- Chimera-users - RBVI Mailing Lists

script command for writing out areaSAS attribute?
by Julius Su 05 Feb '09

05 Feb '09

Hello, Does anyone know what script command could be used to output an "attribute assignment file" in Chimera, specifically for the areaSAS attribute? I am trying to show how the solvent accessible surface area on various residues changes over the frames of a multitrajectory PDB file. To do this I am trying to write a small script in "MD movie" that computes the solvent accessible surface for each frame, then outputs the areaSAS values. I was previously able to do this by loading in all the PDB geometries at once, then using the "Render attributes by ..." dialog, but this method does not scale well to very large proteins (the program runs out of memory trying to compute all the surfaces at once). Thus I am trying to do this task sequentially with a script. Thanks much! Julius

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Is it possible?
by Ahir Utsav Pushpanath 04 Feb '09

04 Feb '09

Hello Dear Sir/Madam, I am very fond of chimera, and everytime I have looked at scripts for doign things, I find that chimera has them already inbuilt as features. There is one particular problem that I am sure chimera has the capability of doing but I am struggling to do it. 1) I want to use structural superposition servers such as Mammoth etc to produce a structural alignment of two proteins, 2nadA and 1ybaB. However, some of these servers do not produce a sequence alignment output in a format compatible with chimera (i.e such as .aln or aligned fasta). But they do produce a .pdb file showing the superposition. 2) If I load the .pdb onto chimera, sometimes in "model list" window, i see the two proteins, wheras in others I only see 1 model(yet there is clearly 2 models there) 3) I was wondering whether you can load the superposition onto chimera, and see the sequence alignment that gives rise to that structural superposition, so that I may save it as a .aln format using multialign viewer. How do I do this? Apologies if this is a very straightforward scenario. Thanks Ahir

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roll command:
by Bui Khanh Huy 01 Feb '09

01 Feb '09

Dear all, I tried the roll command with my model (EM map) open: roll z 30 1 center 50,50,50 Chimera showed msg "wait_frames argument not implemented". Just wonder how to implement that command without the error? Huy

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Calc buried surface area between 2 chains
by Tom Duncan 30 Jan '09

30 Jan '09

I saw an earlier post (Dec. 29, 2008; Digest vol. 68, issue 28) in which Elaine Meng described a procedure for calculating surface area for selected atoms. I did this for atoms on chain A that were selected as contacting atoms on neighboring chain B, but the sum(atom.areaSES) probably includes area buried within the chain A, not just between the 2 chains. I tried checking this by calculating the sum(atom.areaSES) for chain A (all atoms in A) in the whole model, then again for a model from which chain B was deleted before calculating the surface. However, the results indicated a larger areaSES for chain A in the absence of chain B! There were some errors reported in calculating the surfaces; perhaps this contributed. Is there a better way to calculate the buried surface on 1 chain due to contacts with a 2nd chain? Thanks, Tom Duncan

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error message
by Katherine Parra 28 Jan '09

28 Jan '09

Hello! I'm trying to get the hydrogen bonds between some selected residues during a trajectory, using per frame commands from tools. But when I get the possible hydrogen bonds formed between the selected residues I also get the following error message in the Reply Log: *Skipping possible acceptor with bad geometry: #0:2108@O Wrong number of grandchild atoms for phi/psi acceptor #0:2108@O *What could be happening? Thank you in advance. KP

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color zone on command line
by Giulia Zanetti 28 Jan '09

28 Jan '09

Hi all, I would like to make a movie in which areas of my map are coloured while the surface is rotating. Any idea how to use color zone from the command line? thanks Giulia

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fit in map output : coordinate representation of axis, axis point
by Hwang, Youngha,Ph.D. 27 Jan '09

27 Jan '09

Hi, could anyone explain to me what axis points mean in chimera? What unit is used for them? Is it related to the volume dimension? Is the rotation matrix based on Euler-angle representation? Thanks, Youngha. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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3D on Chimera.
by ayassin＠wadsworth.org 27 Jan '09

27 Jan '09

Hello, I am trying to use Chimera to model pdb files into EM maps. When I select the red cyan stereo, the EM map is stereo but the pdb structure is not. -Is there anyway to display pdb in stereo in Chimera, how? -Is there another program that would allow me to do the same thing: fit pdb in EM density map-in stereo(other than "O")? -When I use Chimera on windows VISTA the side view panel does not appear and a message about graphic card appear, anyway to solve this? Thank you all very much. Aymen Yassin. Postdoc Research Affiliate Wadsworth Center, Albany,NY. IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.

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marker coordinates
by Gabor Papai 27 Jan '09

27 Jan '09

Hi, I would like to do the following: I placed markers on density spots. I want to get their coordinates and excise a box around the marked density and save it as a separate file. For this I would like to know how I can retrieve the coordinates of a marker set and possibly how to position exactly a box around a marker to set a subregion (and of course how to set the dimensions of that box). This second feature existed before, but disappeared in the latest releases with the subregion selection tool in the Volume Viewer. Thanks in advance, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-88655748 Fax +33-3-88653201 E-mail: papai(a)igbmc.u-strasbg.fr

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Volume information
by vamsee 26 Jan '09

26 Jan '09

Hello All, I am working on a virus and I am trying to figure out its volume. I would want to find out the volume of the nucleic acid and the water inside the virus capsid. That way, if I am thinking right, that should give me the total internal volume of the virus. This volume would be a constant even with the movement of water in and out. Is it possible to use chimera to calculate any of such data, with no prior information about how the nucleic acid is packed inside? Thanks in advance, Vamsee Graduate Student Dept of Chemistry and Biochemistry Montana State University Bozeman, MT - 59715

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