January 2022 - ChimeraX-users - RBVI Mailing Lists

Surface representation of protein-ligand interactions
by Enrico Martinez 25 Jan '22

25 Jan '22

Dear ChimeraX users! I am working on the surface representation of the protein-ligand contacts. Here is my script: # load pdb of the complex and keep inly the 1st model open pdb.pdb close #1.2-end #calculate electrostatic surface coulombic protein key true #change view of the ligand size ligand atomRadius +.8 color #1.1 & ligand & C gold style ligand sphere #protein-ligand contacts hbonds #1.1 & ligand reveal true log true contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display height 0.8 color orange ~label ligand hide #1 & protein bonds hide #1 & protein pseudobonds Here are my questions: 1) is it possible to set transparency on the part of the displayed surface that overlaps (hide) with the part of the displayed ligand? i've tried: transparency 20 surface, but it change the transparency for whole surface 2) how I may improve further sphere representation of the ligand? it looks very nice but probably there are further modifications ? 3) is it possible to customize the following commands to display amino-acids that within specified distance within the ligand (I would like to display only very closer amino-acids): contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display height 0.8 color orange Many thanks in advance! Cheers Enrico

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Color atoms by RMSD
by Nebojsa Bogdanovic 21 Jan '22

21 Jan '22

Hello, I am looking to color the atoms (cartoon representation) by RMSD values obtained from the matching of the two structures. Is there such a function? I would like to show which part of the target domain is moving the most in comparison to the previously x-ray solved structure of a know ligand state without showing the actual structures overlaid. Thank You very much. Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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Assessment of labeling data using ChimeraX
by Alessio Di Ianni 20 Jan '22

20 Jan '22

Respectable ChimeraX developers, how can I visualize labeling data obtained by Mass Spec Studio into a pdb structure using ChimeraX? A help will be definitely appreciated. Best regards Alessio Di Ianni PhD Student Department of Pharmaceutical Chemistry and Bioanalytics Center for Structural Mass Spectrometry Institute of Pharmacy Martin Luther University Halle-Wittenberg Kurt-Mothes-Str. 3, Entance C D-06120 Halle/Saale Tel: +49 (0)345 55 25224

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selecting and translating / rotating 1 of the models/maps
by Dmitry Semchonok 20 Jan '22

20 Jan '22

Dear colleagues, Quick question. In chimeraX, with multiple models, how can I select and rotate/translate only one/ or two of them? In chimera it was possible to make the selection in the model panel. Kind regards, Dmitry

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view and the center of mass of the selection
by Enrico Martinez 20 Jan '22

20 Jan '22

Dear ChimeraX users! I am using view command to center the camera on the ligand an then, to rotate th whole system to the desired position: view #1.1 & ligand orient clip false; turn z 90; turn y 45; turn x -90; turn x 77 may I rather center the camera on the center of mass of the ligand calculated using measure center ligand If so, how may I combine the both commands together? Thank you in advance! Enrico

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Feature requests
by Ishwar Radhakrishnan 19 Jan '22

19 Jan '22

Hello - I would like to request two features in ChimeraX that we use a lot in Chimera: 1. Render by Attribute 2. Ability to read .poc files created by CASTp Thanks, Ishwar

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service unavailable for toolshed
by Bharti Singal 18 Jan '22

18 Jan '22

Hi , I am trying to install isolde and clipper tools on chimerax 1.3 but the toolshed is giving error for last 24 hours "service unavailable". Is it possible to get the download link of these two tools as I need them for some urgent work? Best regards, Bharti Singal Bharti Singal, Ph.D. Postdoctoral Scholar (Al-Bassam's Lab) Department of Molecular and Cellular Biology| College of Biological Sciences| University of California, Davis| 605 Hutchison Dr, Davis, CA 95616, USA

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labeling of protein-ligand interactions
by Enrico Martinez 18 Jan '22

18 Jan '22

Dear ChimeraX users! I am working on the visualization of the protein-ligand interactions. The two below commands are used to visualize and label amino acids involved in the interactions with the ligand contacts #1.1 & ligand makePseudobonds false reveal true log true label @@display How could I increase the font size and change the colour of the displayed amino acid labels (like Tyr-188)? Is it possible to hide the name of the ligand which always appears after the label command? Many thanks in advance! Enrico

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Alphafold multimer
by Rafael Ponce 17 Jan '22

17 Jan '22

Dear Sir or Madam, I want to predict the structure of a complex in ChimeraX using alphafold, but it seems that this feature is going to be in version 1.4 but version 1.3 is the one that is currently available, so I would like to know if you have an estimation of when the version 1.4 will be available to download. Thank you in advance for the information. Best regards, Rafael Ponce

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zoom on the selection after orientation of the selected object
by Enrico Martinez 17 Jan '22

17 Jan '22

Dear Chimera users! I am using ChimeraX for the visualization of protein-ligand interactions comparing two different pdb structures A - ensemble for doclong; B- X-ray pose: open A.pdb open B.pdb' match #2 to #1.1 # close all docking poses with the exemption of the first pose: close #1.2-end view wait # hide the protein from X-ray pose keeping only ligand for visualisation: hide #2 & protein cartoon hide #2 & protein surface hide #2 & protein #orient view on the model 1.1 and zoom closer view #1.1 orient; turn z 90 zoom 1.5 wait The problem is that when I use zoom 1.5 after view #1.1 it hides completely the representation for the molecule on the current GUI. Otherwise, it works fine if I center view on the both A and B: view orient; turn z 90 zoom 1.5 How could I zoom the screen properly after orientation of the view on the first molecule? Many thanks in advance! Enrico

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