August 2021 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] How to adjust chimeraX's loop display style?
by Elaine Meng 17 Aug '21

17 Aug '21

Hi Xiangan, Sorry no, there is no way to smooth the loops (coil) parts of a ribbon or cartoon. Currently only strands can be smoothed. By "smoothed" I mean that the path of the ribbon may not follow the CA atoms exactly, which can cause problems when the sidechains are displayed. In Chimera when the sidechains were displayed with ribbon, you could get unrealistically long or short CA-CB bonds. So in ChimeraX we decided it was more important to have an accurate CA-CB bond length when sidechains are displayed. In the helix and coil (loop) there is no smoothing option so the ribbon is exactly on the CA positions. Strands have a smoothing option turned on by default, because people expect them to be drawn as mostly straight, and if strands are not smoothed, they are very ripply. In ChimeraX when the strands are smoothed but sidechains are shown, the CA atoms that fall off the ribbon are shown with a connecting "tether" instead of stretching or shrinking the CA-CB bond artificially. This is discussed in the "cartoon" help, see the "smooth" for how to adjust strand smoothing and "cartoon tether": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#tether> I investigated whether I could make a smoother representation with the "shape tube" command, but was unsuccessful. Sorry for the inconvenience -- I'm hoping that explaining the reasons might make it less annoying. :-) Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 17, 2021, at 1:12 PM, Liu, Xiangan <Xiangan.Liu(a)uth.tmc.edu> wrote: > > Hi, > ChimeraX's default loop style shows very cursive. I like the way loop shows in chimera. > Is there any way to make chimeraX's loop display straighter? > Thanks, > Xiangan > > <image.png>

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Chimerax for Ubuntu 21.04
by jobiph 17 Aug '21

17 Aug '21

Dear all, thank you for your fast and thorough answers. I reinstalled lifbffi7 and libllvm6.0 and now Chimerax works. Thanks a lot! Kind regards Jonas

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Re: [chimerax-users] Chimerax for Ubuntu 21.04
by Gabriel Goetten 16 Aug '21

16 Aug '21

Hi, I was able to run chimeraX on ubuntu 21.04 by installing the following package https://answers.launchpad.net/ubuntu/hirsute/amd64/libllvm10/1:10.0.1-6 Then you just need to download chimerax of the following version Ubuntu 20.04 (Linux) 64-bit from their website (deb package). Gabriel

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Chimerax for Ubuntu 21.04
by jobiph 16 Aug '21

16 Aug '21

Dear all, is the current version of Chimera for Ubuntu (20.04) compatible with the 21.04 Ubuntu release? If i try to install the 20.04 version a weird dependency error pops up and I can't install the missing library because on the canonical website it states that this library is deprecated. Thank you for your help and kind regards Jonas

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All-numeric residue names
by Tristan Croll 16 Aug '21

16 Aug '21

Was just looking at 2rg6, which happens to have a ligand with an all-numeric 3-character ID (287)... clearly not much thinking went into allowing that. Anyway, does the residue selection syntax have a way to disambiguate residue *number* 287 from residue *name* 287?

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Coulombic color combined surface
by W. C. 13 Aug '21

13 Aug '21

ChimeraX has no way to color ONE continous surface formed by combining multiple chains with coulombic or hydrophobic. It always color each chain surface separatly . Even though I generated a surface of combined chains by "surface enclose" command, ChimeraX still colors each chian seperately. In Chimera (not ChimearX), I could use surfcat to combine chains, generate one surface for combind chains, and color the surface as one continous. However, that could color large set of molecules. So please make ChimeraX can do the same.

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(no subject)
by Haaris Ahsan Safdari 12 Aug '21

12 Aug '21

Rrg together with the university international realty of

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Morphing with ligands
by Volodymyr Dvornyk 10 Aug '21

10 Aug '21

Dear Colleagues, Tried to do morphing of the following structures: 6rdc, 6rep, and 6rd9. All three have the same ligands: ADP, ATP, Mg, and Zn. However, the resulting model lacks all of them. Any thoughts and/or suggestions? Thank you. Volodymyr ________________________________ DISCLAIMER: This electronic mail transmission contains confidential information intended only for the person(s) named. Any use, distribution, copying or disclosure by any other person is strictly prohibited. If you received this transmission in error, please notify the sender by reply e-mail and then destroy the message. Opinions, conclusions, and other information in this message that do not relate to the official business of Alfaisal University shall understand to be neither given nor endorsed by Alfaisal University. The contents of any attachment to this e-mail may contain software viruses, which could damage your own computer system. While "Alfaisal University" has taken every reasonable precaution to minimize this risk, we cannot accept liability for any damage which you sustain as a result of software viruses. You should carry out your own virus checks before opening the attachment.

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Trying to open .py files on Windows gives cPickle error
by Carnes, Jason 09 Aug '21

09 Aug '21

Hello, I am collaborating with someone using ChimeraX on a Mac. Their only option to save modified files results in a .py file extension. When I try to open .py files on my Windows install of ChimeraX I get an error: "ModuleNotFoundError: No module named 'cPickle'" Is there a way to manually install cPickle on my Windows computer that will allow me to open the .py files, or are Mac & PC not compatible? Thanks, Jason Jason Carnes, PhD Research Scientist IV | Center for Global Infectious Disease Research Seattle Children's Research Institute 206-884-3137 OFFICE CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Difficulties Visualizing Isosurfaces from Cube File - Nathan Wood
by Nathan Wood 09 Aug '21

09 Aug '21

Dear ChimeraX I was having difficulty attempting to visualize computationally generated electrostatic potential isosurfaces originating from a Gaussian *.cube file. I tried to open the cube file from the shell only for it to incompletely visualize. I can provide an image if necessary. I found the following correspondence concerning cube files and isosurfaces, but unfortunately I am unable to resolve the issues of the cube file visualizing. https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-April/002126.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-April/002126.html> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001110.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001110.html> I was curious if anyone has had experience with cubefiles. Any assistance would be greatly appreciated, Very Respectfully, Nathan Wood

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