[Chimera-users] connectivity

[Eric Pettersen]

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 at uab.es
>
> ----- Missatge original -----
> De: chimera-users-request at 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)
>>
>>
>> --------------------------------------------------------------------
>> --
>>
>> Message: 1
>> Date: Tue, 17 Jun 2008 15:44:57 -0700
>> From: Thomas Goddard <goddard at cgl.ucsf.edu>
>> Subject: [Chimera-users] Find contour level to enclose a specified
>> 	volume
>> To: "'Chimera BB'" <chimera-users at cgl.ucsf.edu>
>> Message-ID: <48583E69.5090608 at 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
>> -------------- next part --------------
>> An embedded and charset-unspecified text was scrubbed...
>> Name: findlevel.py
>> Url: http://www.cgl.ucsf.edu/pipermail/chimera-
>> users/attachments/20080617/d7aef5ee/findlevel-0001.ksh
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Wed, 18 Jun 2008 11:02:46 -0700
>> From: Tom Goddard <goddard at cgl.ucsf.edu>
>> Subject: Re: [Chimera-users] Find contour level to enclose a  
>> specified
>> 	volume
>> To: "'Chimera BB'" <chimera-users at cgl.ucsf.edu>
>> Message-ID: <48594DC6.3000801 at cgl.ucsf.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> The script I posted calculates the contour level but does not show
>> it.
>> To set the contour level and display the new surface use Python code:
>>
>>   v.set_parameters(surface_levels = [level])
>>   v.show()
>>
>> Tom
>>
>>
>> ------------------------------
>>
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>> End of Chimera-users Digest, Vol 62, Issue 18
>> *********************************************
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