November 2021 - ChimeraX-users - RBVI Mailing Lists

Color volume series by per voxel variance?
by Oliver Clarke 24 Nov '21

24 Nov '21

Hi all, Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame? When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way. Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume. Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible? Cheers Oli

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ChimeraX import multiple positions of the same .pdb structure
by Frey, Lukas 23 Nov '21

23 Nov '21

Dear Elaine, I have an external file with a transformation matrix (orientation and translation) for a .pdb structure and I would like to apply the transformation in ChimeraX to a .pdb file. I’m aware that ChimeraX needs a matrix like [[1,1,1],[2,2,2],[3,3,3],[x,y,z]], where the first 3 columns are the orientation the last column the x,y,z translation positions. One can load a new orientation/translation into chimeraX with the „open“ command: https://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html in the command line of chimeraX I had to type in: open path-to-file/test.positions models #1 childModels true matchNames true my test.positions file is a .txt file containing the name of the .pdb structure and transformation matrix and I already loaded the .pdb structure before I applied the transformation matrix. Below you can find the input of the transformation matrix file, called text.positions: 6y2l.pdb,-0.6515591636522021,-0.6041757901381976,-0.45873987277293393,0.09148867345316551,-0.662890582358989,0.7431055769199559,-0.7530607405054541,0.44220774578318395,0.48718767500700594,30.0,20.0,30.0 If I apply the open command in chimera somehow it leads to a distortion of the .pdb protein structure. If I check the transformation position of the model with „view matrix“, then I have the following output: view matrix camera position: 0.94464,-0.25925,-0.20113,-578.87,-0.29451,-0.94014,-0.17144,1242.4,-0.14464,0.22118,-0.96445,-8143.8 model positions: #1,-0.65156,-0.60418,-0.45874,0.091489,-0.66289,0.74311,-0.75306,0.44221,0.48719,30,20,30,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0 Somehow the transformation matrix is only applied to #1 but not to #1.1 and #1.2, do you have an idea what I have to change? If I save the transformation matrix of the distorted .pdb structure via the save command: save path-to-file/test_2.positions models #1 childModels true I have the following output: 6y2l.pdb,-0.651559163652,-0.604175790138,-0.458739872773,0.0914886734532,-0.662890582359,0.74310557692,-0.753060740505,0.442207745783,0.487187675007,30,20,30 metal coordination bonds,1,0,0,0,0,1,0,0,0,0,1,0 missing structure,1,0,0,0,0,1,0,0,0,0,1,0 The goal in the future is to load several positions (1 … 100) of the same .pdb structures. Best, Lukas Lukas Frey Visiting Postdoctoral Associate UMASS Medical School Worcester Grigorieff Laboratory

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Re: [chimerax-users] meshmol in chimeraX
by Tom Goddard 23 Nov '21

23 Nov '21

Hi Vijay, The meshmol command from Chimera which converts a surface mesh from wire edges to cylinder edges (making a fake molecule) is not yet in ChimeraX. But I can add it pretty easily, maybe tomorrow if time permits. Tom Icosahedral cage shown with wires and with meshmol cylinders > On Nov 18, 2021, at 2:38 PM, Vijay Reddy <reddyv(a)scripps.edu> wrote: > > Hi Tom, > > Greetings! Hope are staying safe and healthy. > > I am finally transitioning to chimeraX. > > Could you please tell me what is the equivalent of > > the chimera command “meshmol #26 6” in chimeraX > > Many thanks, > Vijay >

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Toolshed
by Moustafa, Ibrahim M. 23 Nov '21

23 Nov '21

Dear ChimeraX, Trying to install iSolde but toolshed page seems to be down! Is there another link to https://cxtoolshed.rbvi.ucsf.edu ? ChimeraX Toolshed<https://cxtoolshed.rbvi.ucsf.edu/> Resource for Biocomputing, Visualization amd Informatics (RBVI), and its precursor, the Computer Graphics Laboratory (CGL), develops cutting-edge interactive software tools and advanced web-based computational resources that provide integrated visualizations and analyses of molecular structures and related non-structural biological information. cxtoolshed.rbvi.ucsf.edu Thanks, Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. Millennium Science Complex University Park State College, PA16802 Phone: (814) 863 5940 Fax: (814) 865 7927

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Question about Chimerax
by JANE LEE 22 Nov '21

22 Nov '21

Hi, I was wondering how/if I could open saved session files from Chimera in Chimerax? Also, when I tried to open a protein in Chimera, it opened. But when I tried to open the same protein in Chimerax, it only showed up as atoms and I received the message "start residue of secondary structure not found." I was wondering if you have any suggestions for troubleshooting? Thank you! Regards, Jane

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ChimeraX AlphaFold2
by Ichcharisma 20 Nov '21

20 Nov '21

Hi ChimeraX Dev I wondering if I can run oligomer prediction on ChimeraX AlphaFold features. As we can do it with others colabfold version out there. Thank you

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Feature request: windowsize to be stored with session
by mailman-bounces＠cgl.ucsf.edu 18 Nov '21

18 Nov '21

From: Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> Date: November 18, 2021 at 8:47:33 AM PST Dear all, I would like to suggest that the current windowsize is associated with a ChimeraX session. This is particularly useful when making figures in a reproducible manner (if I am not mistaken, when opening a .cxs file it will open it with the same windowsize that has been used for the last chimera session, rather than the one that was used when the session was created). I am aware that the windowsize can be specified in a script file. Thanks a lot for your consideration : ) Best, Matthias

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Re: [chimerax-users] [Chimera-users] chimera, H-bonds
by Elaine Meng 18 Nov '21

18 Nov '21

> On Nov 18, 2021, at 11:37 AM, Rio Aquarius via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Developer, > I have a specific task for ChimeraX. I want to show H-bonds and hide all amino acid residues. But when I hide amino acid residues, all H-bonds I need disappear. Is there a way to do what I want? Dear Rio, The H-bond displays are lines (pseudobonds) drawn between atoms. When you hide those atoms, the H-bonds are also hidden. I don't understand why you would want to display a bunch of lines in space without any atoms, as you won't be able to see most of the valuable information from the calculation. However, I will explain how to do it: In ChimeraX, there is no pseudobond option to display even when its atoms are hidden. The only way to make it look like the H-bond lines are shown when you can't see the atoms (and/or ribbons) is to make the atoms (and/or ribbons) 100% transparent with the "transparency" command. Example commands: open 2gbp hbonds reveal true transparency 100 target ar <https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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getting sequences into the Structure Prediction
by Marc Pusey 17 Nov '21

17 Nov '21

Hi - I may be missing something very obvious, but... I am trying to input and use protein sequences for structure predictions using the AlphaFold feature of ChimeraX. I've not had any problems when the sequence can be obtained from a UniProt file, but several of the proteins I'm working with do not have such a file available. Additionally, there is going to come a time where I will want to see what the consequences are from making mutations to those sequences that are available from UniProt. The input gives the option of either Paste or UniProt, but I've not found a way to do a simple cut and paste to put in the sequence. I'm using a Mac running Mojave, version 10.14.6. Thanks! Marc Pusey -- Marc Pusey

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Viewing all frames of trajectory at once
by German Barcenas 17 Nov '21

17 Nov '21

Hello, I've made a trajectory of some similar frames that are stored as an .xtc file. I can upload this with my defined topology file (.pdb) and see each frame individually. Currently I can create a picture of each frame with the frame centered on some residue (SQA) with: perframe "save ~\snapshot_$1.png" frames 10;coordset #1 holdSteady /A:SQA This creates individual pictures for each frame which is nice. I was wondering how one makes a picture with all 10 frames superimposed on each other. I'd also like to change all but the 1st frame to be transparent. I'm aware of the transparent command, which I presume I'd apply to all frames except the 1st, but I'm not sure how to display all frames at once. I'm also struggling on the 1st frame only condition. This is my current attempt: perframe "transparency 0 ALL" frames 1;perframe "transparency 25 ALL" frames 9;coordset #1 holdSteady /A:SQA Thanks, -- German Barcenas Ph.D Candidate | Materials Science and Engineering Materials Modeling and Theory Group Boise State University

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