January 2022 - ChimeraX-users - RBVI Mailing Lists

Help viewer is blank after upgrading to Fedora 35
by Nicholas R Silvaggi 27 Jan '22

27 Jan '22

Hello, I am just getting started with ChimeraX. I installed the latest production release (Centos 8 version, ucsf-chimerax-1.3-1.el8.x86_64) on my Fedora 33 workstation. It worked great. I installed Isolde and Clipper through the help viewer winder and everything was great. Yesterday I upgraded the operating system to Fedora 35, and now the help viewer no longer works. It is just blank. I can't get it to show other web sites, files from my hard drive - nothing. I installed ChimeraX on 3 other workstations, and all have the same problem. This is very curious and there is no error output that I can find to help point me to the problem. Has anyone else experienced this? Thanks for your help, Nick Silvaggi P.S. I also tried uninstalling the production release and installing the Centos 8 version of the latest nightly build - same problem persists. Nicholas R Silvaggi, Ph.D. University of Wisconsin, Milwaukee Department of Chemistry and Biochemistry 3210 North Cramer St Milwaukee, WI 53211 Office: Chemistry 372D Phone: 414-229-2647 silvaggi(a)uwm.edu

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Modeller python script
by Mary Liu 27 Jan '22

27 Jan '22

Dear Chimera X team, I'm using Modeller in ChimeraX to build a homology model. Is there a way to look at the python script to know how it works? Thanks Mary

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3Dconnexion
by Wang, Difei (NIH/NCI) [C] 26 Jan '22

26 Jan '22

Hello ChimeraX team, Thanks for developing the ChimeraX! It is easier to use than Chimera. However, I noticed that my 3Dconnexion could not work anymore when I use ChimeraX. Will it be possible to include such a function in the future version of ChimeraX? Thanks, Difei ======================== Difei Wang, Ph.D. Bioinformatician (Contractor) BB/DCEG/NCI/NIH 9609 Shady Grove Rd. Rockville MD 20850 USA Tel: 1-240-276-5092 ========================

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Surface coloring
by Enrico Martinez 26 Jan '22

26 Jan '22

Dear ChimeraX users! I am working on the protein-ligand binding visualizations using surface representation for the protein. In this case (please see enclosed example) I used mlp palette moccasin:sienna:sandybrown range -55,55 to make this expression of the protein in the Mountain style :-) Two questions: 1) how can I introduce more "dark" gradients into the cavities (similar to the vulcan) ? 2) is it possible to switch the coloring pattern from such a "realistic" view to the animated "cartoon" style ? 3) Any additional advice for the surface visualisations ? Many thanks in advance! Enrico

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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 26 Jan '22

26 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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