December 2023 - ChimeraX-users - RBVI Mailing Lists

augment mousemode center with cofr centerofview; alter animation frames
by leeyang+chimerax＠gmail.com 11 Dec '23

11 Dec '23

Hi, I find the mousemode center function very useful when navigating around a model. One of the features I loved about the original Chimera. Would it be possible to have the option to augment it with a cofr centerofview feature so that the pivotpoint then follows subsequent translation? Also, would it be possible to define a custom number of frames over which the animation occurs? Cheers, Yang

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Re: AlphaFold to run .pkl file and the tax error
by Tom Goddard 11 Dec '23

11 Dec '23

Hi Serhat, AlphaFold does not provide docking scores or energy minimization scores as far as I know. AlphaFold estimates pTM (predicted TM) and ipTM (interface predicted TM) scores related to prediction accuracy. You might want to google molecule TM score to learn about those. And googling Alphafold iptm gives as the top hit a paper describing those scores Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes https://academic.oup.com/bioinformatics/article/39/7/btad424/7219714 ChimeraX does not show you those scores but does have ways of visualizing the pLDDT (predicted local distance difference test) and PAE (predicted aligned error) generated by AlphaFold, described here https://www.rbvi.ucsf.edu/chimerax/data/pae-apr2022/pae.html And you may be interested in ChimeraX videos about visualizing AlphaFold confidence https://youtu.be/oxblwn0_PMM https://youtu.be/TMcjEecFHaI and more ChimeraX AlphaFold videos here https://www.rbvi.ucsf.edu/chimerax/docs/videos/ The .pkl (Python pickle) files contain data such as PAE scores. ChimeraX can read pkl file to show the scores as described in the above links. The alphafold issue #629 you reference about AlphaFold inserting jax data structures into .pkl files was long ago fixed in both AlphaFold and ChimeraX 1.5 as described in the link you sent. The solution is of course to update the version of ChimeraX and AlphaFold you are using. If you are using any ChimeraX version to run AlphaFold it is using a current AlphaFold. But ChimeraX AlphaFold runs don't produce .pkl files so I guess you are running an old AlphaFold in a different. Tom > On Dec 11, 2023, at 4:23 AM, serhat inceer <serhatinceer(a)yahoo.com> wrote: > > Dear Tom Goddard > > > My name is Serhat Inceer Researcher at the University of Vienna department od Molecular Biology, and I am reaching out to seek assistance regarding the interpretation of docking scores and multimer energy minimization scores in AlphaFold. > > Additionally, I have questions about running ".pkl" files to analyze plDDt graphs for the predicted and ranked models that I have already predicted models. > > Specifically, I am interested in understanding the methodology and significance of the docking score and multimer energy minimization score provided by AlphaFold. Could you please provide more information on how these scores are calculated and what they signify in the context of protein structure prediction? > > Furthermore, I have generated ".pkl" files for my predicted models, and I am interested in running them to obtain plDDt graphs. Could you please guide me on the steps to run the ".pkl" files for this purpose? Any documentation or resources that outline the process would be greatly appreciated. > > According my research on GitHub you got also same error and I am wondering about how could you fit it this situation > > https://github.com/google-deepmind/alphafold/issues/629 > > Thank you very much for your time and assistance. I look forward to your response. > > Best regards, > > Serhat Inceer > >

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Smooth-MD script for a trajectory visualisation
by Enrico Martinez 08 Dec '23

08 Dec '23

Dear Chimera-X users. I am trying to record a md trajectory loaded as multi-pdb file: open ./stripped_traj2.pdb coordsets true I have the issue with smooth-md script (enclosed), which produces the following error: open smooth_md_chX.py open /home/test/Bureau/MOVIE_CHIMERAX\/smooth_md_chX.pyTraceback (most recent call last): File "/home/test/Bureau/MOVIE_CHIMERAX\/smooth_md_chX.py", line 23, in <module> avg += weight * coord_sets[j] ValueError: operands could not be broadcast together with shapes (6120,3) (6112,3) (6120,3) Should something be fixed in the script in order that I could observe the MD movie with smooth details ? Thank you in advance Enrico

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Re: Following Up on Drawing Outlines
by Tom Goddard 07 Dec '23

07 Dec '23

Hi André, There is only one selection outline in ChimeraX so you cannot show different color outlines directly in ChimeraX using the selection outline. Here are a couple ideas. You could select all your sites and make one outline around all of them in green and then in Photoshop change the color of parts of the outline to the appropriate colors. Another idea is you can select each patch and make its outline in the correct color and then just save that outline but not the surface. To show just the outline and not the surface you would make the surface 100% transparent and hide atoms transparency 100 hide atoms save outline1.png transparentBackground true. Save each outline as a separate image and then layer them on top of your surface in Photoshop. A problem with both of these methods is that your patches border each other so the outlines will overlap. In fact the selection outline extends outward when you make it thicker (ChimeraX avoids covering the patch with the outline). So two adjacent patches with different outlines are going to draw the outlines intersecting and crossing each other where they adjoin each other. Making the outlines extend inward could be done in Photoshop by fattening the individual layer outlines. This gets into a lot of hand work. Tom > On Dec 7, 2023, at 1:15 PM, Andre Leon <aleon(a)scripps.edu> wrote: > > Hello Tom, > > Thank you for the response! I'm guessing the answer to my next question is no, but I was wondering if there's a way to create these selection outlines around multiple regions to create figures similar to the one below, highlighting all the major antigenic sites on influenza HA. That way I can simultaneously outline the epitopes and also color the figure by sequence conservation as opposed to doing one or the other. If that's not possible, than I will pseudo outline in Illustrator or Photoshop, but it would be ideal to be able to specifically highlight the exact residues using ChimeraX. > > Again, thank you so much for your rapid response! > > > Best Regards, > André Nicolás León > Graduate Student - Ward Lab <https://ward.scripps.edu/> > https://www.linkedin.com/in/andrenicolasleon/ > From: Tom Goddard <goddard(a)sonic.net> > Sent: Thursday, December 7, 2023 12:25 PM > To: Andre Leon <aleon(a)scripps.edu> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] Following Up on Drawing Outlines > > Hi André, > > Making a thick colored outline around an epitope on a protein surface is easier in ChimeraX using thick selection outlines. The link you mentioned from 2014 is from our old program Chimera which could only draw thin 1 pixel wide outlines. Here is an example in ChimeraX where I make a thick (10 pixel wide) red outline around some residues. > > open 2x7r > hide ~/C atoms > surface /C > select /C:670-681 > graphics selection color red width 10 > > Tom > > > >> On Dec 7, 2023, at 10:53 AM, Andre Leon via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hello Chimerax, >> >> I was wondering if there has been any progress on making outlines of specific epitopes in ChimeraX since this thread back in 2014? <https://www.cgl.ucsf.edu/chimera/data/outline-may2014/outlines.html> Thank you in advance. >> >> Best Regards, >> André Nicolás León >> Graduate Student - Ward Lab <https://ward.scripps.edu/> >> https://www.linkedin.com/in/andrenicolasleon/ >> _______________________________________________ >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

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Following Up on Drawing Outlines
by Andre Leon 07 Dec '23

07 Dec '23

Hello Chimerax, I was wondering if there has been any progress on making outlines of specific epitopes in ChimeraX since this thread back in 2014?<https://www.cgl.ucsf.edu/chimera/data/outline-may2014/outlines.html> Thank you in advance. Best Regards, André Nicolás León Graduate Student - Ward Lab<https://ward.scripps.edu/> https://www.linkedin.com/in/andrenicolasleon/

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Add charge to PDB fails
by Daniel Hsu 06 Dec '23

06 Dec '23

Hi All What might cause this action to fail, pH=7.4, H added to protein before adding charge? No errors were thrown. Both DOCK-Prep, and adding H then charge both do not change the PDB file (no charges added to respective atoms). Log reports "Using Amber 20 recommended default charges and atom types for standard residues" Alternative command 'addcharge standardizeResidues 5BU,CSL,MSE,UMS' reports "Using Amber 20 recommended default charges and atom types for standard residues" and no errors but don't add charges to saved PDB file. Charges are added with another structure editor. Thanks for insights! **CONFIDENTIALITY NOTICE** This e-mail communication and any attachments are for the sole use of the intended recipient and may contain information that is confidential and privileged under state and federal privacy laws. If you received this e-mail in error, be aware that any unauthorized use, disclosure, copying, or distribution is strictly prohibited. If you received this e-mail in error, please contact the sender immediately and destroy/delete all copies of this message.

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Surphace representation of multi-model pdb and moovie recording
by Enrico Martinez 06 Dec '23

06 Dec '23

Dear Chimera-X users ! I am working on molecular visualization of membrane system from the md trajectory loaded in the Chimera-x using the open coordset true command. The issue is with the surface representation of the membrane: transparency :OL,PA,PE,PC 80 target s which are applied only on the current frame (not on the whole trajectory). Also when I try to make a movie of the system the presence of the surface does slow down everything. Which options could be useful e.g. to decrease the quality of the surface representation ? Many thanks in advance Enrico

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ChimeraX & ConSurf
by martin.brehm＠univie.ac.at 05 Dec '23

05 Dec '23

Dear ChimeraX developers, I have a question regarding a potential upgrade of ChimeraX. Would it be possible to include the functionality of ConSurf, a tool to plot the degree of sequence conservation onto a model, into ChimeraX? The code for this is publically available on GitHub: https://github.com/Rostlab/ConSurf See this publication for more information: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987940/ Thanks a lot in advance and have a nice day! Best regards Martin Brehm Martin Brehm - PhD Student Falk Lab - Max Perutz Labs Vienna Room 1.624 - Phone +43 14277 74361 martin.brehm(a)univie.ac.at

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ISOLDE on Mac M1/M2/M3 or on Linux CentOS 7
by Mark Hilge 05 Dec '23

05 Dec '23

Hello, Could you please tell me whether your latest Version of ISOLDE would either run on a Mac with an Apple Silicon chip (M1, M2, or M3) or on a Linux box with CentOS 7 installed? Many thanks in advance! Kind regards, Mark

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Missing tools in ChimeraX
by Lars Backman 05 Dec '23

05 Dec '23

Hi, In Chimera, a tool named “Viewing” was available. It was an excellent tool to adjust appearance of the final png or jpg figure. I have looked for a similar tool in ChimeraX, but it seems to be absent. Or is there a way to create something similar? Best regards, Lars Backman [signature_2226121467] Lars Backman Professor Department of Chemistry, Biochemistry Umeå University SE-90187 Umeå, Sweden Tel: (46) 070 833 9946 e-mail: lars.backman(a)chem.umu.se<applewebdata://6E905793-FDA7-4651-8DC6-A97D8021B9DD/lars.backman@chem.umu.se> http://staff.chem.umu.se/lars.backman/research/ När du skickar e-post till Umeå universitet så innebär detta att Umeå universitet behandlar dina personuppgifter. För att läsa mer om hur detta går till, gå till www.umu.se/gdpr<http://www.umu.se/gdpr> By sending an email to Umeå University, the University will need to process your personal data. For more information, please read www.umu.se/en/gdpr<http://www.umu.se/en/gdpr>

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