Chimera-dev June 2008

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by Virginie Lafont 01 May '09

01 May '09

Hi, I am a new user of chimera and I already have a question. I have an protonated aspartic acid in my protein and I was wondering, is it possible to add hydrogen atom to aspartic acid with chimera? Thanks Virginie

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problem with solvate
by Jean-Didier Maréchal 19 Jun '08

19 Jun '08

Hi Guys, I tried the solvate module on the alpha build of the 15/06/2008 on windows. And I have the following error: Running sleap command: C:\Archivos de programa\Chimera2\bin\amber10\exe\sleap -f d:\docume~1\jd\config~1\temp\tmpi8eph7\solvate.cmd (solvate) [gtkleap]$ source leaprc.ff03 (solvate) Error: can not find file leaprc.ff03 in all the search path. Failure running sleap Check reply log for details I made a search of the mentioned file and it does not pop up. Cheers JD -----Mensaje original----- De: chimera-users-bounces(a)cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] En nombre de chimera-users-request(a)cgl.ucsf.edu Enviado el: miércoles, 18 de junio de 2008 21:00 Para: chimera-users(a)cgl.ucsf.edu Asunto: Chimera-users Digest, Vol 62, Issue 18 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. Find contour level to enclose a specified volume (Thomas Goddard) 2. Re: Find contour level to enclose a specified volume (Tom Goddard) ---------------------------------------------------------------------- Message: 1 Date: Tue, 17 Jun 2008 15:44:57 -0700 From: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: [Chimera-users] Find contour level to enclose a specified volume To: "'Chimera BB'" <chimera-users(a)cgl.ucsf.edu> Message-ID: <48583E69.5090608(a)cgl.ucsf.edu> Content-Type: text/plain; charset="iso-8859-1" Ed Brignole asked about setting a volume contouring level so that the resulting surface encloses a desired volume (cubic Angstroms). Attached is a Python script that does this in two ways. The first way is fast but approximate finding the level such that the number of enclosed grid points times the voxel volume equals the requested volume. Estimating the enclosed volume of the surface this way can give a much different result than actually computing analytically the volume within the surface. The second approach computes surfaces at different contour levels and calculates analytically the volume. It uses bisection to find the correct contour level. This approach can be slow, about 30 seconds for a 256^3 volume (sfv.mrc virus map) with ~2.5e6 surface triangles. Most of that time (80%) is actually computing the enclosed volume. That should be very fast but the code is checking for holes in the surface in a rather slow way. Both methods use the step size (subsampling) set in the volume dialog. Tom

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