- ChimeraX-users - RBVI Mailing Lists

volume zone - unexpected behavior when newMap false
by Alexis Rohou 11 Feb '19

11 Feb '19

Hello, I've been playing with volume zone and having good fun, but... I've noticed that if I set newMap to false, then the invert option is ignored (behavior is as though invert is false, even when I specify invert true). When newMap is set to true, or not set at all, the invert option has the effect I expected from reading the documentation. Am I missing something? Hopefully description above is unambiguous but let me know if you need step-by-step. Cheers, Alexis

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Can ChimeraX add noise (Brownian-like motion) in morphing?
by Steve Chou 11 Feb '19

11 Feb '19

Dear ChimeraX support, When morphing from one structure to another unaligned structure, ChimeraX follows a smoothly curved path? Can it add noise (Brownian-like motion) to the path? All the best, Steve -- Steve Chou

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equivalent to "move cofr"
by Alexis Rohou 08 Feb '19

08 Feb '19

Hello, Switching to ChimeraX, I find myself looking for an equivalent to "move cofr <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html#cofr>". Is there one? The use case is: I'm working on a particular part of a map & structure, I open a structure of a homologuous domain from the PDB, but its coordinates are way off, and I want to move it to the region I'm working on without having to zoom out and drag it. My apologies if this is in the documentation somewhere, I'm still finding my way around. Cheers, Alexis

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Output motion prickle magnitude
by Scott, Brandon L. 08 Feb '19

08 Feb '19

Using the measure motion command I am able to generate the prickles on the surfaces correctly, which is great for visualization. Is it possible to write the magnitude of those prickles, and the index to a file so we can do further analysis on the distributions? Cheers, -Brandon ____________________ Brandon Scott, PhD SDSMT, Nanoscience

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How to align two molecules using a subset of atoms in ChimeraX?
by Steve Chou 08 Feb '19

08 Feb '19

Dear ChimeraX support team, I tried the following command first - it worked well. ================== match #1/A to #2/A ================== Then I tried to align the two molecules using parts of them - it didn't work and complained that "No chains in reference structure PROT.pdb #2 compatible with BLOSUM-62 similarity matrix." ================== matchmaker #1/A:10-20@CA to #2/B:10-20@CA ================== System Info: ================== Platform: Linux-3.10.0-862.el7.x86_64-x86_64-with-redhat-7.5-Maipo ChimeraX version: 0.9 (2019-02-05) ================== Thank a bunch! Steven -- Steve Chou

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How to re-define the secondary structure info in ChimeraX?
by Steve Chou 08 Feb '19

08 Feb '19

Dear ChimeraX developers and users, In Chimera, I can use the following commands to redefine the secondary structure info. ============================ setattr r isHelix false : setattr r isSheet false : setattr r isSheet true :8-12,16-21 setattr r isHelix true :55-61,78-92 ============================ What's the ChimeraX equivalent? By the way, I can also delete the hydrogen atoms using "delete element.H" in Chimera. Is there an equivalent in ChimeraX? Many thanks in advance! Steve -- Steve Chou

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Bio-Formats with ChimeraX?
by Matthew Akamatsu 07 Feb '19

07 Feb '19

Hi, I just started using ChimeraX to render and save 3D time lapse microscopy data as a high-performance replacement of Fiji. I am wondering how flexible ChimeraX can be in opening different TIF-derived file formats - particularly hyperstacks (multi color, multi Z, multi time). Other desired formats would be proprietary formats like .nd2 and .sld . Bio-Formats does all of this in an open-source manner - how feasible would it be to have bio-formats type functionality in ChimeraX? Thanks, Matt

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VR in ChimeraX and Dell Visor
by Lewandowski, Jozef 24 Jan '19

24 Jan '19

Hi, Has anyone tested Dell Visor for VR in ChimeraX? If yes are there any issues you have run into? I am assuming that the experience should be similar to what Tom has described for Samsung Odyssey but I would appreciate if anyone had specific feedback on this particular piece of hardware. Thanks, Józef

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color by conservation
by George Ghanim 16 Jan '19

16 Jan '19

Hello, Is it possible to color amino acids by conservation from an alignment file? Thanks, George Ghanim —— PhD Student Rio Lab Molecular and Cellular Biology, University of California Berkeley

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ChimeraX crashes from time to time on Lenovo Y530
by Yehuda Halfon 02 Jan '19

02 Jan '19

Hi All, I bought a new laptop, Lenovo Y530 which has GTX 1050Ti as well as the intel 8750H which has UHD 630 and 16 GB of ram with windows 10. Chimerax is installed on m.2 drive. Sometimes, without any correlation it freezes and crashes, when I restart the error in the picture. All the drivers are updated. I run chimerax with the GTX as the GPU. I think it's something with the dual GPUs, is there a fix for it? I tried both 0.7 and the new 0.8 (not daily). On my other laptop, an old Macbook pro it run perfectly. Thanks, Yehuda Halfon

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Movie recording error
by Carlos Escalante 21 Dec '18

21 Dec '18

Dar all, Trying to make a morphing movie. Everytime I run it, it comes out with the following error: Unknown command: coordset #3 1,21 And there is no sign that is recording. The same error occurred when I created the morphing, but it did created the morphing. Also, if I try to change anything and run the command again, it says ‘already recording a movie’ Any suggestions? Thank you Carlos R. Escalante Assistant Professor Department of Physiology and Biophysics VCU School of Medicine 1220 East Broad Street MMRB 2040 Richmond VA 23298 carlos.escalante(a)vcuhealth.org 804-628-1202

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version 0.7
by jingdong cheng 21 Dec '18

21 Dec '18

Hello, Could you provide me the older version 0.7? I tried the new 0.8, it is good, fixed a lot of bugs, but it runs super slow slow. It is better to change back to 0.7, but on your website I can’t find it anymore. Cheers! Merry Christmas! Jingdong

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FW: hi
by Williams, Joanne 21 Dec '18

21 Dec '18

From: mosbah amine <aminemosbah(a)hotmail.com> Date: Thursday, December 20, 2018 at 11:24 AM To: "chimerax(a)cgl.ucsf.edu" <chimerax(a)cgl.ucsf.edu> Subject: hi dear colleague trying to download chimiraX , no way to get to the right page !!! would you please send me the zip file , i agrre to licesing requarements also i have a windows10 for compatibility regards Dr mosbah amine TN

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scale bar in chimerax
by Xu Jingwei 13 Dec '18

13 Dec '18

Hi, I recently installed the ChimeraX in my centos 7 and it is really powerful software to make beautiful figures. I really like it! However, one question before I setup for figures is how could I make a scale bar in ChimeraX? I did not find the relative information in the web. Could you please help me about that? I am really appreciated for that. Best, Jingwei ETH Zürich Dr. Jingwei Xu Postdoc Institute of Molecular Biology & Biophysics Department of Biology HPK D17 Otto-Stern-Weg 5 8093 Zürich, Switzerland

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Dual GPU VR support
by Lewandowski, Jozef 11 Dec '18

11 Dec '18

Hi, A quick question. Does implementation of VR in ChimeraX support dual GPU? Or dual GPU would give no advantage? Thanks, Józef

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transparentBackground doesn't seems to work on save
by Yehuda Halfon 09 Dec '18

09 Dec '18

Hi all, We are trying to save an image without a background using save image filename format png transparentBackground true but we get the error: transparentBackground expected key word. What are we doing wrong? Thanks, Yehuda Halfon

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Incrementing value in perframe
by Scott, Brandon L. 09 Nov '18

09 Nov '18

I am attempting to use the measure convexity on each frame, and seem to have a mismatch between the frame number which goes from [0 - (N-1)] and the volume child which goes from [1 - N]. Is there a way to augment the $1 value to be $1+1? Attached are the command calls. This displays the convexity properly on the called frame: vseries play #1 jumpTo 1; measure convexity #1.2 smoothingIterations 12 palette cyan-gray-maroon range -1,1; The does not display it because of the mismatch: movie record; perframe "vseries play #1 jumpTo $1; measure convexity #1.$1 smoothingIterations 12 palette cyan-gray-maroon range -1,1;" range 1,200; wait 200; movie encode C:\Users\LLSM\Desktop\Convexity.mp4 quality highest framerate 25 Thanks in advance. -Brandon ____________________ Brandon Scott, PhD SDSMT, Nanoscience

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Render images in nogui mode
by Lukas Pravda 07 Nov '18

07 Nov '18

Hi all, I was wondering if there is a way how to generate images from linux terminal. I’ve come across a couple of very old posts in the mailing list stating that this was not possible at that time. So, I wonder if anything has changed. If I use cif files only, chimerax gives “Unable to render images to save them” message. If I try to include volumetric data from cryo-EM overlaid on the structure I get an exception during opening a *.map file. Please see the script below. The exception is in the attachment Best, Lukas open emd_8909.map volume #1 color white transparency 0.7 level 0.1 step 1 zoom 1.2 open 6ds5.cif set bgColor white hide selAtoms show selAtoms ribbons color bychain ribbons light full light shadow true save image default.png width 1600 height 1600 supersample 5 transparentBackground true turn y 90 save image y.png width 1600 height 1600 supersample 5 transparentBackground true turn z 90 save image z.png width 1600 height 1600 supersample 5 transparentBackground true

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chimeraX questions on representation
by Dr. Eddie 16 Oct '18

16 Oct '18

Hi, I have a few small n00b questions that would really help me along. 1) How do I change the "ball scale" property in chimeraX using a command for the sphere representation? 2) When I do "select protein" (which is represented as a cartoon) it highlights it but clicking on any of the buttons to change the representation does nothing. I need to click first on the show atoms and then I can click on those but many of the H are not connected (for LYS I have two white dots floating above the carbon with no bond to them, but a bond to other C's and it is only for one CH3 group, the other is fine). This is true in all three representations. How do I fix this? 3) Can I increase the resolution in VR? 4) After clocking on the label tool with a VIVE controller and using it, how to I change it back to the original mode so I can scale the model (using both triggers)? Thank you very much for your help! Eddie

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Re: [chimerax-users] chimeraX questions on representation
by Eric Pettersen 16 Oct '18

16 Oct '18

Hi Eddie, ChimeraX (and Chimera for that matter) connect atoms in standard residues using a connectivity template. Therefore the atoms have to have standard names. Some hydrogens in your file don’t have their PDB-standard names, and therefore wind up unconnected. I have committed a fix for this — if there are unconnected hydrogens after the template pass then Chimera(X) does an additional connect-by-distance pass. A second problem with the file is that it uses ATOM records for everything, including solvent, ions, and the lipid bilayer. ATOM records are for polymeric residues and imply connectivity between consecutive residues with the same chain ID. Therefore the non polymeric components of the file should have been using HETATM records. I have attached an edited version of your file with appropriate HETATM records. It should work much better in tomorrow’s fixed build. —Eric > On Oct 16, 2018, at 11:31 AM, Dr. Eddie <eackad(a)gmail.com> wrote: > > Thanks for the help! As for the pdb, I've attached it. It shows fine in vmd and pymol. > Thanks, > Eddie > > On Tue, Oct 16, 2018 at 1:19 PM Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >> On Oct 15, 2018, at 8:35 PM, Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >> >> I don’t know why your H’s are disconnected specifically, but it’s almost surely some issue with the input file. > > If you provided the input file, we might be able to offer advice on how to get ChimeraX to handle it better. One thing you might try sight unseen is to remove the LINK/CONECT records in the file (assuming it’s a PDB file). > > —Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > > > > > -- > Eddie > <popc.3a4.ionf.pdb>

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Question about measuring the distance of helix axis
by ze li 16 Oct '18

16 Oct '18

Dear ChimeraX supporting team: I try to measure the distance between two helix axises, but in the "distance" command there is only atom-to-atom usage in Chimera X. Is there any command and plugin for this function, such as in Chimera? Thank you. Best,

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symmetric function from different template in chimera x
by Alexei Hernandez 09 Oct '18

09 Oct '18

Good morning, I am currently utilizing chimera x for different modeling features. Right now I am trying to use the symmetric option for a file created by a peer of mine titled ppar.pdb. I added the file here and trying to use the sym function by using the template of a close protein blast result, one called 3DZU, also added it. I want to use the template of the 3dzu to create a structure for ppar. I am confused as to which command line to use out of all of them and if it is possible to use 3dzu as a template for the ppar file created. Could you please help me with the command line. Have a nice day... Alexei Hernandez

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Re: [chimerax-users] [Chimera-users] FW: Contributing to ChimeraX ?
by Tom Goddard 01 Oct '18

01 Oct '18

Hi Nicholas, The ChimeraX OBJ reader is all in Python with source code included in the distribution. Windows chimerax/bin/lib/site-packages/chimerax/wavefront_obj Linux chimerax/lib/python3.6/site-packages/chimerax/wavefront_obj Mac ChimeraX.app/Contents/lib/python3.6/site-packages/chimerax/wavefront_obj The ChimeraX git repository is here https://www.rbvi.ucsf.edu/trac/ChimeraX/browser <https://www.rbvi.ucsf.edu/trac/ChimeraX/browser> I don’t think the repository can be cloned due to access restrictions, but here is some info about that and you can try and see if it works. https://www.cgl.ucsf.edu/chimerax/docs/devel/conventions.html Tom > On Oct 1, 2018, at 7:52 AM, Williams, Joanne wrote: > > > > From: Nicholas Yue > Date: Sunday, September 30, 2018 at 3:40 AM > To: "chimerax(a)cgl.ucsf.edu <mailto:chimerax@cgl.ucsf.edu>" <chimerax(a)cgl.ucsf.edu <mailto:chimerax@cgl.ucsf.edu>> > Subject: Contributing to ChimeraX ? > > Hi, > > I took ChimeraX for a spin and when I save out to OBJ, the geometries looks connected up wrongly. > > I was hoping I can take a look at the source code to attempt to fix it myself. > > I see git being mentioned in the documentation. Is there a git repo I can clone and contribute to? > > If I need to sign any documents before contributing, let me know :-) > > I have other geometry format I'd like to write out to and also I am hoping to write out quads rather than triangles for use with OpenSubdiv in rendering software like RenderMan, Arnold, Mantra etc. > > Cheers > -- > Nicholas Yue > Graphics - Arnold, Alembic, RenderMan, OpenGL, HDF5 > Custom Dev - C++ porting, OSX, Linux, Windows > http://au.linkedin.com/in/nicholasyue <http://au.linkedin.com/in/nicholasyue> > https://vimeo.com/channels/naiadtools <https://vimeo.com/channels/naiadtools>_______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

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Re: [chimerax-users] [Chimera-users] chimerax mesh commands doesn't work
by Elaine Meng 20 Sep '18

20 Sep '18

Hi Yehuda, I don’t think you are doing anything wrong; in ChimeraX, the lineThickness option doesn’t work for me either, although it works fine in Chimera on the same computer — we will look into it. Sorry for the inconvenience and thanks for reporting, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. there is a chimerax-users(a)cgl.ucsf.edu mailing list too <http://rbvi.ucsf.edu/chimerax/docs/contact.html> > On Sep 20, 2018, at 4:56 AM, Yehuda Halfon <yehuda.halfon(a)weizmann.ac.il> wrote: > > Hi all, > I wanted to use chimeraX to use some commands on mesh display. > Some works like meshLightning but others like lineThickness doesn't > I use volume #1 lineThickness 10 (or any other integer) but nothing seems to change. What am I doing wrong? > Yehuda Halfon

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Ca trace
by v.kalienkova＠bioc.uzh.ch 19 Sep '18

19 Sep '18

Dear all, I was wondering, is there an option to just show a Ca trace in ChimeraX? If yes, can one modify the width of it? Thanks a lot in advance, Valeria

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