- 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

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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

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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

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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

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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

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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!

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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

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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

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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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