January 2009 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Question regarding saving PDB in Chimera
by Pancera, Marie (NIH/VRC) [E] 24 Nov '09

24 Nov '09

Hello, I am using Chimera to fit coordinates into EM density. However I have problems when I save with Chimera as the coordinates that I am saving are not the one I see on the screen. Here is what I do: File Save PDB chose the folder A file name A file type The model that I want to save, i.e the one I see on the screen And then I have to select save relative to model, otherwise I am saving the original molecule, the problem is that I am not sure relative to which model I have to save it. IS there an easier way to just save what I can see on the screen? Thanks, Marie

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color scale bar
by Yao Cong 17 Jul '09

17 Jul '09

Hello Chimera developer, I am rendering a PDB file colored according to B-factor value by "render by attribute" tool. How can I generate a color scale bar besides the structure labeling the color scale used? Many thanks, Yao Cong

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sequence viewer
by Gatsogiannis, Christos 13 Jul '09

13 Jul '09

Hi all, i ve just installed the latest daily build version and i´ve noticed that the sequence viewer has a new "look". However, i have difficulties to get used to it... Some examples: -when i want to view the sequence of a pdb file containing seven chains, i get seven different pop-up windows (...) showing the sequences corresponding to the seven different chain ID´s.... -Moreover, it isn´t so "easy" anymore to select aminoacids directly in the sequence viewer (e.g. too many colors) and therefore now i´m selecting residues using only the command line.. My colleagues also prefer the older version.. is there a simple way to install the latest chimera version but keep the old version of the sequence viewer? Thanks! -Christos ------------------------------- Christos Gatsogiannis Insitute of Zoology, Dpt. II cryoEM Lab, AG Markl Joh. v. Müllerweg 6 Johannes Gutenberg University Mainz, Germany +49-6131-3923091 ------------------------------- ________________________________________ Von: chimera-users-bounces(a)cgl.ucsf.edu [chimera-users-bounces(a)cgl.ucsf.edu] im Auftrag von chimera-users-request(a)cgl.ucsf.edu [chimera-users-request(a)cgl.ucsf.edu] Gesendet: Mittwoch, 17. Dezember 2008 21:00 An: chimera-users(a)cgl.ucsf.edu Betreff: Chimera-users Digest, Vol 68, Issue 22 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Re: (Thermal ellipsoids) anisotropic temperature factor ellipsoids (Eric Pettersen) 2. Re: (Thermal ellipsoids) anisotropic temperature factor ellipsoids (Eric Pettersen) 3. possibilities to save parts of models (selection)? (Sebastian Kruggel) 4. Re: possibilities to save parts of models (selection)? (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Tue, 16 Dec 2008 14:59:34 -0800 From: Eric Pettersen <pett(a)cgl.ucsf.edu> Subject: Re: [Chimera-users] (Thermal ellipsoids) anisotropic temperature factor ellipsoids To: Tom Goddard <goddard(a)cgl.ucsf.edu> Cc: 'Chimera BB' <chimera-users(a)cgl.ucsf.edu> Message-ID: <9A34751B-6356-4AF4-A8C7-31757E5FFBF1(a)cgl.ucsf.edu> Content-Type: text/plain; charset="us-ascii" On Dec 12, 2008, at 10:40 AM, Tom Goddard wrote: > Hi David, > > Ok I see now, it's a matter of choosing the size of each ellipsoid to > have a 50% chance of finding the atom in that volume. This > shouldn't be > too hard but I'll let Eric tackle it if he has time. Hi David, This is one of those things that I'll endeavor to get into Chimera's production version of thermal ellipsoids, but that I can't spare the time for until then. My guess is that the eigenvectors/values of the U matrix are at the 50% probability level, but verifying that would require some research. If you do look into and find that that's not the case, just change the setting of the 'scale' variable of the start of the script to change the ellipsoid sizes to whatever size encloses 50%. --Eric

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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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Chimera-users January 2009