October 2023 - ChimeraX-users - RBVI Mailing Lists

Distinct clipping planes per model
by Dorien Pastoors 24 Oct '23

24 Oct '23

Hi, Thanks for maintaining such a nice software package! I'm still learning, and I'm currently stuck on clipping. I'm trying to clip models differently in ChimeraX. My aim is to have a global clipping plane to visualize two drugs binding to two domains (in the image in yellow/blue). Now I would like to offset the clipping plane slightly for surrounding protein (in beige). I would like to do this to increase the depth in my image and to emphasize that these domains are embedded in a bigger protein. As it is in fact a huge protein (its an alphafold predicted structure) making the entire protein transparent will still obscure the view on the compounds in their domains. As you can see, by using clip model I've been able to turn off clipping for the drugs in their binding pockets. However, with clip model I can only switch on or off the entire clipping plane , not offset it for a particular model. I've tried: clip model #2.3 front -10 clip model #2.3 offset -10 With clip model I can't specify an offset as it gives an error, I can only turn clipping off completely with "clip model #2.3 false", while "clip front -10" affects the total clipping plane, and I cannot specify a particular model for this clipping plane. (the beige protein model is #2.3) Hope this is clear enough and you have a solution! Thanks in advance! Kind regards, Dorien Pastoors

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Image rendering artifacts with silhouettes and pixelSize value
by Vorländer,Matthias Kopano 24 Oct '23

24 Oct '23

Dear ChimeraX team, I am having issues when using silhouettes and saving an image while specifying the pixel size, as I get the artefacts shown in the attached image. If I don’t use silhouettes or don’t specify the pixel size things look fine. I updated to the latest daily version and uninstalled Isolde and ArtiaX, but the problem persist. I work on a MacBook Pro under Mac OS Ventura 13.5.2. Any ideas for fixes? Many thanks, Matthias [A white structure with colorful strands Description automatically generated with medium confidence]

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Difference maps in chimerax?
by Francisco Murphy Pérez 23 Oct '23

23 Oct '23

When I open a map* in chimerax, how do I specify it is a difference density map? * maps are generated with `phenix.mtz2map finalpdb.pdb finalmtz.mtz` ... both files from the pdb-redo. Thanks

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Morphing problem
by Raphael Bader 23 Oct '23

23 Oct '23

Dear all, I would like to ask for some information/help for a problem I am facing at the moment: I am currently working on a pentameric protein (C5 symmetric) that undergoes a big conformational change (translational & rotational movement) and would like to utilize the morph function in ChimeraX to come up with a good animation for it. For one single protomer the animation works fine – however, for the full pentamer the subunits follow both directions, clockwise and counterclockwise, during their rotational movement which obviously leads to a lot of clashes and therefore does not look very convincing. Since I tried almost all options listed as parameters for the morph (linear & corkscrew method, cartesian true and false, rates, coreFraction, etc.) and it did not affect the direction of rotation at all, I was wondering whether there are additional values I could modify or any other trick that might equalize the movement? Thank you very much in advance! Best regards, Raphael P.S.: I would be happy to provide data if it might help solving the problem.

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Selection with coordinates
by Siyoung Kim 23 Oct '23

23 Oct '23

Hello, Would there be a selection keyword that selects atoms based on their coordinates? For instance, is there a way that I can select atoms whose x coordinates are below 0 (e.g., x < 0)? Thank you. Best, Siyoung

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Re: [Chimera-users] How to obtain transformation matrix between protein structures
by Elaine Meng 22 Oct '23

22 Oct '23

Hi Qiancheng Xia, Please use the chimerax-users(a)cgl.ucsf.edu address (CC'd here) for ChimeraX questions so that people don't get mixed up between Chimera and ChimeraX. Chimera does not have the reportMatrix option. As for ChimeraX, you didn't show the exact command that you tried so I can only guess what went wrong. My guess is that you need to include "reportMatrix true" not just "reportMatrix" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 20, 2023, at 4:39 AM, 夏前程 via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > I want to use chimera to obtain the transformation matrix between two protein structures. I know that matchmaker can superimpose them together, but I still want to obtain the transformation matrix. I've noticed that matchmaker in chimerax (https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html) offer a keyword "reportMatrix" to do that. But when I use that keyword in chimerax, "Expected a keyword" will be returned without match or a matrix. > With Regards, > > Qiancheng Xia > > National Institute of Biological Sciences > > Beijing, China > > 2023/10/20 >

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Export Isolde residue paramters (xml) for phenix
by Sean Connell 21 Oct '23

21 Oct '23

Hello, Sorry If this has been asked recently and I missed it, but is there a way to convert the residues parameter XML file created by Isolde (for a ligand) into a restraints file that can be used in the phenix realspace refinement? Sean

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Re: Movie Record/Encode with GPU?
by Tom Goddard 20 Oct '23

20 Oct '23

No. The only way to show multiple frames of a trajectory in ChimeraX is to open them as separate models. Tom > On Oct 18, 2023, at 9:37 AM, Alexander Hung Lee <Alexander.Lee(a)uga.edu> wrote: > > Oh, and I forgot to ask… Is there an option in command line to show all the hbonds in a trajectory concurrently, even if the bond shows up at a different point in time but not current frame? >

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Surface calculation in ChimeraX
by Dennis Dannecker 20 Oct '23

20 Oct '23

Hello Chimera/ChimeraX team I recently asked already a question regarding the saving/exporting of vertices generated during the surface calculation in ChimeraX and the associated parameters with this surface generation. On a related note, I wanted to ask whether it is possible to also extract the surface (SESA and/or SASA) on a per atom basis. MSMS calculates not only the vertices for each atom (usually several vertices per atom) but it also calculates the SESA and SASA on a per atom basis. Now, I was wondering whether something is possible in ChimeraX too. As I was parsing through the docs, I was wondering whether ChimeraX calculates the surface no longer using MSMS. The vertices density supported by ChimeraX is considerably higher than what I can get with my standalone MSMS program (at least factor 6). So, if ChimeraX does not longer employ MSMS, what else does it use? With "MEASURE CONVEXITY" I get the surface vertex positions, normals, convexity values, and triangles. Unfortunately, the association with the corresponding residue is lost (however, can be regained with a little bit of work I guess, simply using euclidean distance). Question: Is there something similar for the SESA or SASA of the different atoms in the model/chain. In theory, this information should be available, at least the SESA. I am just wondering whether there is a way to write this out as a raw txt file in ChimeraX The closest I found in the save command is the .obj or .vtk format. However, both are semi-satisfying in that that they both do not provide the data looked for and are in somewhat special formats, at least the vtk. The .obj file is much much bigger than what MSMS or "measure convexity" generates, and not really handy for then working with the data in other programs, mainly python. As always, I very much appreciate any help and wish to thank the team for their contributions to the field. Best regards Dennis

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ChimeraX Help
by Bani Kaur 20 Oct '23

20 Oct '23

Hi, I hope you are well! My name is Bani Kaur and I am a ChimeraX user. I wanted to ask you about how I can specify labels on ChimeraX, specifically with finding the names of the residues on a protein. Additionally, how does info residues work and info resattr. I would appreciate any help and guidance! Thanks! Best, Bani Kaur

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