August 2015 - Chimera-users - RBVI Mailing Lists

Mirror image proteins
by Sarko, Dikran 03 Aug '15

03 Aug '15

Hello, is there any way to generate mirror image proteins (All AA in D-form) from an already exsist pdb file. Thank you in advanceDikran

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Average structure
by George Tzotzos 03 Aug '15

03 Aug '15

Hi everybody, I’m analysing the Principal Components of an Amber trajectory. I have generated a number of representative pdb files which are concatenated for each PC. Question: Is there a way to generate an average structure in Chimera from the concatenated PDB files? I know this can be done using MD movie but this solution requires that I generate a new topology file for my complex (the original topology file contains ligands and water molecules). Thank you in advance for any suggestions Regards George

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Re: [Chimera-users] Chimera-users Digest, Vol 148, Issue 6
by feisun＠ibp.ac.cn 03 Aug '15

03 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 5
by feisun＠ibp.ac.cn 03 Aug '15

03 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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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

1 0

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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Chimera-users August 2015