- Chimera-users - RBVI Mailing Lists

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

25 Sep '24

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

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

23 Sep '24

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

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

22 Sep '24

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

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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

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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

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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

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Python script to add hydrogens to selected carbon atoms
by Mandelli, Davide 19 Sep '24

19 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 --------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------

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Error when opening session file cross-platform
by Alexander Lee 18 Sep '24

18 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]

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

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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

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