- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] error with open :: 'foreach' has no suffix
by Rangarajan, Amith 08 Feb '22

08 Feb '22

Hi, I am trying to run a script and want to use foreach ( open script.cxc foreach *.pdb) to iterate through several pdb files in the working directory. I had no issues with running it earlier, but since last few tries, i am getting an error stating that ""'foreach' has no suffix"" I am not able to figure out how to debug this. I am using the latest build of chimerax. I will highly appreciate your suggestions on fixing this. best amith

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Extract densities option not available on Segment Map
by Andre LB Ambrosio 08 Feb '22

08 Feb '22

Dear all, probably a silly question: I want to generate a mask o ChimeraX to use later on a local refinement job elsewhere. I managed to segment the cryoEM map and group the regions of interest. However, the "Extract densities" option is unavailable on the "Regions" menu. Likewise, these are unavailable on "Other tools" shortcuts options: Extract, iSeg, ProMod, and ModelZ. Please, what am I missing? I appreciate any help you can provide. -- Andre LB Ambrosio Associate Professor, IFSC/USP - Brazil www.ifsc.usp.br/alba

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extraction of certain cryo-em density
by Dmitry A. Semchonok 08 Feb '22

08 Feb '22

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Next/previous buttons?
by Oliver Clarke 07 Feb '22

07 Feb '22

Hi, The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over? Cheers Oli PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc?

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keeping multi-chain models locked between chains
by Martti Tolvanen 07 Feb '22

07 Feb '22

Dear ChimeraX gurus and demi-gods, I have created a hypothetical multimer model for a protein which has a dimeric structure in PDB (with a large protein-protein interface, considered real), but misses the C-terminal part of the full protein sequence. AlphaFold predicts there to be an amphipathic helix in the missing part, as we also did in our theoretical work. The hypothesis is that the protein could form larger multimers by binding either via the face-face interactions, as in the PDB dimer of catalytic domains, or via helix-helix interactions (tail-tail) as in coiled coils, to create multimers of type AB-BA-AB-BA-AB-BA etc., A being the helical domain and B the catalytic domain. I have created antiparallel coiled-coil-like helix dimers from the helix predicted by AlphaFold with the help of zdock (big thanks for adding the zdock file open functionality in the daily build!) and built a hexamer model using 3fe4 and my best-looking zdock helix pair as templates for orienting the six copies of the monomeric alphafold model. The helix is randomly placed outside of the confident catalytic domain structure in the AlphaFold model, and there is a linker of poor confidence between the domains. With the original orientation of the helix my first-effort hexamer has the catalytic domains partly overlapping, and I'd need to rotate some bonds manually to orient the subunits into realistic positions. I wouldn't care even if I create some serious Ramachandran plot outliers there, when the goal is just to get a visualization for the multimer hypothesis. The problem is that when I rotate any bond in the linker, I either swing one helix out of a coiled-coil pair or one catalytic domain out of the face-to-face dimer interface (depending if I use move small of move large, respectively, in the torsion command). How could I get all six chains into a single chain? I assume that then I would be moving the whole rest of the multimer as a rigid body if I rotate any main-chain bond in the linker regions. ChimeraX session file attached. Cheers, -Martti Tolvanen U of Turku, Finland

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Re: [chimerax-users] chimeraX on wynton ( UCSF-specific)
by Rangarajan, Amith 04 Feb '22

04 Feb '22

Hi, This question is relevant for UCSF only. I have a set of docked poses that i want to analyze using chimera x script ( check ligand RMSDs, distances etc...) . My laptop is not that great, so i can use Wynton, if possible, to do this . is chimerax available on Wynton nodes? if so, please give me a short intro to get started on using chimerax on Wynton. thanks, amith I

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Automate calculation and saving of residues' structural attributes
by André 04 Feb '22

04 Feb '22

Hello! I'm working on an automated pipeline (in Python) for the structural analysis of proteins. In particular, I'm using Chimera to calculate and save to .txt files some structural properties of residues (namely: areaSAS, areaSES, relSESA, bfactor, kdhydro, phi, psi). These files are the inputs of the pipeline. However, currently the files are exported manually, and, for the purpose of building a fully automated pipeline, it would be great to also automate this step of calculating the attributes and exporting their respective files. I searched a lot, and tried some ways to achieve such an automation (using Chimera), but nothing worked. And I also considered using ChimeraX. In particular, I went through ChimeraX Programming Manual ( https://www.cgl.ucsf.edu/chimerax/docs/devel/index.html#) but, if I understood correctly, I'd only be able to import chimerax and use its functions in the Python interpreter within ChimeraX (Tools >> General >> Shell). At first, I'd like to import chimerax as a module in a Python interpreter outside of ChimeraX, so that manually opening ChimeraX wouldn't be necessary in order to save the files with the residues' attributes. But, from some other threads in the mailing list, I found that it wouldn't be possible (right?) But I also found out that I could write a .py script which calculates and exports the files with the residues' properties, and then run it with ChimeraX application from the command-line, something like: *chimerax --nogui myscript.py* If that works, I think that my automation problem would be solved! The only problem is that I really couldn't figure out the Python code to calculate and export the aforementioned residues' properties (I took a look in ChimeraX Recipes (https://rbvi.github.io/chimerax-recipes/) but I couldn't find what I need, nor more detailed documentation). Given that, I'd like to know if anyone has done something like this, and/or have any guidance on how I could proceed. I really appreciate any help you can provide! (And thanks to Tom Goddard for suggesting moving the discussion here to the ChimeraX mailing list). Thank you so much, André.

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Is there an output directory command for spin movies or morphs?
by Ralph Loring 03 Feb '22

03 Feb '22

Hi, I've given my students an assignment due on Monday which includes making a spin movie. About a third of the class tells me that they can see the molecule spinning while the movie is compiling, but that they can't find where the mp4 file goes. I have no trouble using my laptop, but if I use my office desktop computer, I have the same problem (see picture). The first two error messages were endogenously generated by ChimeraX, the last 3 were me trying to force the output directory. When I spoke to our IT people, they informed me that university computers are not allowed to save files to the public desktop, but prefer that it go to the user desktop in Onedrive. My question is whether there's a command that I can give before running a spin movie that specifies in what directory the output file should be put? Thanks, Ralph Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring(a)northeastern.edu

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Change default palette for sequential coloring?
by Oliver Clarke 03 Feb '22

03 Feb '22

Hi, I really like the option to use custom palettes from colorbrewer etc in ChimeraX for sequential coloring. Would it be possible to allow users to change the palette used as the default for sequential coloring? E.g. I really like "RdYlBu-5 (3-11)", but I can never remember the name or syntax, and for quick jobs I would love to be able to to set the default coloring scheme so it is just set up the way I like it. Cheers Oli

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Coloring Chains Sensitive to Case After Combine
by Anderson, Jacob 03 Feb '22

03 Feb '22

Dear ChimeraX, Really loving the implementation of the combine command in 1.3! After using the combine command to create a model with >30 chains, the resultant model has some chains with the same chain ID but with a lowercase (i.e. #6/D and #6/d are in the model). When I color #6/D (i.e. color #6/D green), this also is coloring chain #6/d. Is this the expected behavior? When I read help:user/commands/atomspec.html it seems that the chain identifier should be case sensitive if both upper and lowercase chain IDs are present. Curious if there is a way to force the case sensitivity.

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