- ChimeraX-users - RBVI Mailing Lists

coloring clipped surface only separately
by Y. Mutum 02 Dec '21

02 Dec '21

Hi Elaine and Team My question relates on how we can color the 'clipped surface only' using a different color independently. This is without messing up the color of the outer surface of the model. Suppose the outer surface of the pdb-model has been colored by hydrophobicity (mlp). Then, I slice the model using the 'side view' tool. Now, using the 'surface cap' command, I can get a clipping plane which is colored 'bychain'. However, if I try to color the clipped surface using a different color, the entire hydrophobicity surface is no longer there. These are my commands below. Is there a way to color the clipped surface by a different color? If not is there a way around? The commands I have used are: >>> open 6g2j; hide all; >>> color #1 green; color /B-G,I,Q,P,R,W,q yellow; Then using the side view tool, clip the surface of the model to get a slice. I am trying to clip in the plane containing Chain D and B. >>> mlp #1; >>> surface cap true; Then, I can get a clipping plane colored by-chain. If I then type >>>color zone #1 near #1 distance 5 Then, I can get the clipped surface to change its color but this messes up the hydrophobicity of the outer surface. Thus, 1. Is there a way to color the clipped surface separately, while not messing up with the outer surface coloring (hydrophobity in this case)? 2. Suppose I want to remember this clipping plane for another ChimeraX session and would like to avoid the manual clipping using the 'Side view'. Using command line, is there a way to get back to the clipping plane? Similar to 'camera matrix' command, but, with the 'sectioned plane' also included. Thanks Yaikhomba

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measuring rotation between two homologous PDB models
by Y. Mutum 28 Nov '21

28 Nov '21

Hi Elaine and ChimeraX Team My query relates to measuring rotation between two subunits from homologous models in ChimeraX. Here, I have first aligned the two models on one of sub-domains of these multi-domain complex. Then, without moving the models, the plan is to calculate the rotation in another domain, between the 2 models, apart from measuring the translational shift. So, * Align Chain /L,M (model #1, PDB:6g2j ) and Chains /5,4 (model #2, PDB:6rfr). * Calculate rotation of Chain /F (model #1, PDB:6g2j) and Chain /B (model #2, PDB:6rfr). I am using the following commands: -- open 6g2j; open 6rfr; -- match #1/L,N to #2/5,4 pair ss; -- measure rotation #1/F toModel #2/B coordinateSystem #1/F showAxis true showSlabs true; The log report is: Position of 6g2j #1 relative to 6rfr #2 in 6g2j #1 coordinate system: Matrix rotation and translation 0.80441124 0.40360431 -0.43591986 67.76279700 0.18783349 0.52334489 0.83116106 -121.82969657 0.56359661 -0.75047565 0.34517410 202.31442783 Axis -0.83978100 -0.53070022 -0.11456502 Axis point 0.00000000 87.13355460 206.39866592 Rotation angle (degrees) 70.33834463 Shift along axis -15.42901832 Thus, ChimeraX is calculating a rotation of ¬70 degrees, which is clearly the case. The visual inspection suggests, that the rotation should be no more than ~15-20 degrees. I am not sure where I am going wrong. Could you please help? Thanks Yaikhomba

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Exporting Measure and Color Blob data
by BINGHAM Dominic 25 Nov '21

25 Nov '21

Hello, I am wanting to get the volumetric data of several blobs in a manner I can easily export and analyse. I am using the Measure and Color Blobs tool and I can see the data I need. However, I have lots of models, with lots of blobs. That means me stopping and writing down the volume data each time I click is not very efficient. So is there anyway I can export all the volume data per each selected blobs per each image into one file? Thanks, Dominic Bingham

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Match the scale of OBJ and volume
by Roden Deng Luo 24 Nov '21

24 Nov '21

Hi, As shown in the screenshot, I have opened one volume and one obj. But they should have the same scale. How can I achieve this? Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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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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