- Chimera-users - RBVI Mailing Lists

Question about using Chimera
by Zhuangwei Zhang 16 Sep '21

16 Sep '21

Hello, Dear Chimera developers， I encountered some problems when dealing with complexes of peptide-protein docking，Chimera could not correctly recognize the peptide as a single ligand, but recognized the peptide as model 2 and the receptor protein as model 1. Like this: I would appreciate it if you could help me answer this question. Thank you. Zhuangwei zhang Zhejiang Oeacn University

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local docking
by Yanhe Zhao 08 Sep '21

08 Sep '21

Greeting, I tried sequential fitting to fit 3 models to my maps. I was wondering that if I want to fix one model and do local fitting of another models with limited shift and rotation, what command with options should I use? Thanks and regards, Yanhe

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Fwd: Split, Crash out
by Tom Goddard 07 Sep '21

07 Sep '21

MJ reports that rebooting the computer fixed the Chimera crashes. > Begin forwarded message: > > From: Jeremy Jin > Subject: Re: [Chimera-users] Split, Crash out > Date: September 5, 2021 at 10:28:02 PM PDT > To: Elaine Meng <meng(a)cgl.ucsf.edu>, Tom Goddard <goddard(a)sonic.net> > > Hi Elaine adb Tom, > Sorry to bother, I tried again today, it worked, seems something wrong with my system or reboot several times works. I am also will try ChimeraX! Thanks! > > Best Regards! > MJ > > MJ, Mingliang Jin > Postdoc of Yifan Cheng’s Lab > Genentech Hall, UCSF Missionbay > Main Email: m.jin(a)msg.ucsf.edu > Tel: 415-2835-171 > > > >> On Sep 3, 2021, at 12:53, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi MJ, >> >> Most Chimera crashes are caused by graphics driver bugs. Updating your graphics driver is the usual fix. You might try our newer program ChimeraX. We have only done basic maintenance on Chimera for the past 5 years. ChimeraX does a better job reporting diagnostics if a crash happens. >> >> Tom >> >>> On Sep 3, 2021, at 12:26 PM, Jeremy Jin via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >>> >>> Hi, >>> >>> When I use chimera, I want to split a mode, as long as I split, the software just crashes out. >>> >>> It works very well before. Also it worked this morning, but after I split the model, fit to my map, it crashed out, then I restart, it showed the same problem. Then I re-installed the program, 2020-12-08 version, it crashed out even when I do split command. >>> >>> Best Regards! >>> MJ >>> >>> MJ, Mingliang Jin >>> Postdoc of Yifan Cheng’s Lab >>> Genentech Hall, UCSF Missionbay >>> Main Email: m.jin(a)msg.ucsf.edu >>> Tel: 415-2835-171 >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >>> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > >

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Copy protein orientation
by SANDOVAL, KENNETH 06 Sep '21

06 Sep '21

Hello, I wish to generate two images. The first is of protein A which is in session 1. The second is of protein A aligned with protein B using TM-Align which is in session 2. I wish for the alignment of the second image to be in the same orientation as the first with respect to protein A. Is there a feature which lets me do the following: 1) Identify orientation of protein A in session 1 2) Copy that orientation 3) Apply that orientation to protein A in session 2 4) Have protein B in session 2 remain aligned to protein A despite the new orientation Thank you, Kenneth Sandoval

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Split, Crash out
by Jeremy Jin 03 Sep '21

03 Sep '21

Hi, When I use chimera, I want to split a mode, as long as I split, the software just crashes out. It works very well before. Also it worked this morning, but after I split the model, fit to my map, it crashed out, then I restart, it showed the same problem. Then I re-installed the program, 2020-12-08 version, it crashed out even when I do split command. Best Regards! MJ MJ, Mingliang Jin Postdoc of Yifan Cheng’s Lab Genentech Hall, UCSF Missionbay Main Email: m.jin(a)msg.ucsf.edu Tel: 415-2835-171

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matchmaker for more than one chain
by manikandank 02 Sep '21

02 Sep '21

Hi ChimeraX-users, I have used recently the mmaker cmd to align two pdb each have multiple chains as below. mmaker #12/L,M,N to #5/S,A,B matrix blosum-62 showAlignment true But the sequence view shows only the alignment of chain L and S. 1. I would like to have aligned sequences of all chains used in mmaker alignement. 2. Is it possible to open the saved RMSD header values in a file later just to color the pdb? 3. Do mmaker align entire pdb based on selected chains and Can calculate RMSD for all residues in the pdb? 4. I also would like to change the displayed text for the sequence name. Presently it puts the filename as sequence name. [similar to 'Edit sequence name' in the sequence viewer in chimera] Please let me know how this can be done. thank you very much with kind regards Mani.

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Ribbon scaling in a script
by Esser, Lothar (NIH/NCI) [E] 01 Sep '21

01 Sep '21

Hi, despite a good amount of search in the documentation, I was unable to find a way to set the dimensions of a ribbon coil, helix width etc. with a commandline statement. I can do it in Ribbons Style Editor but I need to be able to do it from a script. I am sure it is terribly obvious but I just think it may be easier if I get a hint at this point. Thanks, Lothar Dr. Lothar Esser National Institutes of Health 37 Convent Dr. Rm2122B Bethesda, MD 20892

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Re: [Chimera-users] Making oligomers from Alphafold predictions
by Tom Goddard 01 Sep '21

01 Sep '21

Hi Tiru, If the center of symmetry is at 0,0,0 for your model and it just needs 6 rotated copies placed use Chimera command sym #0 group c6 where #0 is the model number of your monomer. If you do not know the center of symmetry or how the monomers interface with each other (ie their orientation in the hexamer), then that is a protein-protein docking problem and the sym command does not solve that. For that case you would need to fit in a cryoEM or X-ray map of the hexamer, or align the monomer to a known homologous hexamer, or find some amazing oligomeric structure prediction tool. Tom > On Sep 1, 2021, at 11:24 AM, Tiru Hcu <tiru.hcu09(a)gmail.com <mailto:tiru.hcu09@gmail.com>> wrote: > > Hi Tom, > > Thank you for your response. My protein symmetry is a hexamer. Please would you mind sharing a little elaborate how to to do in chimera. Thank you. > > Best regards, > Tiru > > On Wed, 1 Sep 2021, 21:10 Tom Goddard via Chimera-users, <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: > Hi Smith, > > Do you know the symmetry of the oligomer you are trying to make? Is it just a matter of applying positions that you already know? Or do you need some computational protein-protein docking to figure it out (a vastly harder problem)? If you know the symmetry you want the Chimera and ChimeraX sym command can place copies of a structure using standard symmetries or a list of position matrices (rotation + translation). > > tom > > >> On Sep 1, 2021, at 1:29 AM, tim smith via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >> >> Thank you, Elaine and Kevin, for your response. >> The Rosetta Symmetry docking is up to 400 amino acids, and mine is 800. I can't use it as it is. Wondering there is any other server for predicting symmetry. >> >> Thank you. >> >> Best >> Smith >> >> On Tue, Aug 31, 2021 at 7:02 PM Kevin Jude <kjude(a)stanford.edu <mailto:kjude@stanford.edu>> wrote: >> Hi Smith, you can use Rosetta Symmetric Docking. It's available on the ROSIE server >> >> https://rosie.rosettacommons.org/symmetric_docking <https://rosie.rosettacommons.org/symmetric_docking> >> -- >> Kevin Jude, PhD (he/him/his) >> Structural Biology Research Specialist, Garcia Lab >> Howard Hughes Medical Institute >> Stanford University School of Medicine >> Beckman B177, 279 Campus Drive, Stanford CA 94305 >> Phone: (650) 723-6431 <tel:%28650%29%20723-6431> >> On Tue, Aug 31, 2021 at 4:30 AM tim smith via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: >> Hi All, >> Apologies for the nonrelated question!! >> >> Wondering if there are any tools (can make in chimera/chimerax/Pymol) that predict or build protein oligomers based on alphfold structure. Please let me know. I will be grateful for your kind responses. Thank you >> >> Best >> Smith >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users> > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>

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Making oligomers from Alphafold predictions
by tim smith 01 Sep '21

01 Sep '21

Hi All, Apologies for the nonrelated question!! Wondering if there are any tools (can make in chimera/chimerax/Pymol) that predict or build protein oligomers based on alphfold structure. Please let me know. I will be grateful for your kind responses. Thank you Best Smith

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Capture click event
by jeni_zen2004＠yahoo.co.in 30 Aug '21

30 Aug '21

Hi, Is there a way to capture the Chimera click event or a way to work around?I'm trying to do something from python code like., when a user clicks on a residue, it pops up a tooltip or shows the centroid. Thanks,Catherine

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