January 2022 - ChimeraX-users - RBVI Mailing Lists

artistic cartoon visualisations
by Enrico Martinez 26 Jan '22

26 Jan '22

Dear ChimeraX users! I am working on the improvement of the cartoon visualizations. Here are some options that I have found very cool: preset 'overall look' publication cartoon style coil thickness 0.22 set silhouettes t; set silhouetteColor firebrick; set silhouetteDepthJump 0.02 could you please suggest me something, which may further develop these ideas? In particularly I would like to improve representations of the beta-sheets making the arrow-ends more elongated and cylindrical Many thanks in advance Enrico

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Debian 10 Installation
by Martin Urban 25 Jan '22

25 Jan '22

Dear ChimeraX users, I have a problem with the installation of ChimeraX under Debian 10 buster. I downloaded the ucsf-chimerax_1.3ubuntu18.04_amd64.deb from the official website. I installed it one time with: /sudo dpkg -i //ucsf-chimerax_1.3ubuntu18.04_amd64.deb /and also with /sudo apt-get install .///ucsf-chimerax_1.3ubuntu18.04_amd64.deb./ Both times I get the same error message: qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in " " even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. The full error message is as attachment in this mail. I searched the web for an answer and came up with three entries of this mailing list. I followed the described way in these mails, but nothing worked for me (1st mail: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002797.html; 2nd mail: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002770.html; 3rd mail: https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-June/002339.html) Do you have an answer or a solution to my problem? Greetings from Germany -- Martin

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Ribbon Thicken
by Cameron Larson 25 Jan '22

25 Jan '22

Hello, Is there a way to thicken ribbons so I can 3d print a structure? What do you recommend for 3d printing a structure? -Cameron Larson

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Re: [chimerax-users] rename a ligand from UNK 999
by Rangarajan, Amith 25 Jan '22

25 Jan '22

Dear ChimeraX users, When i add a pdb file to chimera , the resulting model displays the ligand as UNK 999 and when i am having multiple models , it will help to be able to edit the UNK to name the ligand. is there a way to do it ? thanks , amith

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Displaying secondary structure elements
by Enrico Martinez 25 Jan '22

25 Jan '22

Dear ChimeraX users! Could you suggest to me the command which will 1) hide all loops from the selected object? 2) hide all loop regions which contain more than 10 residues (=hide long loops)? Thank you in advance! Enrico

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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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ChimeraX-users January 2022