January 2011 - Chimera-users - RBVI Mailing Lists

how to delete saved state in the "savepos list"
by jinghua 21 Jan '11

21 Jan '11

The savepos is a very useful command to save the state of the graphics. But after a while, the "savepos list" contains a long list. Is there a way to delete some of the states in the list? Thank you in advance, Jinghua

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Display only selection
by Damien Larivière 20 Jan '11

20 Jan '11

Dear Chimera team, I'm identifying a complex between two proteins thanks to crosslink data. I have the following questions: 1/ I would like to select two residues that belong to two different chains and highlight them in the viewport. By using the sequence tool and then ctrl/shift+drag, I can select two residues (ex: 45 and 246 of chain A), they are highlighted in the view. But when I operate this way with res 45 of chain A and res 246 of chain B, only one remains highlighted in the view port. One way to sort this out would have been to rename all the chains with the letter A. But once the residues are highlighted, I have to measure the distance between them, then to make one chain active and then to move it and try to fit crosslink data (I hope I'm clear:-\ ). Is it possible to directly select and highlight in the viewport residues of interest belonging to different chains? 2/ Supposing that I can select and highlight in the viewport residues of interest belonging to different chains: How can I display only them in the viewport (and hide all the others)? The technical goal behind these questions is to better appreciate visually the distance between residues of interest and, thanks to the distance tool, to move one protein with respect to the other and fit crosslink data. Many thanks for your help. Damien

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Chimera 1.5.1 on CentOS 5.5
by Yohei Norimatsu 18 Jan '11

18 Jan '11

Hi all, I just installed the latest version of Chimera (1.5.1 x86_64) on CentOS 5.5. I'm having a problem with MSMS surface representation. It doesn't show the surface for all the atoms and it just looks messed up. I installed the same version of Chimera on RedHat Linux 5 and it works without any problem. I don't know what the problem is. Does anyone use Chimera on CentOS? Any comment is appreciated. Thank you! Yohei

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TZD Tautomer Distributions
by Nancy 17 Jan '11

17 Jan '11

Hi All, For pioglitazone, are the two tautomers depicted in the attached figure the major forms at pH 7.0? Also, are there any published articles, or other evidence that would confirm that this is indeed the correct tautomeric distribution at pH 7? Thank you, Nancy

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Fwd: distance between 2 residues
by Damien Larivière 17 Jan '11

17 Jan '11

Hi everyone, As explain in the Chimera user guide, I used the command such like distance #0.2:246@N#0.5:131@N to measure the distance between two atoms of interest. To be more explicit regarding my first email, it was necessary to re-edit the pdb file and to assign a model number to each chain. In the example above, the chain B is named model 2 (then model 0.2 in Chimera) and the chain D is named model 5 (then model 0.5 in Chimera). It works fine but I suppose that there is a simpler and more direct way to specify the chain in the command? Many thanks Damien -------- Message original -------- Sujet: distance between 2 residues Date : Mon, 17 Jan 2011 18:09:11 +0100 De : Damien Larivière <damien.lariviere(a)fourmentinguilbert.org> Pour : chimera-users(a)cgl.ucsf.edu Dear all, I would like to know the (mean or approximative) distance between two residues within a protein (let's say Res 5 of chain A and Res 246 of chain C). I suppose that I have to select one atom in each of the residues and use the Distance tool. I confess I have trouble to do so, either by picking in the viewport or by using the atom identifier. May you tell me a simple way to achieve such a distance? Many thanks for your help Damien

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distance between 2 residues
by Damien Larivière 17 Jan '11

17 Jan '11

Dear all, I would like to know the (mean or approximative) distance between two residues within a protein (let's say Res 5 of chain A and Res 246 of chain C). I suppose that I have to select one atom in each of the residues and use the Distance tool. I confess I have trouble to do so, either by picking in the viewport or by using the atom identifier. May you tell me a simple way to achieve such a distance? Many thanks for your help Damien

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Cavities
by Beale, John 12 Jan '11

12 Jan '11

Is it possible to find cavities in a protein structure using Chimera? Thanks in advance! John John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale(a)stlcop.edu<mailto:jbeale@stlcop.edu>

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Tautomer Prediction
by Nancy 11 Jan '11

11 Jan '11

Hi All, Using MarvinSketch v5.3.3 (ChemAxon software), the predicted pKa value of the acidic hydrogen on the thiazolidinedione ring of pioglitazone is 4.57 (see attached "Figure_1.gif"). Therefore, the predominant species at pH 7.0 predicted by MarvinSketch is the one depicted in "Figure_2.gif". The different tautomeric forms predicted by MarvinSketch are shown in "Figure_3.gif". Can anyone explain where these predictions come from, and if they are correct? Also, are there other programs that can accurately predict tautomeric forms? Thanks, Nancy

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Pioglitazone Tautomers
by Nancy 10 Jan '11

10 Jan '11

Hi All, I am performing molecular docking and molecular dynamics simulations of the thiazolidinedione pioglitazone binding to the PPAR-gamma receptor protein (PDB ID: 1ZGY). The thiazolidinedione ring can exist in numerous different tautomeric states; I have attached a figure depicting several of them. Which tautomer would be dominant at the physiological pH of ~7.0? Also, are there any software programs that can predict which tautomer would be correct? Thanks in advance, Nancy

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Morphing surface
by Sumitro Harjanto 05 Jan '11

05 Jan '11

Hi elaine, Thanks for the prompt responses on earlier queries. I have one more question: Is it possible to morph between 2 surfaces? Basically, I would like to show the effect in the surface contour due to a residue change. Thanks, Sumitro Institute for Infocomm Research disclaimer: "This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you."

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Chimera-users January 2011