[Chimera-users] connectivity

[Jean Didier Pie Marechal]

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
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> 
> ------------------------------
> 
> 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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