March 2023 - ChimeraX-users - RBVI Mailing Lists

AlphaFold best_model.pdb could not visually overlap the input sequence using matchmaker
by Cheng Fei Phung 31 Mar '23

31 Mar '23

Hi, I am trying do "matchmaker #2 to #1" between colab output ( best_model.pdb which is pasted here at http://ix.io/4rRO ) and https://www.rcsb.org/structure/7CR5 However, as seen in https://i.imgur.com/gHL8to3.png , there is not really much visual overlapping since the structures are not rotated properly to match each other. The log for doing matchmaker command is available here at https://i.imgur.com/78h5CLq.png The colab notebook is also saved as a screenshot here at https://i.imgur.com/LSTdyZe.png Manually doing "turn z 1 270 model #1 center #1" or similar rotations commands also do not help. Please advise. Regards, Phung Cheng Fei

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question about chimerax
by 12119007 30 Mar '23

30 Mar '23

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MICROTUBULE AND SYM COMMAND
by Aleck Dwyer 29 Mar '23

29 Mar '23

Hi, I am trying to model a microtubule Cryo-EM map (my first time).in Chimera I was following the example https://www.cgl.ucsf.edu/chimera/videodoc/MicrotubuleSym/index.html I was able to do the example but when using my data I see issues. The spacing is way off. If anyone has modeled a microtubule in Chimera and/or ChimeraX please let me know.. Thanks, Aleck [image: image.png] <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Virus-free.www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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MICROTUBULE AND SYM COMMAND
by Victor Dwyer 29 Mar '23

29 Mar '23

Hi, I am trying to model a microtubule Cryo-EM map (my first time).in Chimera I was following the example https://www.cgl.ucsf.edu/chimera/videodoc/MicrotubuleSym/index.html I was able to do the example but when using my data I see issues. The spacing is way off. If anyone has modeled a microtubule in Chimera and/or ChimeraX please let me know.. Thanks, Aleck [image.png] ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Re: [chimerax-users] Removing unwanted models from the chimerax panel
by Elaine Meng 29 Mar '23

29 Mar '23

Hi Boaz, I don't know what .ctx files are. At first I thought you meant open models in the Models Panel, but I am pretty sure that you already know how to close models. However, my coworker suggests that you actually meant the previously opened files and thumbnails in the File History or Rapid Access panel. If the files no longer exist, you can easily clear them by using the context menu in that tool (File History or Rapid Access), shown with right-click (or on a Mac with trackpad or single button mouse, Ctrl-click): Remove deleted files <https://rbvi.ucsf.edu/chimerax/docs/user/tools/filehistory.html> However, if the files still exist but you don't want to see them in this tool, you would need to delete the specific preferences file that has the file history. The File History help link above says how to figure out what directory on your system contains this file, which is named file_history I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 25, 2023, at 2:25 PM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi, > Excuse the trivial question: I am experimenting with various options and end up filling the panel of sessions with unwanted models. Do I have to delete the .ctx file of the session from outside Chimerax to make it disappear from the panel or is there a way to do this from within the program (i.e. the equivalent of of the Edit option in chimera)? I couldn't find such an option in the 'help' or documentation. Sorry. > Thanks, > > Boaz

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Coloring H bonds black
by McClean, Phillip 28 Mar '23

28 Mar '23

Hi Everyone, I am developing a publication image that shows the hydrogen bonds between two chains. How can I ensure that the dashed lines that show the H+ is displayed in black. From the papers I see in refereed publications, black seems to be the color of dashed lines showing these bonds. Thanks for any help Phil McClean

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Values at atom positions
by Gőcze Máté 27 Mar '23

27 Mar '23

Hello, I have an issue with saving values at atom positions from the command line. I can attach the attributes to the atoms but when i use: save filename attrName a:mapvalue format defattr matchMode 1-to-1 I get: One or more attribute values aren't integer, floating-point, string or None (e.g. 3.8542745); skipping those Saved attribute 'mapvalue' of 0 atoms using match mode: 1-to-1 to filename can you please help me resolve the issue. I have tried reformatting the headers of my map but it didn't help. Thank you for your help.

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Changing line thickness of individual selections
by Raulf, Karoline 27 Mar '23

27 Mar '23

Hi everyone, I have a question about the graphical representation of my model in ChimeraX. Here, I have colored individual proteins and to make them even more visible, I would like to increase the line thickness of the silhouette of these proteins. But when I try this with the combination of the keyword graphic silhouette and sel, I don't get anywhere. Is there any way to change the line thickness of individual selections without changing the line thickness of the silhouette of the entire model? Thanks in advance for the help! Best Karoline

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commandline to change the step and threshold of all the maps
by Rayees Mattoo 23 Mar '23

23 Mar '23

Hi, If there is one, could you please share the command lines for changing the step and threshhold of all or the selected maps in chimeraX. Best

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Integrating Vina into ChimeraX
by Andy Tong 22 Mar '23

22 Mar '23

Hi, So I recently began using ChimeraX on my Windows PC and I'm stuck on how to integrate Vina into ChimeraX. I know that it's no longer automatically included in ChimeraX so I downloaded it separately, but where do I need to insert Vina's files for it to show up in the "tools" section under binding analysis, or how can I add a command to run Vina through Chimera? Thanks

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