- Chimera-users - RBVI Mailing Lists

Crashes during Dock Prep
by Justin Trickett 27 Sep '21

27 Sep '21

Hello, I am prepping 43 structures for docking using the "Dock Prep" feature in Chimera 1.15, and it crashes every time it gets to "Retrieving rotamers from Dunbrack library." Am I doing something wrong? Many thanks, Justin -- Justin Trickett Graduate Student College of Pharmacy, University of Rhode Island (603) 505-1061

2 1

question on protein structure change after matchmaker (position-change) operation
by Lei Qian 27 Sep '21

27 Sep '21

Dear users, After aligning protein A to protein B using matchmaker, I found the protein A structure slightly changed compared with its original structure (RMSD: 0.001). Could I ask how I can keep protein A structure unchanged after matchmaker (position-change) operation? Thanks! Lei

2 2

Running 3D-FSC script causes freeze
by Oliver Clarke 23 Sep '21

23 Sep '21

Hi, Running the chimera command file included with the example data for 3D-FSC (https://github.com/LyumkisLab/3DFSC/tree/master/Example/Results_T40-3DFSC/C… <https://github.com/LyumkisLab/3DFSC/tree/master/Example/Results_T40-3DFSC/C…>) causes the latest daily build of Chimera to freeze - it executes lineplot.py, but then just locks up and does not respond. This happens whether I run it as `chimera 3DFSCPlot_Chimera.cmd` or load the command file after opening the GUI. Am I doing something wrong, or has something changed in Chimera that has broken this script? Cheers Oli

2 1

Connecting ends of a peptide
by Nicole Ostrovsky 22 Sep '21

22 Sep '21

Hello, I am trying to connect two sides of a peptide together to make it cyclic. Is there a way to do this that doesn't involve adding in another amino acid? I have been adding a glycine by individual atom using the modify structure tool but I'm wondering if I can do it a different way. Best, Nicole Ostrovsky

2 2

Visualize chain break in Chimera
by Yu Zhou 22 Sep '21

22 Sep '21

Dear all, I am going through a Rosetta protein-protein docking tutorial using Chimera as the structure viewer. There is a chain break in the structure used for this tutorial (3gbn), which is caused by a severed connection between residue 127 and 128. Such chain break needs to be identified and fixed in a structural model before it could be used for Rosetta simulation. This chain break can be easily identified in Pymol as it is displayed as a dotted line. However, I cannot see this chain break in Chimera (and ChimeraX) as the segment is rendered as a beta-sheet. Is there a way to visualize such chain break in Chimera? Thanks, Yu Zhou

2 2

question about label chain?
by 朱玉威 22 Sep '21

22 Sep '21

Dear developer， Could you kindly tell me how to label each chains. I need it to make a movie. Thank you very much. Best wishes!

2 1

How to sequentially open PDB files using a "for loop" in the UCSF chimera's command line?
by Prathvi Singh 18 Sep '21

18 Sep '21

Greetings, Is it possible to use a "for loop" in the UCSF chimera's command line to open a PDB file, perform an action (say delete an atom), save the PDB file & close it, open the next PDB file, perform the same operation, save it & close it and so on. Thanks, Prathvi

2 2

Setting Default Colors
by joshloecker＠icloud.com 16 Sep '21

16 Sep '21

Hello, I have recently started using Chimera and I am having a problem setting a default color when starting a session (if this is possible). When I open a model, it opens in a tan color, which I like because it is easy to pick out other molecules, such as SO4, etc. However, when closing the session and opening the same model, it opens in a variety of other colors, such as bright red, pink, purple, orange, etc. that are distracting to what I am trying to do. I have found the section in Preferences > New Molecules to not use a new color for each model, but then if I load multiple models I cannot distinguish between them. I was wondering if it was possible to set a default color to open models in, or if I have to quit Chimera each time I open a single model in order to get the easy-to-see tan color? -- Thank you, Josh Loecker

2 2

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

2 3

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

3 3

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 >>> >> > >

1 0

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

3 8

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

3 2

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.

2 1

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

3 6

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>

1 0

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

4 4

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

2 1

ITasser model looks different once PDB opened in UCSF Chimera
by Athena Andreosso 25 Aug '21

25 Aug '21

Hi, I recently submitted a sequence to get a model in PDB format. When I opened the PDB file of model 1 in Chimera it looked completely different than the model on the ITasser results page - it had less beta strands. When I clicked on model 2 it was better but there's still a visible discrepancy. Am I doing something wrong? Am I supposed to give chimera more info than just the PDB file ? Any help is appreciated. Cheers Athena Andreosso, D.Phil. | Research Officer Mucosal Immunology QIMR Berghofer Medical Research Institute e AthenaAndreosso(a)qimrberghofer.edu.au<mailto:AthenaAndreosso@qimrberghofer.edu.au> | www.qimr.edu.au<http://www.qimr.edu.au/> 300 Herston Road, Herston QLD 4006

2 4

3D Visualization
by Song, David 25 Aug '21

25 Aug '21

Hi, My name is Dave Song, and I am a graduate student interested in visualizing protein structures in 3D. I was wondering if you had any recommendations in regards to computer hardware requirements for maximum performance while using Chimera/ChimeraX. Additionally, do you have any suggestions on monitors and 3D glasses that work well with Chimera? Thank you for your time, and I look forward to hearing from you. Best, Dave

2 1

Chimera not responding
by Pritam Dey 23 Aug '21

23 Aug '21

Cannot execute 'gzip': no automatic decompression of .Z files Return code: -1073741819 Press return or enter to to exit

2 1

Hollow Sticks When Exporting as STLs?
by Josh Moon 17 Aug '21

17 Aug '21

Hello, I hope to make this question as direct and simple as I can! When I export a scene of a molecule displayed as a ball-and-stick as a STL, I find that many of my "stick" portions are hollow. This creates thin, weak walls for 3D printing. I've included a screenshot of an intended plane cut from Meshmixer so that you can see the internal structure. What am I doing incorrectly? Is there something I can do in Chimera to export a solid object with no "hollow tubes." Fixing this with 3d programs can be time consuming. Sincere thanks, Josh ----------------------------------------- Josh Moon, Ph.D. (he/him/his) Educational Technology Specialist Kalamazoo College (269) 337-7415

2 1

Fc dimer fall apart after fusion with a GS linker
by tiger wang 16 Aug '21

16 Aug '21

Dear Ms/Mr helper: I encounted an issue when I try to fuse one (G4S)x linker to one of the Fc "C" terminal using "join bond". Once selected the "C" atom on Fc C terminal and "N" atom on (G4S)x N terminal and hit "apply" button, the Fc dimer fall apart but the (G4S)x linker was connected to the C terminal of Fc. How to avoid the Fc dimer from falling apart? Thanks very much for your help Sincerely TW

2 1

How to get random velocities?
by Seera Suryanarayana 11 Aug '21

11 Aug '21

Dear chimera users, Dear VMD users, I was asked to do simulations five times with the same starting structure and number of processors. But the velocities should be different. Here my query is "How do you generate velocities in the gromacs?". I request you to guide me how to do it. Thanks in advance Surya Graduate student India.

2 2

Problems with installing on a Windows 10 expedition Dell laptop
by Alice Chen 10 Aug '21

10 Aug '21

Hello, I'm on a Dell XPS 9500 laptop running Windows v. 10.0.2.1000. When my IT specialist tried to install it, it would run the install program but at the very end the install would fail. We were able to install the old non-X version of Chimera. Is there something we should/can do to check, settings-wise? Cheers-Alice Kitterman Alice Y Chen AY Chen Illustration and Design https://www.facebook.com/AYCIAD https://vimeo.com/user13507144/videos www.aliceychen.com

3 9