- ChimeraX-users - RBVI Mailing Lists

Multichain comparative modelling
by Prof. Dr. Kay-Eberhard Gottschalk 06 Apr '23

06 Apr '23

Hi There, I am interested in a complex formed by a protein with two domains connected by a long loop in complex with a second Protein, that binds this loop, causing it to form a short helix. I have two pdb stuctures: One with the two domains in the correct relative domain orientation, connected by an unstructured loop, and one with the part of the loop forming a helix in complex with a second Protein. I am sure that comparative modelling can do the trick, but somehow I dont understand the workflow. Do I need do load both templates into chimeraX, oben sequence file conatining both Proteins and load that also, if so in which format? I went over the Manual, but somehow it is not clear to me. Thanks a lot for your help! Best, Kay

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About displaying electron density maps (MTZ format) in chimerax
by Laurent 05 Apr '23

05 Apr '23

Hi, I am currently trying to display an electron density map (from a MTZ file) in ChimeraX, but it seems that the display box size is limited. I would like to display the maps around ligands in an oligomeric protein, where the ligands are quite far from each other. Is there any way to increase the box size of the displayed map so that it covers all ligands ? Thanks ! Laurent Laurent Maveyraud Professor of Biophysics | University of Toulouse | Structural Biophysics Team Doctoral School Biology - Health - Biotechnologies +33 5 61 17 54 35 | +33 6 46 04 21 11 | Laurent.Maveyraud(a)ipbs.fr <mailto:Laurent.maveyraud@ipbs.fr> | L. Maveyraud <https://fr.linkedin.com/in/laurent-maveyraud-8b394a5> | L. Maveyraud <https://orcid.org/0000-0003-4610-8319> UMR5089 | CNRS - UT3 | 205 Route de Narbonne BP 64182 - 31077 Toulouse Cedex 4 ipbs.fr <https://www.ipbs.fr/>| Team Website <https://www.ipbs.fr/structural-biophysics>| pict.ipbs.fr <https://cribligand.ipbs.fr/> @IpbsToulouse <https://twitter.com/IpbsToulouse> ipbs.cnrs <https://www.facebook.com/IPBS.CNRS/>

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Virtual Crash Course - Understanding PDBx/mmCIF | May 3rd | REGISTER NOW!
by Brian Hudson 04 Apr '23

04 Apr '23

Virtual Crash Course The RCSB Protein Data Bank will provide a course, "Use PDB data to their full extent: Understanding PDBx/mmCIF" on Wednesday, May 3rd 2023 from 1:00-3:00 EDT. Understand the basics of PDBx/mmCIF data dictionary and file format that underpin archiving of more than 200,000 experimentally determined three-dimensional biostructures in the PDB. Learn about software tools for generating and working with PDBx/mmCIF files, and programmatic access for harvesting PDB data. The program: https://iqb.rutgers.edu/sites/iqb.rutgers.edu/files/crashcourses/mmCIF-cras… Free registration: https://go.rutgers.edu/u3vpwjet If you have questions, please contact Michelle Sanghera: msanghera(a)iqb.rutgers.edu

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AlphaFold best_model.pdb could not visually overlap the input sequence using matchmaker
by Cheng Fei Phung 30 Mar '23

30 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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