- Chimera-users - RBVI Mailing Lists

MD on Chimera
by Manon Bulliard 20 Sep '24

20 Sep '24

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

3 3

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

20 Sep '24

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

2 1

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

19 Sep '24

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

3 8

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

18 Sep '24

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

2 2

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

17 Sep '24

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

3 3

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

12 Sep '24

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

2 1

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

12 Sep '24

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

1 0

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

10 Sep '24

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

2 2

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

09 Sep '24

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

2 1

Chimera interface to Modeller
by Vonderviszt Ferenc 03 Sep '24

03 Sep '24

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

4 4

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

29 Aug '24

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

3 6

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

27 Aug '24

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

2 1

Problem of starting Chimera
by 郭家瑞 24 Aug '24

24 Aug '24

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

2 1

Mac Version
by Gonzalo de Prat Gay 22 Aug '24

22 Aug '24

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

3 5

chimera
by 2719354821＠qq.com 13 Aug '24

13 Aug '24

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

2 1

Chimera
by Kotin, Robert 13 Aug '24

13 Aug '24

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

2 2

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

05 Aug '24

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

2 8

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

01 Aug '24

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

1 1

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

22 Jul '24

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

2 1

molmap onGrid option
by Hernando J Sosa 18 Jul '24

18 Jul '24

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

2 1

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

17 Jul '24

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

2 1

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

15 Jul '24

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

2 1

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

14 Jul '24

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

4 3

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

12 Jul '24

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

2 1

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

09 Jul '24

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

2 7