April 2020 - ChimeraX-users - RBVI Mailing Lists

deleting sidechain in ChimeraX
by Joel Meyerson 22 Apr '20

22 Apr '20

Hi, What is the command or sequence of commands which can be used to delete the sidechain on an amino acid or range of amino acids? I reviewed the ChimeraX atom spec page but could not find a way to do this. Thanks, Joel

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Problem with showing 4 Fe-4S in pdb with chimerax
by Meinan Lyu 22 Apr '20

22 Apr '20

Dear chimerax-users(a)cgl.ucsf.edu, There is a 4 Fe-S in my structure, it shows a little bit funny when I open it with chimerax. It should only have links between Fe and S, but between 2Fe shows a link line two. Do you know how to show it normally like in pymol, or remove the links between 2Fe? I really want to draw some figures in chimerax. The attached are 4 Fe-S shown in chimrax,also shown in pymol. PDB id 2WDQ is also attached, which 4 Fe-S is in /B,F,J:303. Thanks very much. Be safe and Best, Meinan Postdoc from CWRU

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shape tool in ChimeraX
by Joel Meyerson 20 Apr '20

20 Apr '20

Hi, Chimera has a “shape” command that I find quite useful. Does ChimeraX have this feature? I could not find it in the online documentation. Thanks, Joel

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Re: [chimerax-users] [EXT] Re: passing arguments to python scripts with command runscript
by Philipp Milkereit 15 Apr '20

15 Apr '20

Hi Eric, thanks for your fast help, works now as expected! Philipp Von: Eric Pettersen <pett(a)cgl.ucsf.edu> Gesendet: Mittwoch, 15. April 2020 22:19 An: Philipp Milkereit <philipp.milkereit(a)vkl.uni-regensburg.de> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Betreff: [EXT] Re: [chimerax-users] passing arguments to python scripts with command runscript Hi Philipp, In ChimeraX, the arguments will be in sys.argv — namely sys.argv[1:] since sys.argv[0] will be the name of your script file. --Eric Eric Pettersen UCSF Computer Graphics Lab On Apr 15, 2020, at 12:47 PM, Philipp Milkereit <philipp.milkereit(a)vkl.uni-regensburg.de <mailto:philipp.milkereit@vkl.uni-regensburg.de> > wrote: Dear all, in Chimera 1 it was possible to pass arguments with runscript to python scripts which could be read out there by arguments[index]. In ChimeraX I am not anymore able to read passed values using arguments[index] in python scripts called by runscript. Was that feature dismissed or was there a change in the naming? Thanks for your help, Philipp _______________________________________________ ChimeraX-users mailing list <mailto:ChimeraX-users@cgl.ucsf.edu> ChimeraX-users(a)cgl.ucsf.edu Manage subscription: <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

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passing arguments to python scripts with command runscript
by Philipp Milkereit 15 Apr '20

15 Apr '20

Dear all, in Chimera 1 it was possible to pass arguments with runscript to python scripts which could be read out there by arguments[index]. In ChimeraX I am not anymore able to read passed values using arguments[index] in python scripts called by runscript. Was that feature dismissed or was there a change in the naming? Thanks for your help, Philipp

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syntax on marker and marker link placement
by Joel Meyerson 12 Apr '20

12 Apr '20

Hi, I have a question about marker and marker link syntax. Suppose model #1 has chains A and B, and that chains A and B form a homodimer where each subunit has the same residue numbering. I would like to place a marker at the midpoint between alpha-carbons of position 10 on A and 10 on B. In turn, I'd like another marker at the midpoint between position 20 on each of the two subunits. I would then like to draw a linker between the two markers. I would expect the following syntax to work, but I get an error. marker #2 #1/a,b:10@CA color yellow radius 1 marker #2 #1/a,b:20@CA color yellow radius 1 marker link #2:1,2 color yellow radius 0.5 Gives the error: Missing or invalid "position" argument: Expected 3 floats or object specifier Any suggestions on how to fix the syntax, or is there an alternative approach? Thanks, Joel

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Move Z plane backside
by Aritz Roa Eguiara 09 Apr '20

09 Apr '20

Dear ChimeraX team, I would like to ask if there is any command to move the Z plane but not the front, but the back one, while recording a movie. I am familiar with clipping, however when recording a movie it directly appears, is there any way to do the same move z but for the far plane? Thank you in advance and happy Easter, Aritz

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How to do repetitive task using Python or command line in ChimeraX?
by 이서원 09 Apr '20

09 Apr '20

Hello, I think I'm good at dealing with the previous Chimera command line, and I'm learning Python coding and ChimeraX little by little. In Chimera, I was able to apply the Chimera command to a Python script using runCommand. So, I wrote some python scripts for Chimera, such as automatically coloring or cropping maps and/or models based on the target specification list in plain text. However, I think there's no python modules like runCommand, and I don't know how to repetitively input specifications by .cxc files. (Do I have to make as many .cxc files as many as the number of the variables?) Also I tried to understand the ChimeraX developer tutorial, but I failed to import color functions on chimeraX Python Shell. (I didn't understand how to import experimental API) Is there any fancy way to create a .cxc file that executes by sequentially inputting variables in the list? Or, How to import python modules such as color functions? (https://www.cgl.ucsf.edu/chimerax/docs/devel/core/commands/user_commands.ht…) Best regards, Seowon ______________________________________________________________________________________ 이 서 원 | Selcia Seowon Lee selcia20(a)snu.ac.kr Laboratory of Molecular Imaging , Ph.D. Candidate Department of Biological Sciences, College of Natural Sciences Seoul National University, Gwanak-gu Gwanak-ro 1, Bldg105 Rm109, Seoul 08826, Korea

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How to do repetitive task using Python or command line in ChimeraX?
by 이서원 08 Apr '20

08 Apr '20

Hello, I think I'm good at dealing with the previous Chimera command line, and I'm learning Python coding and ChimeraX little by little. In Chimera, I was able to apply the Chimera command to a Python script using runCommand. So, I wrote some python scripts for Chimera, such as automatically coloring or cropping maps and/or models based on the target specification list in plain text. However, I think there's no python modules like runCommand, and I don't know how to repetitively input specifications by .cxc files. (Do I have to make as many .cxc files as there are variables?) Also I tried to understand the ChimeraX developer tutorial, but I failed to import color functions on chimeraX Python Shell. (Experimental API Is there any fancy way to create a .cxc file that executes by sequentially inputting variables in the list? Or, How to import python modules such as color functions? (https://www.cgl.ucsf.edu/chimerax/docs/devel/core/commands/user_commands.ht…) Best regards, Seowon ______________________________________________________________________________________ 이 서 원 | Selcia Seowon Lee selcia20(a)snu.ac.kr Laboratory of Molecular Imaging , Ph.D. Candidate Department of Biological Sciences, College of Natural Sciences Seoul National University, Gwanak-gu Gwanak-ro 1, Bldg105 Rm109, Seoul 08826, Korea

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silhouette scaling and image dimension
by Joel Meyerson 08 Apr '20

08 Apr '20

Hi, I noticed that when I save images in ChimeraX with silhouettes on, the apparent width of the silhouette in the output image seems to scale inversely with the image dimensions. For example, these three commands give slightly different silhouette thicknesses. Images attached. save ~/Desktop/image1.png width 500 height 500 save ~/Desktop/image2.png width 1000 height 1000 save ~/Desktop/image3.png width 2000 height 2000 Is there a way to have a fixed silhouette thickness in output images? I'd also be interested to know why this happens. Thanks, Joel

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ChimeraX-users April 2020