July 2020 - ChimeraX-users - RBVI Mailing Lists

Surface dust command in the .cxc script
by 李泽 24 Feb '25

24 Feb '25

Hi all: I'm trying to use the .cxc script to run the software, I found that the "surface dust" command has never been executed in it. Have anyone met the same problem? Any suggestions. Thank you all. Best, Ze

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Get color code of a custom color
by Ahmad Khalifa 11 Feb '25

11 Feb '25

I created a custom color that I want to use in a different session. is there a way to do that besides trying to match colors by eye? Regards.

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Double and Triple Bond Stick Style
by Smith, Chase 05 Feb '25

05 Feb '25

Dear ChimeraX, I was just wondering why there is no way to represent a double or triple bond in either the ligands or the protein amino acids when viewing as a Stick or Ball-and-Stick representation? I sometimes use Chimera or ChimeraX to make visuals for my lectures, and the students often have difficulty in understanding due to the absence of the multiple bonds. I would love to have the ability to represent the double or triple bonds with multiple lines between the atoms. Thank you, Chase Smith ... ChaseSmith, PhD Chair, Department of Pharmaceutical Sciences & Associate Professor of Medicinal Chemistry School of Pharmacy MCPHS University 19 Foster Street | WorcesterMA01608 T 508.373.5717F 508.890.5618C 978.855.7203 chase.smith(a)mcphs.edu www.mcphs.edu MCPHS University Confidentiality Note: This e-mail, and any attachment to it, is intended to be confidential and might be legally privileged. It is intended solely for the use of the addressee. If you are not the intended recipient, you are hereby notified that reading, copying, disseminating or distributing this email is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.

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Re: [chimerax-users] [Chimera-users] color by zone in chimeraX
by Elaine Meng 20 Nov '20

20 Nov '20

Hi Pranav, I’m Cc'ing the chimerax-users(a)cgl.ucsf.edu list (recommended for ChimeraX questions). I believe the problem is that when coloring the chains you are using “target c” which means to color only cartoons, whereas coloring by zone uses the atom colors. Since you only colored the cartoons, the atoms probably still had heteroatom color-coding. If you use “target ac” instead (even if the atoms aren’t shown), then as long as the color zone distance is big enough, I think you will get the color zones you expect. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 20, 2019, at 10:54 AM, Pranav Shah <p.shah.lab(a)gmail.com> wrote: > > Hi Elaine and Co., > > I am trying to color a virus map with the relevant pdb file, the > series of commands I am running are as follows, > open virus.mrc > open virus.pdb > color /A plum target c > color /B lightgreen target c > color /C dodger blue target c > color zone #1 near #2 dist 3 > However, the resultant surface is rendered in splotches of red and > blue, which leads me to think the it is coloring the surface using > atom type. Could you tell me how I can get Chimera X to color the > surface using the colors of the chains only? FYI, color by zone works > flawlessly in chimera. > > Cheers, > Pranav

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Command line utility for .cmap
by Daniel Asarnow 06 Aug '20

06 Aug '20

Hi all, I have only been able to load volume series data using the .cmap format (using a daily from this week on OS X). Is there a command-line utility, perhaps ChimeraX itself, that can generate a .cmap file from a number .mrc volumes? It would be nice to generate these on my processing machine and then only download the .cmaps to my laptop. Best, -da

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command: symmetry, option: contact
by Roberto Marabini 31 Jul '20

31 Jul '20

Dear all, In chimera I used to use the command sym #0 group i,222r contact 3 to surround an asymmetric unit cell by its neighbors. I see that, in chimerax, "sym" no longer has the option "contact" (or the alternative option "range"). Is there any way to get results similar to the ones obtained using chiera command sym #0 group i,222r contact 3 with chimerax

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Cartoon and ribbon display - change atoms for nucleic acid from C5' to Phosphate
by bertrand beckert 31 Jul '20

31 Jul '20

Dear ChimeraX developper, I was wondering if in ChimeraX it is possible to change the atoms used for the cartoon/ribbon display. According to the online user manual ( https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#top) for the nucleic acid the cartoon path seems to be restricted and guided by only the C5'.... could it be possible to change the C5' to the Phosphate instead? is there already a command existing ? Thanks for the nice software! Best regards Bertrand

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Re: [chimerax-users] ChimeraX command line iterate through models for individual file export
by Tom Goddard 30 Jul '20

30 Jul '20

Hi Austin, Of course I remember you, it was a great trip to Rocky Mountain Laboratories. Thanks for your hospitality! And I see your SARS-Cov-2 images in the media -- very nice. Here's the ChimeraX voodoo to save all your objs in one command perframe "save ~/Desktop/objs/model$1.obj model #1.$1" frames 23 It uses the perframe command that runs another command once each frame (usually used for recording an animation video). The $1 gets the frame number substituted in 1, 2, 3 and the frames tells it how many frames, in your case use 100 to get the 100 models. Here are the perframe docs https://www.cgl.ucsf.edu/chimerax/docs/user/commands/perframe.html <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/perframe.html> if you need more info. Tom > On Jul 29, 2020, at 10:19 PM, Athman, Austin (NIH/NIAID) [E] <austin.athman(a)nih.gov> wrote: > > Tom, > > I’m Austin Athman, from the NIAID Rocky Mountain Laboratories Visual Arts Department. I took some of your sessions on ChimeraX when you were out to Hamilton MT in the past, and I believe you assisted my colleague Ryan Kissinger on some ChimeraX questions he had. I have one for you I hope you can help. > > I have received a morphing model of the spike protein on RSV for an animation project we are working on for Barney Graham and Jason McLellan. The morph is in 100 steps, and I have 2 different morphs (one for attachment, and another for fusion), making 200 steps total. I am exporting the surface model of each step to an OBJ file for use in our animation software. I have managed to write a single command line that I copy/paste in over and over, changing just the id and file number for export to get the files I need. > > Is there a way I can automate this further, so that ChimeraX will iterate through each id and export to individual files for me without copy/pasting the command each time and modifying it? It would save me hours of time. > > Unfortunately, I am very new to ChimeraX, and know only enough to get me into trouble, specifically, how to show/hide surfaces, and export! > > Here is a screenshot of my model, and also the Excel doc I use to keep track and build my command for each file export, just so you can see what I am doing at the moment. It takes some time for each to save as well, so I don’t know if that delay will make it difficult for the command line to wait and continue each time for each export. There may be some additional commands I can just add between each line in the excel, and I can just copy and past the entire thing and let it run, but that is where I hope you might be able to tell me what I am missing. > > Hope you are well in these times. Also, thank you for your work and videos on coronavirus. Good informative stuff. > > -Austin Athman > > > > <image006.jpg> > > <image008.jpg> > > > > > -- > <image009.png> > ..................................................................... > Rocky Mountain Laboratories NIH/NIAID > Research Technologies Branch <http://myrtb.nih.gov/> > 903 South 4th Street > Hamilton MT 59840 > Phone: (406) 375-7480 > > DISCLAIMER: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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source code of ChimeraX
by Сергій Кущ 29 Jul '20

29 Jul '20

Hello! How to download source code of ChimeraX?

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VOP cover command?
by Megan Mayer 29 Jul '20

29 Jul '20

Hi chimeraX forum, I am trying to get an electron density map (.mrc) to overlap with atomic structure (.cif) file of a small organic molecule. When I open my electron density map in ChimeraX, only one rectangle ( i am assuming one lattice piece) appears, which does not encapsulate the entire small molecule. I am thinking to use the "vop cover" command to get the density to expand to multiple lattices, but I am not sure what numbers to enter. When I try "vop cover atomBox #2" (#2 is the ID of the .cif structure), I get a "Missing or invalid 'volumes' argument: invalid density map specifier" response. Thanks in advance for any help!! Megan

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