December 2022 - ChimeraX-users - RBVI Mailing Lists

ISOLDE and secondary structure restraints
by Guido Hansen 17 Nov '23

17 Nov '23

Hi all, I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess: Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script? Cheers, Guido -- PD Dr. Guido Hansen Group Leader UNIVERSITÄT ZU LÜBECK INSTITUT FÜR BIOCHEMIE Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen(a)biochem.uni-luebeck.de www.biochem.uni-luebeck.de [1] Ratzeburger Allee 160 23562 Lübeck Links: ------ [1] http://www.biochem.uni-luebeck.de

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select displayed atoms via command line / transfer saved views
by Helge Paternoga 18 Jan '23

18 Jan '23

Dear ChimeraX users, I have to unrelated questions: 1) Is there a way to select displayed atoms via the command line? 2) Is it possible to transfer saved views from one session to another one? Many regards and thank you for reading, Helge

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Extracting the color name/hex code of a colored ribbon
by Theodora Bruun 23 Dec '22

23 Dec '22

Hello, I am just curious if there is a command for listing the current color name or hex code of an atom/ribbon that is colored in ChimeraX. For example, I open a previously colored structure and like the color of chain A and now I would like to use that same color and maybe apply to other chains in the structure. Is there a way other than just eye-balling it? Best, Theo

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using atomic coordinates to measure volume
by Harrison, Daniel P 23 Dec '22

23 Dec '22

Hello: I would like to calculate the maximum volume made by selection of atoms in a given structure. Can you provide guidance on how to go about this process? It seems like there should be a simple procedure in ChimeraX but I have failed to locate it. My specific problem: I would like to calculate the volume of the void created by ice under various conditions so that my physical chemistry students can quantify and visually understand partial molal volume non-ideality. I would greatly appreciate any assistance you can provide. Dan

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PDB upload TER card error
by HONG ZHAN 21 Dec '22

21 Dec '22

Dear all, I saved my protein coordinates in ChimeraX as pdb (it has multiple chains), however, when I was doing upload on the PDB, it shows this error, I am using ChimeraX 1.5rc202211091945 on Linux ubuntu 22.04 LTS. Coordinates issues: ERROR: There is no TER card at the end of polymer chain 'X'. All polymer chains should have a TER card at the end of each chain. Please add TER card and restart again. Many thanks! Hong

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phosphorylation
by Fabian Glaser 21 Dec '22

21 Dec '22

Dear experts, I would like to mutate a ser and a thr to phospo-serine and phospho-threonine, what is the easiest way to do it? Thanks a lot, fabian -------------------------- Fabian Glaser, PhD Structural and Computational Biology Unit The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel

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ChimeraX linux binary problems
by Добромир Калчевски 19 Dec '22

19 Dec '22

Hello, I have installed Chimera linux from binary and everything was OK from the get-go. ChimeraX however, fails to start for library dependencies. As I understand the source depends on around 50 packages. I don't know (and I can find no indication on internet) how many libraries am I missing, but I'm also kind of limited in terms of disk space / linux size and my distro does not have a very nice package manager - Clear Linux (it installs entire bundles of similar packages, instead of single packages and once removed the disk size does not go down). Is it possible to make a ChimeraX linux binary which is as easy to run as the Chimera linux binary - universal for all distributions and including all necessary dependencies ? Best Regards, Dobromir

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ChimeraX linux binaries too inconvenient
by Добромир Калчевски 19 Dec '22

19 Dec '22

Hello, Can you provide ChimeraX linux binary as useful as the Chimera linux binary ? - without all of the dependencies being outside of the package. Also, can the package simply install in the /home/username/.local/CHIMERAX... directory, just as Chimera or in a similar path ? (makes uninstallation easy, saves disk space). Many distros do not have package managers as convenient as those of Red Hat or Debian. For example I use Clear Linux (for the performance) and the dependencies are not even in the package manager. There is also no explicit list of dependencies and according to your web site there are about 50 of them, anyway. Basically whatever I do there is always a missing library I cannot easily find / compile / have no time for it, etc., so ChimeraX for me is out of reach. I tried Chimera from the linux binary and it ran just fine, but it lacks something in the GUI, which ChimeraX does not. The visualization settings fields can be scrolled up and down, so if I load let's say 12 molecular orbitals - I can easily hide / show the ones I need, instead of having them all on the screen and using the "Data set list" to manually show / hide each one. Best Regards, Dobromir

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Re: [chimerax-users] color
by Elaine Meng 19 Dec '22

19 Dec '22

Hi Guan, To ensure you get an aswer, we recommend sending ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here). You can click the square "color well" for each model listed in the Model Panel to open your system color browser, which will show the code. See also this page for the names of the initial model colors... <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html> ...and then this page which shows the codes for the names <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html#builtin> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 18, 2022, at 5:46 PM, Guan, Lan <Lan.Guan(a)ttuhsc.edu> wrote: > > Dear Elaine: > I like the color usage in chimeraX. I wonder if we could know the color code for the color auto-painted when we open it. > Thanks, > Lan

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Aligning atoms
by Noriega, Heather 18 Dec '22

18 Dec '22

Hello, I have a question about the alignment. Is there a way to get the glycans to align, one has a PEG docked to it and I was hoping to place the PEG and delete the glycan #2. I am unsure if it is possible. It gives me an error because the number of atoms are not equal. I attached the session. Thanks in advance. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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ChimeraX-users December 2022