- Chimera-users - RBVI Mailing Lists

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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