July 2022 - ChimeraX-users - RBVI Mailing Lists

a question about CMM files
by Pranav Shah 15 Jul '22

15 Jul '22

Hi Team, How are XYZ coords represented in ChimeraX? I have a volume of 794x794x272 sampled @15Å/px. When I place markers in the volume and save the resultant marker file, the coords for the points are as follows- <marker_set name="markers"> <marker id="1" x="6950.3" y="6659.4" z="2010" r="1" g="1" b="0" radius="15"/> <marker id="2" x="6977.7" y="6381.5" z="2010" r="1" g="1" b="0" radius="15"/> <marker id="3" x="9747.8" y="3926.7" z="2010" r="1" g="1" b="0" radius="15"/> </marker_set> Such large numbers seem to imply that the dimensions are measured in physical units (Å in this case). Is this correct? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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How to view swiss docking results in ChimeraX
by Fernando Luis Cônsoli 15 Jul '22

15 Jul '22

Hi! I am a very excited biologist that has been eagerly trying to use ChimeraX to generate hypotheses for the work I collaborate in insect resistance to pesticides by analyzing the predicted structure of proteins and their interactions with ligands. I have been able to generate a 3D model of my protein of interest using the *alphafold* tool as available in *ChimeraX*. I then proceeded using the *Swiss Docking* tool to predict the interactions of selected ligands with the 3D protein model. I can see the results in swiss page, but was not able to use the link available to *uscf chimera*, and neither identify why my browser would not launch web chimera when requested. I downloaded all the data produced by Swiss Docking, but I can not open the *clusters.dock4* file generated in my installed version of *ChimeraX* to display the results as it is shown in the video available when selecting the link of the *uscf chimera* in the swiss web page. How can I do that to select for the best ligand-protein interaction predicted? Alternatively, I have uploaded my protein and ligand pdb files in my ChimeraX and calculated clashes and contacts under Structure Analysis in the Tools tab, as explained in some of the videos I have been watching with the Chimera old version. But I am not confident that what I see reflects the prediction data I was able to obtain with the Swiss Docking tool. How can I be sure that the ligand-protein interaction predicted this way is the best choice? Sorry for the long message! Hope someone will bring me some light as I struggle with python command lines! My best! Fernando Consoli

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downloading and saving maps from EMDB
by Nebojsa Bogdanovic 14 Jul '22

14 Jul '22

Hello, I have a text file list of 30-40 maps from emdb that I would like to download and save using chimeraX. Each map should be named for example 5995.mrc, where 5995 is the actual EMDB id. Is there a way to do this using CLI to make it faster than downloading 1 by 1? I am not sure how to instruct chimeraX to take the file name from the open models. open 5995 from emdb #opens the file and assigns #1 save ???.mrc models #1 #save the model 1 but how to instruct chimerax to take the model's name Ideally would be something like this: Input: emdb-ID.txt Output: 40 single .mrc maps named according to their EMDBIDs. open emdb-ID.txt from emdb save all, models #1-40 name=???? Please let me know if I can implement this. Thank you and best regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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Stereo view does not work with chimerax 1.4
by Gong, Zhen 14 Jul '22

14 Jul '22

Hi, Good morning. I would like to generate a stereo view in ChimeraX 1.4 but it did not work. Here is the error message: camera stereoCould not switch graphics mode. Graphics driver did not create OpenGL context. And there is the graphics driver information: graphics driverOpenGL version: 4.1 INTEL-18.7.4 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc Any helpful suggestion is greatly appreciated. Best regards, Zhen

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Issue with loading large trajectory topology and coordinate file
by Shubham Devesh Ramgoolam 12 Jul '22

12 Jul '22

Hi all, I hope you are doing well. I have a PSF file of size 62 MB and a DCD coordinate file of size 423 MB that I am trying to load in chimeraX. However, chimeraX remains unresponsive during the loading process. As such, I tried loading a subset of the coordinate file using start stop step option. However, this did not fix the issue. This is an example of the command I used: open myfile.psf coords file.dcd start 1 stop 10 step 2 Is there an alternative approach I could use? (I don’t know if this is relevant or not but whenever I closed and re-opened chimeraX after it became unresponsive, it did not ask me to send a bug report.) UCSF ChimeraX version: 1.5.dev202206290845 (2022-06-29) OS: Windows 10 Regards, Shubham Ramgoolam Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Copy/pasting
by Dmitry Semchonok 12 Jul '22

12 Jul '22

Dear colleagues, In case I would like to copy/paste the piece of a model - what is the correct way to do that? Thank you Kind regards, Dmitry

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How to complete docking with ChimeraX
by 刘金鑫 11 Jul '22

11 Jul '22

Dears, I want to use ChimeraX to dock. The old version can combine with Vina. But I cann't to find the menu in the ChimeraX. Would it be possible? Best regards Jinxin

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Measuring distance between two atoms in a single protein
by McClean, Phillip 11 Jul '22

11 Jul '22

Hi Chimerax Group, I am trying to measure the distance between two atoms in a protein in Chimerax v1.4. The .pdb file I am working with was generated using Alphafold2 in the ColabFold application. I select the two atoms by using CTRL+SHIFT, go to the TOOL -> Structure Analysis -> Distances. The Structure Measurements panel appears in the lower right of the screen. When I click on the Create button, a Chimerax box appears on screen with the following message: Exactly two atoms must be selected! I was surprised to see this message since I thought I had properly selected two atoms. Any advice on how to calculate the distance would be greatly appreciated. Thanks in advance for any help you can provide. Phil McClean Professor North Dakota State University

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Unable to run the option region all
by Edoardo D Imprima 11 Jul '22

11 Jul '22

Dear all, I saved two sessions with different data to make a movie using the same command lines. However, I am not able to obtain the same result when I use the command volume region. In one instance Chimerax renders the whole 3D volumes I selected with “volume #x-y region all". In a second session, with different data but virtually the same commands, the rendering halts at the step before (~disp #1). I am puzzled because in both instances the logs show the command “volume #x-y region all” as executed. And, in the “faulty session" if I manually input the same command that I passed through the script it eventually shows the complete regions of the volumes. Could you please help me to understand what am I doing wrong? I am using ChimeraX 1.4 on Linux. I am pasting here the piece of the scripts that work and do not respectively, Many thanks in advance, Edoardo Working fly p2 p1 100; wait; volume #2 show style surface level 0.8 color #5555ff; volume #3 show style surface level 0.8 color #aa557f; volume #4 show style surface level 0.8 color #f514fd; volume #5 show style surface level 0.8 color #11ffcc; volume #6 show style surface level 0.8 color #ff9429; volume #2-6 transparency 0.8; wait 20; volume all planes z,1344,60; wait 1284; ~disp #1; volume #2-6 region all; Faulty fly p1 p2 100; wait; volume #2 show style surface level 0.8 color #5555ff; volume #3 show style surface level 0.8 color #aa557f; volume #4 show style surface level 0.8 color #f514fd; volume #5 show style surface level 0.8 color #11ffcc; volume #2-5 transparency 0.5; wait 20; volume all planes z,1604,1594; wait 10; ~disp #1; volume #2-5 region all; ------------------------------------------------------ Dr. Edoardo D'Imprima Postdoctoral fellow Structural and Computational Biology Unit EMBL Heidelberg - Mahamid Group Meyerhofstraße 1 69117 Heidelberg Germany Phone: +49 6221 387-8531

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color zone with markers
by HUI WANG 08 Jul '22

08 Jul '22

Dear Developers, I have a need to color a huge ring-like structure with markers, I used to know that we could color the density by the markers as well as the links between them, so It's not necessary to have too many markers. However, I cannot figure out how to color the density covered by the links now. I am using ChimeraX 1.3. Any comments or suggestions will be appreciated! Thanks! Best regards, Hui

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ChimeraX-users July 2022