glad for your help. I can provide the pdb files of the residue segments if necessary. Thanks Tiglath

2 3

Re: [Chimera-users] Video tutorials
by Tom Goddard 04 Feb '21

04 Feb '21

Hi Cynthia, Ok, I converted all the Chimera video tutorials (about 40 of them) to use standard web browser video playback. https://www.rbvi.ucsf.edu/chimera/videodoc/videodoc.html <https://www.rbvi.ucsf.edu/chimera/videodoc/videodoc.html> Thanks for pointing out that they were using the obsolete Flash plugin for movie playback. Tom > On Feb 4, 2021, at 10:29 AM, Cynthia Page wrote: > > Hi Tom, > Do you all have any plans of porting the tutorial flash videos to another player? I see there are some YouTube videos available for Chimera but I am thinking of the tutorials that are available on the website. > Maybe there is another source of video tutorial I am unaware of? > > Thanks very much, > Cynthia Page > CU Boulder > > Sent from my iPhone >

1 0

MD simulation in Chimera : 10 ns simulation is equivalent to 1 million of production steps 10 fs each?
by Giovanni Roviello 29 Jan '21

29 Jan '21

Dear Sirs, I would like to perform a MD simulation by UCSF Chimera. Should I wish to perform a 10 ns simulation (for example) how could I set the parameters related to time? For example in production a number of phase steps of 1000000 and a time step of 10 fs is OK? Does the relaxation time Nosé thermostat has effect on the overall simulation time? In simpler words if I set 1000000 steps, 10 fs time step, and I leave selected Nosè thermostat with 0.2 ps (but leave unselected the barostat option) will it correspond to a 10 ns MD simulation? Of course if I will publish using Chimera I will cite the program and the reference as indicated in https://www.cgl.ucsf.edu/chimera/docs/credits.html Thank you in advance for your kind help. Kind regards, Giovanni _______________________________________________________ Dr. Giovanni N. Roviello, Ph.D. Researcher at Istituto di Biostrutture e Bioimmagini IBB - CNR; Via Mezzocannone 16; I-80134 Naples; Italy giroviel(a)unina.it giovanni.roviello(a)cnr.it http://www.ibb.cnr.it/?command=viewu&id=387&lang=en https://orcid.org/0000-0001-6065-2367

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less color depth possible?
by Cheng, Tat 27 Jan '21

27 Jan '21

Hi all, We are trying to set up cryoEM data processing in the university HPC. We use X2go for remote accessing the HPC, but it doesn't have enough color depth, so Chimera (24-bit) doesn't start. One workaround is to download the volume from HPC to local machine, but it is less convenient. But I wonder is there a way to use Chimera in less color? Thanks a lot. Best, Tat

3 3

how to color an model by an attribute in chimerax
by sunyeping 27 Jan '21

27 Jan '21

Dear all, I wish to color an model by an attribute in chimerax. The attribute is the entropy which is calculted by an external software. I wrote the entropy values of each residue in a text file (attr.txt) like the following: attribute: entropy match mode: 1-to-1 recipient: residues :1 0.0 :2 0.0014948 :3 0.0090952 :4 0.0004805 :5 0.1102497 :6 0.0095258 :7 0.0008226 :8 0.0042205 :9 0.0037255 :10 0.0006678 :11 0.0027988 :12 0.0193925 :13 0.0153925 :14 0.0052115 :15 0.0020136 .......... However, when I input the command "color byattr attr.txt", I get the following error information: "No known/Registered attribute attr.txt" Could anyone tell me what is the correct way to do this? With many thanks. Best regards

2 3

coloring the volume series
by Arto Pulk 26 Jan '21

26 Jan '21

Dear all, I would like to make a movie using volume series. I have 10 maps (from Relion) that I upload to volume series. Now I would like to color the moving parts of the map. One can use zone coloring, but it does not do the precise job to color specific volumes of the map as it is radius specific. Then there is "surface coloring" by "volume data value". I can make a mask and color the mask region, but it makes the color gradient and I do not have control of the region outside of the mask at it will be mixture of colors. The best way to color is to use "segment map" and then go to "Regions" and "color density map". It does good job to color specific map volumes but the colors are not permanent. If you Play the Volme Series then colors vanish. So, is there any good way to color Volume Series? Regards, Arto Institute of Technology University of Tartu Nooruse 1 50411, Tartu Estonia Dr. Arto Pulk email: arto.pulk(a)ut.ee phone: 58244846

2 2

Chimera RMSD
by Elaine Meng 25 Jan '21

25 Jan '21

> From: "Sharyn Endow, Ph.D." <sharyn.endow(a)duke.edu> > Subject: Chimera RMSD > Date: January 23, 2021 at 11:27:17 AM PST > > Thank you for your work in developing Chimera. We are trying to use Chimera RMSD to quantitate twisting of a beta-sheet and would like to know what the syntax is to list rmsd values for specified residues corresponding to a beta-strand, not just for single residues. Is it possible to list these values using RMSD? If so, we would greatly appreciate knowing how to get started. > > Sincerely, > Sharyn Hi Sharyn, You can specify any sets of atoms/residues that you like in the RMSD command, as long as there are equal numbers of atoms in the two sets that you specify (from two different models). They will be paired in the order specified. We have a command-line "atom specification" syntax for that kind of thing. There is a longish page with lots of examples here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> In your case, you may need to specify residue numbers, chain ID, and possibly atom names if you just want to use alpha-carbons or backbone as opposed to all atoms of the residues. E.g. something like rmsd #0:12.A,57-63.A #1:14.A,59-65.A ... for all atoms of model 0 residues 12 and 57-63 in chain A vs. all atoms of model 1 residues 14 and 59-65 in chain A. Or to use CA-only or backbone only: rmsd #0:12.A,57-63.A@ca #1:14.A,59-65.A@ca rmsd #0:12.A,57-63.A@n,ca,c,o #1:14.A,59-65.A@n,ca,c,o Of course the numbers could be the same in the two models, I just was trying to give a more general example. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. the chimera-users(a)cgl.ucsf.edu address CC'd here is recommended for general Chimera how-to or is-it-possible types of questions

1 0

adding chimera-trimmings alias
by Dmitry A. Semchonok 25 Jan '21

25 Jan '21

2 3

command line > vol all surface level 0.1 colour gradient
by Dieter Blaas 20 Jan '21

20 Jan '21

Dear Elaine, please forgive me for asking again, I cannot find your previous mail and my notes: How can I, in command line, do the following, i.e. what is the correct syntax? vol all style surface level 0.1 colour by gradient colours 5 palette rainbow set I have a number of volumes loaded and want to colour their surfaces, at level 0.1 by 'volume data gradient norm' with 5 rainbow colours setting them to the full range Thanks a lot, best 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 1

Coloring peptide bonds in Chimera
by Tynan A. Becker 19 Jan '21

19 Jan '21

Good afternoon, I have been trying to figure out how to color just a single peptide bond between 2 residues in a protein. What I have figured out so far is to show chain trace under actions|atoms/bonds. Then invert the selection (whole protein). This shows the bonds. I can select a residue and color the bond on both sides. But I want to color the bond between 2 residues. If I pick the bond by manual selection, the action|color|choice doesn't work. The manual tantalizingly suggests using the "halfbond" setting or "bondcolor" for the command line. The problem that I encounter is that I can't figure out how to tell the program which bond I want. I've read the "atom specifications" page of the manual and tried every logical combination I can figure to tell the program which bond I want to color. But each time, I get the "mangled atom specifier" error. I was told today that there is a way to do this, but I'm stuck. Any input is welcome. Thank you, Tynan

2 6

Problem with electron density
by Elaine Meng 14 Jan '21

14 Jan '21

Dear Francesco, Probably you just need to use "vop cover" as described in these previous posts: <https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009142.html <https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009142.html>> <https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-July/017021.html <https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-July/017021.html>> Details on the "vop cover" command: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>> For future: the recommended address for questions is chimera-users(a)cgl.ucsf.edu (CC'd on this message) ... since I'm not the expert in everything (or might be sick or away from work), it's helpful if more people see the question! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > From: Francesco Papi <Francesco.Papi(a)iit.it> > Subject: Chimera: Problem with electron density > Date: January 14, 2021 at 3:03:55 AM PST > To: "meng(a)cgl.ucsf.edu" <meng(a)cgl.ucsf.edu> > > Dear Elaine, > I am using Chimera to get a picture of a small molecule (cif file) in an electron density map (xplor file). My issue deals with the position of some atoms of the molecule in an adjacent unit cell (see attached image) which prevents me to see some atoms within the map. I thought to simply expand the map beyond the cell boundaries and eventually crop the map, but it didn’t work. I have checked different tutorials and the chimera mailing list for troubleshooting but I haven’t found a solution to this problem. Is there something you can think of? > Thank you. > Regards, > Francesco Papi > > Francesco Papi, PhD > PostDoc > Center for Nanotechnology Innovation@NEST > Istituto Italiano di Tecnologia > Piazza San Silvestro, 12 > 56127 Pisa, Italy > Phone: +39 050 509 495 > E-mail: francesco.papi(a)iit.it <mailto:francesco.papi@iit.it> > Skype: francesco.papi.89 >

2 1

Can't open large .bild files
by Hannah Bridges 13 Jan '21

13 Jan '21

Hi all, I would like to visualize in Chimera the orientations from some angdist.bild files output from relion. I am able to open some .bild files (up to ~5.6MB in size) but I get "not responding" from Chimera when I try to open .bild files ~10-70MB (lots of particles and high angular sampling). I tried on a machine with more RAM but it was the same. Any hints about how to open these or is it just not possible? Best wishes Hannah -- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom Telephone : 01223 252812

4 5

APBS
by mailman-bounces＠cgl.ucsf.edu 12 Jan '21

12 Jan '21

From: benjamintam <benjamintam(a)um.edu.mo <mailto:benjamintam@um.edu.mo>> Subject: APBS Date: January 11, 2021 at 7:28:44 PM PST To: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu <mailto:chimera-users-bounces@cgl.ucsf.edu>> Dear All, I can see that we have to run the APBS locally, however, which default execute file that I need to select in the Chimera in order to run APBS? Best, Ben

2 1