April 2022 - ChimeraX-users - RBVI Mailing Lists

Identifying residues based on PAE plot?
by mailman-bounces＠cgl.ucsf.edu 27 Apr '22

27 Apr '22

From: "Jan Gebauer" <jan.gebauer(a)uni-koeln.de <mailto:jan.gebauer@uni-koeln.de>> Subject: Identifying residues based on PAE plot? Date: April 27, 2022 at 3:04:30 AM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Reply-To: "Jan Gebauer" <jan.gebauer(a)uni-koeln.de <mailto:jan.gebauer@uni-koeln.de>> Hi everyone, love the "new" work in the dailys for ChimeraX and visualising the PAE and pLDTT scores. As I calculate my AF structures on my own, this helps a lot to analyses the structures. I have one question/suggestion however: If I select a region in the PAE plot, it gets coloured in the the "3D-view", however, I found no way to actually get the residues number or a proper selection for the coloured residues. Is there a way? I'd like to colour multiple selections differently... Another nice feature would be a pLDTT plot, as this enables easier detection of unordered stretches... As always: Many thanks for all the good work! Best Jan -- Dr. Jan Gebauer | 💎 Head of C2f |🔬 Member of AG Prof. Baumann Institut für Biochemie | University of Cologne Zuelpicher Str. 47 | 50674 Cologne | Germany 📞 +49 (221) 470 3212 📠Fax: +49 (221 470 5066) 📧 jan.gebauer(a)uni-koeln.de <mailto:jan.gebauer@uni-koeln.de> 🌐http://px.uni-koeln.de/ <http://px.uni-koeln.de/> 💎Visit the Cologne Crystallisation facility (C2f) !🌐http://c2f.uni-koeln.de/ <http://c2f.uni-koeln.de/>

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Trouble running ChimeraX 1.3 on Windows 7
by Yu Zhou 27 Apr '22

27 Apr '22

Hi there, I got this error message "api-ms-win-core-path-l1-1-0.dll is missing" when i tried to run ChimeraX 1.3 after installation. My OS is Window 7 and I have no trouble running ChimeraX 1.2.5. I greatly appreciate your help. Yu Zhou

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Unable to restore session: need to update bundle
by Rafael Molina 27 Apr '22

27 Apr '22

Dear ChimeraX staff, I cannot restore a ChimeraX session and ChimeraX suggests to update atomic bundle to version 1.31 or newer (have 1.13.2). When I go to all bundles (https://cxtoolshed.rbvi.ucsf.edu/apps/all <https://cxtoolshed.rbvi.ucsf.edu/apps/all>) I cannot find the way to update it properly. Could you help me to fix the error? Thx ---------------------------------------------------------- Rafael Molina, PhD Dept. Crystallography & Structural Biology. Institute of Physical Chemistry Rocasolano Spanish National Research Council (CSIC) Serrano 119. 28006-Madrid. Spain Phone: +34 91 561 94 00 ext. 961121 E-mail: rmolina(a)iqfr.csic.es <mailto:rmolina@iqfr.csic.es> My Research Gate Profile <https://www.researchgate.net/profile/Rafael-Molina-11> ----------------------------------------------------------

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Re: [chimerax-users] [Chimera-users] Tomogram display
by Elaine Meng 26 Apr '22

26 Apr '22

Hi Shen, If you are asking whether ChimeraX has similar features to Chimera: (1) yes, ChimeraX has a volume viewer tool and "volume" command for density maps, with many of the same options as Chimera <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html> (2) ChimeraX has the same fitting into maps as Chimera <https://rbvi.ucsf.edu/chimerax/docs/user/tools/fitmap.html> (3) ChimeraX also includes segmentation <https://rbvi.ucsf.edu/chimerax/docs/user/tools/segment.html> (4) similar to Chimera's Volume Tracer, ChimeraX has markers and links and tools for placing them into maps <https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html> Details between the two programs are not exactly the same, however. There may be some specific thing you need that still requires Chimera, but you can certainly use both programs. To ask questions about ChimeraX specifically, you may wish to use the other mailing list chimerax-users(a)cgl.ucsf.edu CC'd here. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 26, 2022, at 5:13 AM, Han, Shen via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > I want to ask some questions regarding displaying tomogram in ChimeraX. is it possible to reveal the density in the tomogram and trace the objects throughout the tomogram (also docking model in the density) in ChimeraX? > Best wishes, > Shen > _________ > Dr. Shen Han > Postdoctoral Researcher > Max Planck Institute for Multidisciplinary Sciences > Department of Molecular Biology / Cramer Lab > Am Faßberg 11, Göttingen > 37077, Germany

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Re: [chimerax-users] [Chimera-users] Creating Bonds between Models
by Elaine Meng 25 Apr '22

25 Apr '22

Hello Draven, You could continue to use Chimera for this, since there is a Join Models section in the Build Structure tool (in menu under Tools... Structure Editing). <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.…> We are at this very moment working on adding this functionality to ChimeraX, so if you get today's daily build, you can form peptide bonds between different models with the command "build join peptide" -- it is not yet available as a graphical interface, however, and the kinks are still being worked out. There is a still a bug if you specify "phi" when the model that is being moved contains more than one chain. If you want to specify "phi" but one of the models has more than one chain, use the "move" option to make the other model move instead. Here is the help for this brand-new command in my personal preview since it is not yet up on the website, although it should appear there tomorrow: <https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/commands/build.html#…> The ability to add other types of bonds (nonpeptide) between models is not available yet. You can combine multiple models into one and then form a bond, but that does not take care of positioning between the models like the joining capability above. Instead you would have to manually move the models into the proper positions first. Both Chimera and ChimeraX have a "combine" command to merge multiple models into one without repositioning. By the way, if you want to ask questions about ChimeraX specifically, there is a separate mailing list chimerax-users(a)cgl.ucsf.edu CC'd here. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 25, 2022, at 12:37 PM, Draven Houser via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello, > I am trying to build a structure in chimeraX that is a combination of several other known structures. To do this I need to be able to create bonds between different models in the software, but this doesn't seem to be possible for the moment. Can anyone suggest a workaround for this? Thanks! > Best regards, > Draven Houser

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Re: [chimerax-users] [Chimera-users] Open Castp file in Chimera X
by Tom Goddard 21 Apr '22

21 Apr '22

Hi Bixia, You will need to download the read_castp.py file from that web page. Then if it is your downloads directory you would use open ~/Downloads/read_castp.py In other words you have to tell it exactly where the file is unless it is in the directory where you downloaded the file. Also you can use the ChimeraX "cd" command to change to a new current directory in ChimeraX. Best to email this question to the ChimeraX mailing list instead of the Chimera mailing list. Tom > On Apr 21, 2022, at 4:42 PM, Zhang, Bixia via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Good afternoon, > I am trying to open .poc file from CASTP server in Chimera X. And I found this chimeraX recipehttps://rbvi.github.io/chimerax-recipes/castp/castp.html <https://rbvi.github.io/chimerax-recipes/castp/castp.html>. However, when I used the command open <help:user/commands/open.html> read_castp.py, it saidNo such file/path: read_castp.py. I am working on a Linux unbuntu box and I don't know if this is making any difference. Could you please help with this issue? > Thank you so much! > Best, > Bixia > > Read CASTP pockets file - ChimeraX Recipes <https://rbvi.github.io/chimerax-recipes/castp/castp.html> > We for the ChimeraX atom specifier from chain identifier, residue number and atom name. For example, the above lines are for atoms /A:45@NH2, /B:27@O, /B:27@CG1 in ChimeraX syntax belonging to pockets 2, 1 and 1. > rbvi.github.io <http://rbvi.github.io/> > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

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Re: [chimerax-users] palettes and color keys
by Martti Tolvanen 21 Apr '22

21 Apr '22

A followup question regarding palettes and color keys: Is there any way to create two color keys for two different properties or for two different models? My motivation to ask this stems from a dimer model I got from AlphaFold multimer. When I use the default alphafold palette, the individual monomers are hard to see, most of the interface being in the dark blue, marking highest confidence. I can apply a different palette to one of the chains, but it would be also nice to show the color keys for both palettes. Martti Tolvanen Lecturer in Bioinformatics U of Turku, Finland -----Original Message----- From: chimerax-users-request(a)cgl.ucsf.edu [mailto:chimerax-users-request@cgl.ucsf.edu] Sent: 12. huhtikuutata 2022 22:00 To: chimerax-users(a)cgl.ucsf.edu Subject: ChimeraX-users Digest, Vol 64, Issue 15 Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users or, via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..."

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ChimeraX command for rmsd color range in angstrom
by Dario Passos 20 Apr '22

20 Apr '22

Dear Chimera community, does anyone know how to add a range of values for the rmsd colors in Chimera X? Something like this (below) in angstrom: => *color byattribute seq_rmsd #1 palette blue:white:red threshold 0:3;6* Thanks, Dario

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Toolshed backend update
by Greg Couch 19 Apr '22

19 Apr '22

FYI, the ChimeraX toolshed will be down this evening (10 p.m PDT, 5 a.m. GMT) to upgrade the back-end. If all goes well, it will be back up within an hour. There should be no user visible changes after the update. However, the back-end change will allow Bundle developers to submit bundles that have commas in the dependencies. -- Greg

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Re: [chimerax-users] Render psuedobonds for RMF models?
by Tom Goddard 19 Apr '22

19 Apr '22

Hi Matthew, Yes. The coarse grain models made from reading RMF files create spheres that are actually atoms, and any atoms can be connected by pseudobonds. I don't know much about RMF in Chimera and ChimeraX. Ben Webb and Conrad Huang worked on that and Conrad retired 2 years ago. It may be that reading RMF creates pseudobonds that are specified in the RMF file. Another way to create pseudobonds is to open a pseudobond file https://www.cgl.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles <https://www.cgl.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles> For that you need to figure out the names of the "atoms" (which may represent coarse grain beads) you want to connect. You can open the RMF and hover the mouse over a sphere and a popup will show its name. Also the ChimeraX distance command can create pseudobonds https://www.cgl.ucsf.edu/chimerax/docs/user/commands/distance.html Tom > On Apr 19, 2022, at 8:41 AM, Hancock, Matthew wrote: > > This Message Is From an External Sender > This message came from outside your organization. > > Hi Tom, > > I am a UCSF graduate student in Andrej Sali's group and have a question about Chimera/ChimeraX functionality. I am curious if it is possible to render psuedobonds for multi-scale structures that are read from RMF files. Similar to how it can be done for pdb structures. > > Best > Matthew

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ChimeraX-users April 2022