- Chimera-users - RBVI Mailing Lists

Some problem with volume coloring
by MAG 14 Jul '09

14 Jul '09

Good day for you, Would be so kind and help me. The problem is I want to color two parts of my volume. So, I have put markers inside of it, color two parts, but now I want to save this colored volume, such that after I would be able to duplicate it and use as a normal volume, but colored. Thank you in advance, Best, Alex

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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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suggestion/transform molecule coordinates
by Dougherty, Matthew T. 13 Jul '09

13 Jul '09

relating to the apply, close & help buttons 1)"reset" button The reset would remove prior transformations 2) "apply once" button. The apply once would function the same as a reset and apply in sequence. 3) display sum of current transformation (Euler & shift) Matthew Dougherty 713-433-3849 National Center for Macromolecular Imaging Baylor College of Medicine/Houston Texas USA ========================================================================= =========================================================================

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Faster raytracing
by "Bernhard Pätzold" 09 Jul '09

09 Jul '09

Hello I love Chimera and the only little bummer to me are the long rendering times for raytraced movies. I managed to get the PovRay version 3.7 which uses multiple cores running on our server. However now I am stuck and here comes my question. Is there away how I can get Chimera to use the newer Version of PovRay? Or can I somehow change my script so that I get only the .pov and .ini files for all the frames while the actual raytracing is skipped and I can do it subsequently with the newer Version? Currently the whole things has to happen on a windows system, but I hope that I'll get my ubuntu version soon up and running again, so hints and advices for both options are welcome. Thanks a lot in advance Berni -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01

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no bug reports
by Eric Pettersen 09 Jul '09

09 Jul '09

Since mail to chimera-bugs eventually gets delivered to crick and crick is down, we won't be receiving any bug reports until crick comes up. --Eric

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thermal ellipsoids
by Michael K. Gilson 08 Jul '09

08 Jul '09

Hi, Chimera and PyMol are showing very different thermal ellipsoid orientations for the same PDB file, and I have reason to believe that the PyMol display is the right one. Here are the first two lines of the PDB file I am reading in: Atom 1 O1 CUC 1 3.345 1.613 0.172 ANISOU 1 O1 CUC 1 619 156 528 150 43 -6 ATOM 2 O2 CUC 1 -1.699 0.125 2.792 ANISOU 2 O2 CUC 1 497 355 848 128 -68 204 I would appreciate help with this because Chimera appears to provide more detailed control of the coloring of the ellipsoids than PyMol does. I'll be happy to provide screenshots or other information. Regards, Mike

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Model translation
by David Chenoweth 08 Jul '09

08 Jul '09

Hi, Can anyone tell me the easiest way to translate an entire model by a defined amount (angstroms) in a defined direction. I have a slice of a nanotube and I would like to open it several times, translate each section, and make bonds between the translated sections in order to create a longer nanotube and then save the new coordinates as a new model. Thanks, Dave

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Re: [Chimera-users] Display Molecule Name
by cdlau＠ucsd.edu 08 Jul '09

08 Jul '09

Hi, Thanks for the response. This would not work for my case because I am writing a plugin for ViewDock for use with a Tiled Wall Display. I was hoping there was a setting that was available to show the molecule name (if a setting does exist I can initiate it with runCommand). Does anyone know if this is possible? Thanks, Chris On Thu, 2 Jul 2009, cdlau(a)ucsd.edu wrote: Hi, I was wondering if there was a way to display the molecule name that is being shown in chimera. A simple display such as "molecule #0.10" below the rendered molecule would be great. Thanks for your help, Chris Just place the mouse over the item you want to know more about and a popup balloon will tell you about it. The text starts with the model number, e.g., #0.10, and may or may not have additional information, i.e., for an atom it includes the residue name and sequence number and the atom name. - Greg

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Thermal ellipsoids
by Michael Day 07 Jul '09

07 Jul '09

Hi, I see thermal ellipsoid rendering was just enabled. This is another point (in a long list of points) in favor of using Chimera. Is there a plan to be able to display ellipsoid axis or octants as in ortep type renderings. This would be extremely useful in small molecule work. I've been using Chimera as an alternate when reporting structures in my lab and it has been very well received. The first question asked when I distributed a report today was about the axis and/or octants. Great work. Keep it up! Cheers, Mike <<< ------------------------------------------------------------------------> >> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday(a)caltech.edu <<< ------------------------------------------------------------------------> >>

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Display of a vector in Chimera
by Charles Letner, Ph.D. 07 Jul '09

07 Jul '09

Hello, Is there a way to display a vector between two sets of coordinates in Chimera? If the approach is to write a python, any chance I could get a nudge in the right direction on chimera commands to work with? I've written a minimal amount of python code but not related to Chimera. Cheers, Chuck Charles Letner, Ph.D. Alpharetta, GA 30004 Email: chuck(a)theletners.com

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