- Chimera-users - RBVI Mailing Lists

Morphing a residue through MD trajectories
by George Tzotzos 02 Aug '15

02 Aug '15

Hi, I have an MD trajectory which I can load successfully on Chimera. My objective is to monitor changes in conformations of one particular residue in the receptor (:123) throughout the trajectory and generate a movie. If I could do this in tandem with a bound ligand so much the better. I’ve tried to follow the instructions but obviously, I get it wrong. I opened the Morph Conformations tool, I selected the trajectory and clicked on Add. This generated a 2nd MD Movie panel of just one frame. Any help would be most welcome Regards George

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 4
by feisun＠ibp.ac.cn 02 Aug '15

02 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 3
by feisun＠ibp.ac.cn 01 Aug '15

01 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 2
by feisun＠ibp.ac.cn 01 Aug '15

01 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 1
by feisun＠ibp.ac.cn 01 Aug '15

01 Aug '15

From: feisun(a)ibp.ac.cn Subject: I am in a vacation. I am now taking a vacation from Aug. 1st to Aug. 9th. I will reply to you after Aug. 10th. Sorry for the delay. Fei

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Open model from pdb with designated model id?
by Oliver Clarke 31 Jul '15

31 Jul '15

Hi all, I would like to write an alias to load a pdb and the associated 2fo-fc and fo-fc maps with a single command (and adjust the contours and appearance of the maps and model). To do this, I need to be able to open the models with specific output ids, so I can issue commands to alter their appearance later in the alias. Looking at the documentation (http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/open.html>), it seems like this should be possible, but when I give an output model id it seems that chimera is ignoring it and still choosing the lowest available id. I have tried the following commands, “open 1bl8 100”, “open 1bl8 #100”, “open 1bl8 model-id:100” but they all either fail or load 1bl8 with model id 1. Am I missing something about the syntax here? Or is there another flag for the output model id? Cheers, Oliver.

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Option to not record duplicates in the command history?
by Oliver Clarke 31 Jul '15

31 Jul '15

Hi all, I like the command history in chimera a lot - it makes it very quick to repeat previous commands. One minor alteration that might make it a little bit better would be to have an option (maybe in the Command Line section of the preferences?) to not record sequential duplicate commands in the history (like the “ignoredups” option for the bash history). I will often repeat the same command a bunch of times (for example “turn x 5” or one of the various aliases I use for navigation and recentering), and so not having all these duplicates recorded in the history would make it a lot faster to find recently used commands. Cheers, Oliver.

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Addh function and fake N, C-terminii
by gaelle garet 31 Jul '15

31 Jul '15

Hi, I want to use Addh function to add hydrogens and protonate N, C-terminii but I don't understand very well how you detect if a terminus is fake or not. For example, for the structure 3L4F, I obtain the following log : Chain-initial residues that are actual N terminii: MET 586.A, MET 586.B, MET 586.C Chain-initial residues that are not actual N terminii: GLY 652.D Chain-final residues that are actual C terminii: LEU 646.A, LEU 646.B Chain-final residues that are not actual C terminii: ASP 638.C, ARG 758.D I don't understand why GLY 652.D, ASP638.C and ARG 758.D are not terminii, can you explain me why and how the algorithm detect that ? Thank you in advance for your answer. -- Gaëlle

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How to explore two protein structures on the same screen?
by Jing Tang 31 Jul '15

31 Jul '15

Hi, I opened two protein structures, say 2JIT and 4WA9 and they were partially overlapped on the screen. How to move one protein so that they can be separated more? I can only move the two proteins as a whole but not individually. Further, I would like to highlight one residue for a particular protein and I could not find a way to first select a protein and then a residue. Thanks, Jing

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Recent problems with linux x64 version
by Peter L. 31 Jul '15

31 Jul '15

Hello, Recently I used Chimera for a internship/volunteer work with my older brother, and it did not start up due to some seemingly graphics drivers problems. I'm running Ubuntu 15.04 on a AMD radion 5450M on this machine and NVidea gtx 760 on another. Both would not start up due to having libGL error: unable to load driver: nouveau_dri.so etc etc, as so documented here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015February/010734.html (Error from the NvIdia machine) and would not load r600. However both had the same fix, that seemigly works by removing the file /Chimera64-1.10.2/lib/libstdc++.so.6, I renamed it to libstdc++.so.6.bak in case I might need it, but it works on both machines now. It seems as some older libs are colliding with mesa drivers, and casung them to break, and removing this fixes the problem. Its been documented before with other programs here, where the fix is simular. http://askubuntu.com/questions/614422/problem-with-installing-steam-on-ubun… I also found that in the chimera mail I found, it was recommend to update some drivers, or Nvidia drivers, however, nvidia drivers for linux tend to break the system a lot or cause other problems. Hope this helps!, Peter

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