- Chimera-users - RBVI Mailing Lists

Euler Angles
by Gabriella Angiulli 29 Jun '20

29 Jun '20

Hi, I’m trying to calculate the transformation between two Cterminal domains in two different conformations and I’ve been using the command “measure rotation”. The rotation is reported in the first three columns of a 4x3 matrix in the log file window and my question is: do I have a way to get the Euler angles of my transformation from that matrix ? Thank you so much, Gabriella

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Intallation
by Joakin Mori 29 Jun '20

29 Jun '20

Hello, I am having trouble with opening the application. I keep getting error message. Please see attached. [cid:447FFFA4-4784-499C-80AC-B4D90E44938F@GuestNet.Tuskegee.Edu]

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adding residues to an existing protein or joining a protein to a small peptide.
by brody deming 26 Jun '20

26 Jun '20

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AutoDock Vina Help
by Ali 24 Jun '20

24 Jun '20

Hi Everyone, As of the end of April 2020, the webserver to opal is no longer working. I have tried to build the PDB2PQR programme locally but have been struggling. Basically, need to align a RNA molecule to a sight within the pdb. If anyone can help, please assist. Thank you, Ali from Cape Town

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New instance opened with each new map
by Melody Campbell 24 Jun '20

24 Jun '20

Hi, Since I installed the 64-bit UCSF Chimera version for Mac Catalina (10.15.5) each time I open a new map, a new instance of UCSF Chimera opens instead of opening the map in the same instance. Could you help me find where the setting is to change this so that by default all new maps and models opened (via double clicking icons) is done in the same instance of Chimera? (I tried re-installing/ restoring all factory settings and deleting my /Users/user/.chimera/preferences file, but still by default, a new session opens for each map). Thanks so much! Melody

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convert .mod to .mrc
by Emmanuel Moebel 23 Jun '20

23 Jun '20

Dear Chimera community, I am visualising a tomogram segmentation with Chimera, the format of the file is .mod and has been obtained with the IMOD software. I would like to get a voxel map from it : a volume with integer values, for ex. '0' for background, '1' for membrane, '2' for filament. Output file format needs to be .mrc or .em. Is this possible to achieve with Chimera? Thanks in advance, Emmanuel Moebel, PhD

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ask a question about the chimera in windows
by Hai Li 22 Jun '20

22 Jun '20

Hi, officer, I am Hai Li at university of texas working on the protein structure and function. Recently I begin to use chimera to show the protein structure. I lean that I need to click and drag a residue in the list in order to show this residue’s sidechain in chimra. However, I have windows and I tried to do the click and drag a residue but it did not work. Could you please tell me how to visualize a residue in windows? Thank you. hai Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Structure Minimization and Molecule Movement (ChimeraX-1.0)?
by Ammar Jastaniah 21 Jun '20

21 Jun '20

Hi, I am not able to find the minimize feature function in ChimeraX-1.0. Is there an equivalent to the regular Chimera version, which is to be found under Tools ==> Structure Editing ===> Minimize Structure? Also. Are you able to move a PDB file ligand molecule around while keeping the other receptor PDB structure stationary/in its place in ChimeraX-1.0? Once again, this is achievable in Chimera by clicking on Tools ==> Movement ===> Movement Mouse Mode. Thank you. Ammar

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Re: [Chimera-users] [chimerax-users] ViewDock script
by Moustafa, Ibrahim M. 20 Jun '20

20 Jun '20

Hi Eric, I'm using Chimera. Is there an equivalent command to use in Chimera? Thanks, Ibrahim ________________________________ From: Eric Pettersen <pett(a)cgl.ucsf.edu> Sent: Friday, June 19, 2020 3:50 PM To: Moustafa, Ibrahim M. <ria2(a)psu.edu> Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] ViewDock script Hi Ibrahim, “ui tool hide ViewDockX” will hide all ViewDockX windows. --Eric Eric Pettersen UCSF Computer Graphics Lab On Jun 19, 2020, at 11:54 AM, Moustafa, Ibrahim M. <ria2(a)psu.edu<mailto:ria2@psu.edu>> wrote: Dear All, I'm trying to run ViewDock from a script using the following command in a loop: runCommand("viewdock " + filename + " AutoDock") It works fine. However, the ViewDock window remains opened after reading each file. For large number of files it is not practical to close them manually. Is there a command to close the opened ViewDock windows to add to the script? Thank you for your help. Ibrahim _______________________________________________ ChimeraX-users mailing list ChimeraX-users(a)cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl…>

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ViewDock in script
by Moustafa, Ibrahim M. 19 Jun '20

19 Jun '20

"re-sending question to the right bb" Dear All, I'm trying to run ViewDock, in Chimera, from a script using the following command in a loop: runCommand("viewdock " + filename + " AutoDock") It works fine. However, the ViewDock window remains opened after reading each file. For large number of files it is not practical to close them manually. Is there a command to close the opened ViewDock windows to add to the script? Thank you for your help. Ibrahim

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Saving volume surface in IMOD .mod
by Long Gui 18 Jun '20

18 Jun '20

Dear all, I was trying to save the surface data of a mrc file in Volume Viewer as the IMOD file type .mod so that it would be read in IMOD. I have searched but could only find the following link about opening IMOD .mod file in Chimera: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/imod… But I want to do the reserve operation. Is that possible that we could generate and save the surface data in Chimera and let it be read by IMOD? Thanks a lot, Long Gui, Ph.D. Postdoc Researcher, Nicastro Lab University of Texas Southwestern Medical Center Long.Gui(a)utsouthwestern.edu Tel: (214)-645-1561 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Modeller function and MD function in Chimera 1.14
by ‍성열승(대학원학생/일반대학원 약학과) 18 Jun '20

18 Jun '20

Daer whom it may concern, Hello, I am a graduate student trying out several features in Chimera for structure prediction. I write to you due to repeated problem during my use of Chimera function. I currently made a slight alteration in one residue of my protein. I have named it as a another residue, other than an amino acid. Then, I tried going to Modeller function so that the program will predict some energetic difference resulting in a structural modification. However, whenever the function ends, my helices and beta sheets are all converted into loop regions.Therefore, I only selected the loop region of my protein and made it go through the Modeller. Now, the modification was only shown in the loop area, but my alteration in an amino acid residue has been cut off. The residue was nowhere to be seen. I guess the Modeller made it go away. Next I tried selecting all the loop regions except the residue that I made the change and started Modeller, hoping that the altered residue will not be cut off. However, I got a result of it getting cut off again. Overall my question could be summed up into the following three: 1. Is there any way making Modeller function to have my altered residue not changed but have the program go through? 2. Is there a way for refining my protein in the helices and beta sheets area? Modeller function seem to change all of those into loops, and showed excellent prediction in the loop region. 3. Do you recommend any other function for my purpose? I built a PTM residue into one of my amino acid and want to see some predicted structure alteration. Thank you so much for your time. I really think the Chimera software is awesome and I just need to get used to it and try to learn some tricks. I hope to hear from you soon. Yours sincerely, Yulseung Sung -- 성열승 연세대학교 약학대학 암대사연구실 (Yulseung SUNG) (Lab of Cancer Metabolism, College of Pharmacy, Yonsei University) 연세대학교 약학대학 인천광역시 연수구 송도과학로85, 연세대학교 국제캠퍼스 진리관D 317-3호, 암대사연구실 College of Pharmacy, Yonsei University 317-3 Veritas D, 85 Songdogwahak-ro, Yeonsu-gu, Inchoen, 406-840, South Korea

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Managing window visibility through scripts?
by Martti Tolvanen 05 Jun '20

05 Jun '20

Hi, I have made scripts in which various models are rendered by mavConservation taken from different alignments. As the scripts proceed, the multialignment viewer windows remain at the front, and I haven't been able to figure out how to bring the main molecular graphics window back to the front (except by clicking). I am aware that the problem would go away if I made the whole thing into a movie, but I would like to run the script in our research group meeting and leave the displayed models available for manual rotations. Are there commands to bring windows behind or in front of other Chimera windows? I run the production version of Chimera 1.14 under Windows 7. Part of my code follows. #single chains of ca6, ca9, ca12, and ca14 as #0-3, superimposed by mmaker, and their copies as #4-7 tile #0-7 columns 4 range kdHydrophobicity min cyan 0 white max maroon novalue green #0-3 open ca6.fasta range mavConservation 0.1 dodger blue 0.55 white 1 orange red novalue green #4 open ca9.fasta range mavConservation 0.1 dodger blue 0.55 white 1 orange red novalue green #5 open ca12.fasta range mavConservation 0.1 dodger blue 0.55 white 1 orange red novalue green #6 open ca14.fasta range mavConservation 0.1 dodger blue 0.55 white 1 orange red novalue green #7 surface #0-7 & protein Cheers, -Martti -- Martti Tolvanen Lecturer in Bioinformatics U of Turku, Finland

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Bottom menu is super small
by h k 05 Jun '20

05 Jun '20

Dear Sir/Madam, I have installed *Chimera-1.14-win64.exe* on my laptop (Windows 10) in order to work on the protein structures. The structures look good, but the bottom menu is super tiny as I can’t see the buttons there at all ! Please look at the following picture (red arrow on that) and let me know how can I solve this issue? I tried different compatibilities by changing High DPI Scaling Override. In this way, I can increase the size of bottom menu but it adversely affect the quality (resolution) of protein structure images! Please help me with this issue. Thank you, Haniyeh [image: image.png]

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Multifit waiting too long for Opal server response
by André Graça 04 Jun '20

04 Jun '20

Hi, I am using Multifit for the first time and wondering if a few hours are not long enough to wait for a server response. The task panel shows from the beginning the status as 'waiting for response from Opal server'. I read on the paper (2011) about Multifit that "The typical running time is about 20 min for assemblies with tens of thousands of atoms", which is the case. I wonder if it is not running yet and it is queued in the server, or if it takes a long time depending on anything that I might have set up wrongly. Could anyone help me to figure this out? Thank you, André Graça

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How to know the cut-off used in ensemble cluster?
by Ibrahim Mohamed 01 Jun '20

01 Jun '20

i am using MD movie to cluster my Molecular Dynamics results. how can i know the cut-off used by chimera to do this? i know that it depends on the data itself, but how can i know this cut-off for specific data? Thanks

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Need instructions how to do MD simulations of Protein-ligand complex using Chimera
by P Srivastava 01 Jun '20

01 Jun '20

Dear Chimera Team I Need instructions on how to do MD simulations of Protein-ligand complex using Chimera. Please give me in details. With regards, Pratibha Srivastava प्रतिभा श्रीवास्तव Scientist वैज्ञानिक Bioprospecting Group जैव पूर्वेक्षण समूह Agharkar Research Institute आघारकर अनुसंधान संस्थान Pune, India पुणे, भारत

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(no subject)
by Preantha Poonan 01 Jun '20

01 Jun '20

Good afternoon, I am writing to you regarding an error I am experiencing with working with Chimera. When I begin the docking process the following appears: Service 'opal:vina_1.1.2 is unavailable . See Reply Log for more details. Kindly assist. Preantha Poonan Sent from Mail for Windows 10

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Conversion of Chimera session .py file to Pymol .pse file
by Joanna Smietanska 01 Jun '20

01 Jun '20

Dear UMSF Chimera Users, I would like to ask how to convert Chimera session .py file into .pse Pymol format? I have a few saved Chimera sessions, my approach was to save protein coordinates in .pdb format and subsequently read them in Pymol 2.0 to save as Pymol session, but during this procedure all informations about specific colouring of chains and other settings are lost. May I ask about possibilities for direct import Chimera .py files into Pymol without losing saved settings? I would be very grateful for any help and advice. Best regards, Joanna Smietanska

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Molecular dynamics
by Сергей Владимиров 01 Jun '20

01 Jun '20

Good day! My name is Sergei Vladimirov, I'm a student at Moscow State University. As far as I know, when running a molecular dynamics of ligand-protein interaction one must use different force fields to the ligand and the protein. There is a mm14ff to calculate interactions within a protein but there are only two different force fields to calculate interactions within a ligand. I've been led into believing that the best ff for small organic ligands is GAFF. So my question is, is there any way to implement the GAFF force field into the production of molecular dynamics? Is there anything I'm missing? I will be awaiting your reply. Best regards, Sergei Vladimirov.

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CHIMERA code in R
by Farzaneh Amanpour 27 May '20

27 May '20

Dear CHIMERA users, I am a PhD student in biostatistics and I want to run this algorithm in R. Can I have access to R code for CHIMERA? Thank you in advance

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Molecular docking
by Schaf, Judith (2017) 27 May '20

27 May '20

Hi everybody, I have a quick question: when I analyse the results of a molecular docking assay (performed with SwissDock) on Chimera I sometimes see a green line between the protein and the ligand. Does someone know what this line represents? [cid:fc8bd8ab-4117-464a-b2fb-0f512e867f88] Thank you, Judith

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Re: [Chimera-users] Adding New Covalent Bond?
by Elaine Meng 26 May '20

26 May '20

> On May 26, 2020, at 9:52 AM, Ammar Jastaniah <ajasta2(a)uic.edu> wrote: > > Hi Elaine, > Is there any way to connect/make new bonds between adjacent, somewhat distant carbon atoms within a ligand structure (perhaps still using the 'Build Structure' feature)? > Thank you. > Ammar Hi Ammar, Assuming this is a Chimera question (we are now developing ChimeraX) the answer is yes, in the Adjust Bonds section of Build Structure, you can choose to add a bond between any two selected atoms regardless of the distance between them. Just choose the "all possible" option. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h…> Or, you could use the "bond" command: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html> The chimera-users(a)cgl.ucsf.edu address (CC'd here) is recommended for Chimera questions, unless private data are included. 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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save images/scene - independent of chimera window
by Dominique Gutierrez 26 May '20

26 May '20

Good Morning, Is there a way to save an image independent of the chimera window size. When I reopened a saved session and saved an image from a scene it was not the same and it seems to be due to change in the chimera window. Best Regards. Dominique Gutierrez

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Color by electrostatic potential
by Francesco Pietra 22 May '20

22 May '20

I was able to open with chimera 1.1.3.1 (linux) electrostatic-potential cube files generated from ORCA package and view them in colors (red lowest, blue highest potential). I can't remember how I succeeded and now, from chimera help, I am no more able. Only a single color. Thanks for putting me on the right way. chiendarret

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