December 2019 - ChimeraX-users - RBVI Mailing Lists

Double and Triple Bond Stick Style
by Smith, Chase 05 Feb '25

05 Feb '25

Dear ChimeraX, I was just wondering why there is no way to represent a double or triple bond in either the ligands or the protein amino acids when viewing as a Stick or Ball-and-Stick representation? I sometimes use Chimera or ChimeraX to make visuals for my lectures, and the students often have difficulty in understanding due to the absence of the multiple bonds. I would love to have the ability to represent the double or triple bonds with multiple lines between the atoms. Thank you, Chase Smith ... ChaseSmith, PhD Chair, Department of Pharmaceutical Sciences & Associate Professor of Medicinal Chemistry School of Pharmacy MCPHS University 19 Foster Street | WorcesterMA01608 T 508.373.5717F 508.890.5618C 978.855.7203 chase.smith(a)mcphs.edu www.mcphs.edu MCPHS University Confidentiality Note: This e-mail, and any attachment to it, is intended to be confidential and might be legally privileged. It is intended solely for the use of the addressee. If you are not the intended recipient, you are hereby notified that reading, copying, disseminating or distributing this email is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.

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Re: [chimerax-users] [Chimera-users] color by zone in chimeraX
by Elaine Meng 20 Nov '20

20 Nov '20

Hi Pranav, I’m Cc'ing the chimerax-users(a)cgl.ucsf.edu list (recommended for ChimeraX questions). I believe the problem is that when coloring the chains you are using “target c” which means to color only cartoons, whereas coloring by zone uses the atom colors. Since you only colored the cartoons, the atoms probably still had heteroatom color-coding. If you use “target ac” instead (even if the atoms aren’t shown), then as long as the color zone distance is big enough, I think you will get the color zones you expect. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 20, 2019, at 10:54 AM, Pranav Shah <p.shah.lab(a)gmail.com> wrote: > > Hi Elaine and Co., > > I am trying to color a virus map with the relevant pdb file, the > series of commands I am running are as follows, > open virus.mrc > open virus.pdb > color /A plum target c > color /B lightgreen target c > color /C dodger blue target c > color zone #1 near #2 dist 3 > However, the resultant surface is rendered in splotches of red and > blue, which leads me to think the it is coloring the surface using > atom type. Could you tell me how I can get Chimera X to color the > surface using the colors of the chains only? FYI, color by zone works > flawlessly in chimera. > > Cheers, > Pranav

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Map "Blobs" tool - Generate objects?
by Christophe Leterrier 11 May '20

11 May '20

Hi, I started using ChimeraX for visualization and quantification of 3D microscopy images. The "blob" tool is particularly impressive to semi-automatically segment objects of interest and measure their characteristics. However, I could not find a way to generate an independent object from the picked blobs. This makes the quantification process unreproducible as it is not possible to store the blobs in the session or automatically measure all the picked blobs. Am I wrong in the intent of the tool, or is there a way to do this? Thank you, -- Christophe Leterrier NeuroCyto lab INP CNRS UMR 7051 Aix Marseille University, France

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volume onesmask usage question
by Alexis Rohou 30 Mar '20

30 Mar '20

Hi there, I was trying to use "volume onesmask" to go quickly from a dusted surface of a low-pass-filtered volume to a mask volume with the same dimensions, spacing, etc. as the input map. I thought "fullmap" might be a way to achieve this (the doc says "The remaining options are the same as described for volume mask"), but I don't think that option actually works with "volume onesmask": volume onesmask #3 fullmap true *Expected a keyword* Is there a "onesmask"-like operation or set of options that creates an output volume that's on the same grid as the input volume? Thanks, Alexis

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differentiating file category
by Anthony James Schaefer 02 Jan '20

02 Jan '20

Hello, Is there any way I can get a bundle to know that I'm trying to open a file from a certain category (e.g. Molecular structure vs. Molecular trajectory) from the File -> Open... menu? I'm trying to build a plugin that will allow me to open Gaussian log files in ChimeraX. I'd like to have it open the optimized structure when I go File -> Open... and change the file filter to "Molecular structure files". When I set the file filter to "Molecular trajectory files", I'd like it to open the log file as a trajectory with each frame being one of Gaussian's optimization steps. The file stays the same, I just want to have my 'open_file' method know that it should open the file differently. So far, I've tried having multiple 'Open' entries in my bundle tags. Here are some relevant tags from my setup.py: "ChimeraX :: DataFormat :: LOG :: Gaussian output file :: Molecular structure :: .log :: :: :: :: :: Gaussian output file :: utf-8", "ChimeraX :: DataFormat :: LOG trajectory :: Gaussian output trajectory :: Molecular trajectory :: .log :: :: :: :: :: Gaussian output file :: utf-8", "ChimeraX :: Open :: LOG :: Gaussian output file ::", "ChimeraX :: Open :: LOG trajectory :: Gaussian output trajectory :: :: coordsets:Bool", My 'open_file' definition line is: def open_file(session, path, format_name, coordsets=False): While I'm testing, I've set up my 'open_file' method to print the arguments that get passed to it. When I use File -> Open..., I can see that 'format_name' is always "Gaussian ouput file" (never "Gaussian output trajectory") and 'coordsets' is always False, regardless of the file filter. When I use the `open` command (`open asdf.log coordsets true`), 'coordsets' is True and 'format_name' is "Gaussian output file". I can work with the open command because of the 'coordsets' argument, but I'd like to know if there's something I can do with the File -> Open... menu. Thanks, Tony

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Superimposition of Carbohydrate Molecules
by Rajarshi Roy 18 Dec '19

18 Dec '19

Dear ChimeraX, I am trying to superimpose multiple carbohydrate chains using chimeraX. Using match command, I am unable to do the same. Here is my command: *match #2:1-4 to #1:1-4* But I am getting the following error: Reference and/or match model contains no nucleic or amino acid chains. Use the command-line 'match' command to superimpose small molecules/ligands. Already I am using match command, still why the same error is showing? Please advise me on how to proceed? Thank you in advance. -- *with regards* *Rajarshi Roy* *PhD Research Scholar* *Biosciences and Biomedical Engineering* *Indian Institute of Technology, Indore* *India*

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Amber trajectories
by Lewandowski, Jozef 16 Dec '19

16 Dec '19

Hi, Quick question. Are there any plans for ChimeraX to support opening also Amber trajectories (as Chimera does)? Thanks, Józef ------------------------------------------------------------------------------------------------------ Józef R. Lewandowski Professor | Department of Chemistry | University of Warwick<http://www2.warwick.ac.uk/> j.r.lewandowski(a)warwick.ac.uk<mailto:j.r.lewandowski@warwick.ac.uk> | External: +44 (0) 24 76151355 | Internal: 51355 Millburn House: F07 | Coventry CV4 7AL | Find us on the interactive map<http://www2.warwick.ac.uk/about/visiting/maps/interactive/> Lewandowski group website<https://www2.warwick.ac.uk/fac/sci/chemistry/research/lewandowski/lewandows…> | Warwick solid-state NMR group website<http://www2.warwick.ac.uk/fac/sci/physics/research/condensedmatt/nmr/>

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Re: [chimerax-users] [Chimera-users] view MD ChimeraX
by Elaine Meng 16 Dec '19

16 Dec '19

Hi Fabian! The “Molecular Dynamics Viewer" tool is available on ChimeraX Toolshed from outside developers, i.e. it is not written by our group. However, the description on Toolshed pretty much says what it does: it is a simple graphical interface for showing multiframe PDB files as a trajectory. It doesn’t read other trajectory formats. <https://cxtoolshed.rbvi.ucsf.edu/apps/moleculardynamicsviewer> After you install it, it will be under Tools… General in the menu. Starting the tool from that menu will open a window in ChimeraX and then clicking the Open button in that tool will allow you to browse to and open a multiframe PDB file, like 1PLX.pdb downloaded from the RCSB PDB (NMR structure, so it has multiple conformations each as a MODEL in the single PDB file). Then you can use the other buttons, e.g. Start to play as a a trajectory. (I wasn’t sure what you meant by “not able to use it.”) However, *without* this tool: Just using ChimeraX without installing anything extra, you can read in a few trajectory formats and then play them with the “coordset” command or using a slider interface shown with “coordset slider". The trajectory formats known to ChimeraX are listed here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory> <http://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html> See also “coordset” and “coordset slider” <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html#slider> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. There is also a chimerax-users(a)cgl.ucsf.edu mailing list, CC’d here. > On Dec 15, 2019, at 1:50 AM, Fabian Glaser <fglaser(a)technion.ac.il> wrote: > > Hi, > I installed Molecular Dynamics Viewer in ChimeraX but I am not able to use it, . I use it successfully in Chimera (no X). But in ChimeraX. > Can you please help me? > Best, > Fabian

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SSL expiry
by James Walshe 13 Dec '19

13 Dec '19

Hi Guys, Hope you’re well. I’m trying to download some ChimeraX plugins. It appears the toolshed security certificate has expired. https://cxtoolshed.rbvi.ucsf.edu/ Just letting you know if you were unaware. Kind regards, James ______________________________________________________________________ The Victor Chang Cardiac Research Institute's Email is scanned by the MessageLabs Email Security System.

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multiple conformations in one pdb chain
by Linda Schulte 12 Dec '19

12 Dec '19

Hi everyone, I have two conformation in a single PDB chain, see example below: ATOM 90444 N APHE z 9 253.604 183.844 259.994 0.50 47.28 N ATOM 90455 N BPHE z 9 253.778 183.499 258.715 0.50 47.28 N Chimera can read in this two conformations of the chain, while chimerax shows only the A atoms of the chain. How can I read in also the B atoms? Thanks a lot for your help. Best, Linda -- Linda Schulte Goethe-Universität Frankfurt am Main Institut für Organische Chemie und Chemische Biologie, AK Schwalbe Max-von-Laue-Straße 7 D-60438 Frankfurt am Main N160/300 +49 (0)69 / 798-29956 schulte(a)nmr.uni-frankfurt.de

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