April 2020 - ChimeraX-users - RBVI Mailing Lists

Surface dust command in the .cxc script
by 李泽 24 Feb '25

24 Feb '25

Hi all: I'm trying to use the .cxc script to run the software, I found that the "surface dust" command has never been executed in it. Have anyone met the same problem? Any suggestions. Thank you all. Best, Ze

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Get color code of a custom color
by Ahmad Khalifa 11 Feb '25

11 Feb '25

I created a custom color that I want to use in a different session. is there a way to do that besides trying to match colors by eye? Regards.

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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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Scroll threshold step size
by Daniel Asarnow 04 May '20

04 May '20

Hi, Is it possible to adjust the step size when using alt + scrollwheel to change the contour level? I'd like to make it coarser for RSI reasons. Thanks, -da

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ubuntu 20.04
by Hua tiger 03 May '20

03 May '20

Please create a download and install package for ubuntu 20.04 Thank you very much. John

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Missing segments
by Daniel Asarnow 01 May '20

01 May '20

Hi all, When I save a CIF from ChimeraX, the missing segment pseudobonds are replaced by real (super unphysical) bonds. Can I do something about it, or is this a bug? Thanks and best, -da

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morph movie with secondary structure and dssp
by Joel Meyerson 30 Apr '20

30 Apr '20

Hi, I am making a morph between two PDB models representing two states of the same protein, and the overall secondary structure does not change much between the models. However, there is a region where the secondary structure does change. I would like to capture the secondary structure change in the morph and have a couple questions. 1. It seems the morph uses the secondary structure from PDB #1. Is there a way to use the two different secondary structure headers from the two PDBs to define the secondary structure endpoints on the morph? 2. If the above is not possible, is there a way to restrict DSSP to update only the region of interest (i.e. a residue range), and not change secondary structure throughout the molecule? Thanks, Joel

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addh and phenix
by Daniel Asarnow 24 Apr '20

24 Apr '20

Hi, Seems like with NAG glycans the addh result is incompatible with phenix real space refinement. It's easy enough to fix by deleting HD2 - the offending hydrogen - manually. I was wondering if anyone had an opinion about this, before I report a phenix bug. Error looks like: Number of atoms with unknown nonbonded energy type symbols: 5 "ATOM 2629 HD2 ASN A 362 .*. H " (4 more similar lines). Best, -da

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