- Chimera-users - RBVI Mailing Lists

Loop through pbd files (ligand poses) and find hydrogen bonds against one template receptor
by Samuel Kyobe 13 Apr '22

13 Apr '22

Dear Chimera (and ChimeraX) team I have run a large docking experiment using several ligands to determine the best binders for further analysis in Molecular Dynamics studies and possible wetlab evaluation. I need to find some python example or code snippet capable of looping over hundreds of files and find several .pdb poses from a docking run and find Hydrogen bonds in each one using one receptor. In the process of finding the H bonds, I would like to add Hydrogens, and the protonation state is unspecified. Then at FindHBond, I want to find intermodal Hbonds and write the results to a file. Thanks Samuel Dr. Samuel Kyobe Department of Medical Microbiology, 3rd floor, Pathology/Microbiology BLDG, School of Biomedical Sciences College of Health Sciences, Makerere University. Box 7072, Kampala, Uganda. Mob: +256775468605 Skype: samuelkyobe

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Chimera X color by attribute middle range value
by Zimanyi, Marcell 12 Apr '22

12 Apr '22

Hello Chimera Community, I have a .defattr file where I have assigned a value to a few residues on my protein. I'd like to set the range to be 0.2, 1, and 4 so that values with 1.0 will be the middle color. I currently don't see a way to set the middle value for the range. In Chimera, I could set the middle range value in the define attribute GUI. In Chimera X, I'm using color byattribute range 0.2,4 because the range argument will only accept two values. I see that I can bring up the color key gui, but when I change the color key I don't see a way to update the coloring on the residues themselves. Could you please help me figure out how to set attribute range with 3 values as in Chimera? Thanks, Marcell

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Align two structures
by Catherine Jenifer Rajam Rajendran 11 Apr '22

11 Apr '22

Hi, I'm trying to use the "match" command to align two protein pdb structures. Instead of specifying which chains or atoms or residues to align, Is there a way to align the whole structure from the command line? Thanks, Catherine

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Problem running Chimera on MacBook
by Levine, Judy 08 Apr '22

08 Apr '22

Hello all – I’m having trouble doing the ViewDock tutorial on my MacBook. I am able to open the ras.mol2 file in ViewDock, but when I then open the setup file the program freezes – and in fact the only way to exit the program at that point is to do a force quit. I have done it successfully several months ago and wanted to refresh my memory but now am experiencing this problem. I installed the latest version (1.16) in case that was the problem, but that didn’t help. I also considered using ChimeraX instead but was unable to figure out whether the ViewDock feature is available in that. I’m able to do the tutorial on my home desktop PC, but at work I only have the MacBook so it’s frustrating not to have Chimera working properly. Has anyone else experienced this problem? (In case it’s not obvious, I am quite the novice Chimera user. I’m using it in undergraduate biochemistry teaching, primarily to analyze results from SwissDock.) Thanks! Judy Levine ***************************************** Dr. Judy Levine Center for the Natural Sciences; Program in Biochemistry and Molecular Biology Goucher College 1021 Dulaney Valley Rd. Baltimore, MD 21204 410-337-6525; judith.levine(a)goucher.edu<mailto:judith.levine@goucher.edu> *****************************************

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Openning XYZ files with ChimeraX
by Henrique Castro 07 Apr '22

07 Apr '22

Hello, everyone, I'm trying to adapt to ChimeraX and when trying to open an XYZ file I'm receiving the message "Opener for format 'XYZ file' is not installed; see log for more info". Is it possible to work with his format as in the Classic Chimera? -- Henrique C. S. Junior

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Creating distances using the command line
by Lucic, Iva 07 Apr '22

07 Apr '22

Hello, I would like to measure distances between atoms in a structure by using the command line, and not manually by clicking on the atoms and then clicking on "create" button in the Structure Measurements tool. I would like to map many distances on the same structure (I performed a crosslinking experiments, so I would now like to map the crosslinks on the structure of my protein of interest). I tried something like distance #1 :347.A@ca - :323.A@ca and similar variations, hoping that I could get the distance between CA atoms of residues 347 and 323 of chain A (there are 12 chains in my protein) from model 1. But I couldn't find a good combination of commands to give me a distance. I would highly appreciate any advice. Otherwise, I would have to map manually over 20 crosslinks for each chain... Thank you in advance, Iva

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Re: [Chimera-users] Assembling 2 protein subunits into a heteromer
by Elaine Meng 05 Apr '22

05 Apr '22

> On Apr 4, 2022, at 11:32 PM, SANTOSH RAMA BHADRA RAO TATA <19807877(a)students.latrobe.edu.au> wrote: > > Good evening, Meng, > > I'm trying to bind to protein subunits A and B with the stoichiometry of A-A-B-A-B pentameric form how can I do that in chimera? I have both A and B PDB files single chains. > > Thanking you, > > With best wishes, > Tata Santosh Rama Bhadra Rao, > PhD Scholar, > C/O Prof Helen Irving, > La Trobe university, > Bendigo, Vic-3550, > Australia. > Email: 19807877(a)students.latrobe.edu.au; > S.Tata(a)latrobe.edu.au > Phone: 0499263974 Hello, The recommended address for Chimera questions is chimera-users(a)cgl.ucsf.edu CC'd here. Chimera doesn't predict how A and B would bind each other. Instead you have to use any other information you might have. If there is a similar structure already known in pentameric form, then you could: - open the known pentamer - open the A structure 3 times and the B structure 2 times - superimpose each of your structures on one monomer of the known pentamer, e.g. with matchmaker See matchmaker (GUI tool or command) and other methods for superimposing structures: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Question regarding chimerax module
by Prathvi Singh 04 Apr '22

04 Apr '22

Hello again Elaine, Is it possible to install the chimerax module in anaconda for usage in jupyter notebook? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Extracting secondary structure residue info
by Prathvi Singh 03 Apr '22

03 Apr '22

Hi Elaine, I have a PDB file which only has rows starting with ATOM. When I open it in UCSF chimera, it displays all the secondary structures which the residues form. Is it possible to extract the starting & ending residues of each alpha helix (or any other secondary structure for that matter)? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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How to run a script in ChimeraX
by Shanti Pal Gangwar 30 Mar '22

30 Mar '22

Hi I am trying to run a script in chimeraX but it did not work. I even downloaded the example files and that also did not work. I wonder if a script can be run in ChimeraX as we do in PyMol. Any help would be appreciated. Thank you Shanti Pal

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