June 2023 - ChimeraX-users - RBVI Mailing Lists

opening multiple csx files at same time
by stevensb＠ufl.edu 26 Jun '23

26 Jun '23

How can you open 2 or more csx files simultaneously in order to have the all contents of both *.csx files showing and superpositioned. This can be done for opening multiple *.pdb files which then shows all the chains of all the opened files superpositioned on the same page. But when I try to open multiple csx files, the second one completely deletes and replaces the currently open csx file and deletes what was showing from the originally open csx file.

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Re: [Chimera-users] downloading and saving multiple PDB's
by Elaine Meng 26 Jun '23

26 Jun '23

Hi Dmitry, You sent this to the chimera-users list but chimerax-users(a)cgl.ucsf.edu (CC'd here) is the better address for ChimeraX questions. We try not confuse Chimera users with ChimeraX answers and vice versa. Since your text said "Chimerax" I will answer for ChimeraX. Not sure what you mean by "multiple" ... of course you can fetch structures from the PDB using their IDs, e.g. commands: open 1zik open 2gbp 2fw0 1plx 1plz <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> If by "multiple" you mean a huge number that is not practical to put in a single command, that is a different matter. Also, a single "save" command only saves one file and it does not have option to automatically figure out filename from model name. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> However, ChimeraX does allow writing a single command script (.cxc file) and applying it to multiple input files when the .cxc file is opened with the "open" command and "forEachFile" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile> It also allows substituting part of the input file name as the output file name. However, it was intended for the case where all the input files are local files. So as far as I know you would have to first fetch all the files from the PDB so that they are in your local cache (~/Downloads/ChimeraX/PDB/ ) and then in a separate step, use your .cxc file with this forEachFile mechanism. To do so, you would probably also need to segragate these files into their own directory since you don't also want to run the script on all of the other structures you've previously fetched from the PDB using ChimeraX. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 26, 2023, at 9:39 AM, Dmitry Semchonok via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear colleagues, > > Is there a way to > > • download the multiple pdb/mmcif using Chimerax knowing their ID entry? > • save multiple opened pdbs using their corresponding original names in Chimerax? > Thank you in advance. > > Kind regards, > Dmitry

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Electrostatics
by Ryan Gardner 26 Jun '23

26 Jun '23

Hello, I just want to verify that the electrostatic potential is measured in volts (V). Is this correct? Here's an example of my analysis: [image: image.png] Sorry to be a bother! -Ryan

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error opening Swissdock generated output file
by Fussner-Dupas, Eden 26 Jun '23

26 Jun '23

Hello, I am having trouble using ViewDockX with a file generated by Swissdock. When I open the clusters.dock4.pdb file it opens without issues - but when I try to use the ViewDockX tool to view each predicted pose one at a time I get the error “No suitable models found for ViewDockX” Any help warmly appreciated Cheers, Eden

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Save Image Dialog box
by McClean, Phillip 25 Jun '23

25 Jun '23

Hi Everyone, I am using ver 1.6 of Chimerax. I want to save an image for print publication, so I want to save it as 300 dpi. I used the Snapshot icon from the toolbar and it saved a 72 dpi image. In the user guide, there is mention of a Save Image dialog. The guide sounds like I can make use the dialog to select the dpi. But, I cannot find the Save Image menu. Can someone point me to it and add any help/hints on save a 300 dpi image. As always, thanks for your help. Phil McClean

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Aligning two ligands
by Karim Rafie 25 Jun '23

25 Jun '23

Hi all, I was wondering if there's a command that will allow me align two ligands to each other? Couldn't find anything online and when I try the match command I constantly run into an error, even when specifying certain atoms between two ligands. Any help would be greatly appreciated. All the best, Karim ############################################## Karim Rafie; PhD, MRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå, Sweden [cid:e5366e3a-666f-40ea-9f71-eb5b2b395016]

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Changing spin movie default save location?
by Daniel Gilliam 21 Jun '23

21 Jun '23

Hi, How can I change the default filepath that 'Spin movie' saves to? The default for me saves to location without save permissions, so I have been unable to save images or movies. Apologies if I missed an easy answer to this in the documentation. Thanks, Daniel Gilliam

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Invert selection
by Leonardo Talachia Rosa 20 Jun '23

20 Jun '23

Dear ChimeraX community Apologies for the very naive question. In old chimera, there was a "Select - Invert selected models" command which would invert the selection solely in the selected model, whereas in chimeraX I could not find an equivalent command or option in the menu. The select invert menu will invert the selection for all open models. Is there a way to invert selection only in one model? Thank you for your time Kind wishes, Leonardo -- ************************* Leonardo TALACHIA ROSA, PhD Associated professor Department of Biochemistry and Tissue Biology (DBBT) Biology Institute Universidade Estadual de Campinas - UNICAMP Rua Monteiro Lobato, 255 - Campinas - SP - Brasil - CEP 13083-862 **************************

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ChimeraX - Without NVIDIA
by Nguyen, Tuan /US 16 Jun '23

16 Jun '23

Hi, I'm trying to install the ChimeraX 1.6.1 on Ubuntu 22 without NVIDIA driver, I can launch the chimerax, but it gives me an error about the graphic driver, and I'm trying to open a pdb file, I don't see the image at all. Please see attached below. Would you please help? Thanks, Tuan [cid:image001.png@01D9A02C.7D05AF30]

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600 DPI Quality Images
by Dillon P Cao 15 Jun '23

15 Jun '23

Hello, How would I save an image on ChimeraX as 600 dpi? Apologies if this has been answered before. Sincerely, Dillon P. Cao

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