- Chimera-users - RBVI Mailing Lists

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

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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

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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

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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.

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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?

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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

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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

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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

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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

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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.

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Bug
by Anoop B S 09 Apr '24

09 Apr '24

Sometimes its not responsive.How to resolve that

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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

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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]

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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]

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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> -----------------------------------------------------------------------------

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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

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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

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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?

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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

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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.

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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

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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,

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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.

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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

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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

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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> --

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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

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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 |

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[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

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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

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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

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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.

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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

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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

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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

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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

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