Dear all, I would like to use chimera to generate inputs for gaussian QM/MM calculations (ONIOM). One of the element I need is the connectivity of the atoms. I looked around the programmer's guide but couldn't find the right module that takes this in charge. what is the way to have access the connectivity of a given molecule? All the best, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es ----- Missatge original ----- De: chimera-users-request@cgl.ucsf.edu Data: Dimecres, Juny 18, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 62, Issue 18
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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)
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Message: 1 Date: Tue, 17 Jun 2008 15:44:57 -0700 From: Thomas Goddard <goddard@cgl.ucsf.edu> Subject: [Chimera-users] Find contour level to enclose a specified volume To: "'Chimera BB'" <chimera-users@cgl.ucsf.edu> Message-ID: <48583E69.5090608@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
Hi JD, For a Molecule model "m", m.bonds is the list of bonds. Each Bond "b" has the bonded atoms in b.atoms. Conversely each Atom "a" lists its bonded neighbor atoms in a.neighbors. Is this basically what you wanted? --Eric On Jun 18, 2008, at 3:50 PM, Jean Didier Pie Marechal wrote:
Dear all,
I would like to use chimera to generate inputs for gaussian QM/MM calculations (ONIOM). One of the element I need is the connectivity of the atoms. I looked around the programmer's guide but couldn't find the right module that takes this in charge.
what is the way to have access the connectivity of a given molecule?
All the best, JD
Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es
----- Missatge original ----- De: chimera-users-request@cgl.ucsf.edu Data: Dimecres, Juny 18, 2008 9:00 pm Assumpte: Chimera-users Digest, Vol 62, Issue 18
Send Chimera-users mailing list submissions to chimera-users@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@cgl.ucsf.edu
You can reach the person managing the list at chimera-users-owner@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@cgl.ucsf.edu> Subject: [Chimera-users] Find contour level to enclose a specified volume To: "'Chimera BB'" <chimera-users@cgl.ucsf.edu> Message-ID: <48583E69.5090608@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
participants (2)
-
Eric Pettersen -
Jean Didier Pie Marechal