[chimera-dev] problem with solvate

[Jean-Didier Maréchal]

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 at cgl.ucsf.edu
[mailto:chimera-users-bounces at cgl.ucsf.edu] En nombre de
chimera-users-request at cgl.ucsf.edu
Enviado el: miércoles, 18 de junio de 2008 21:00
Para: chimera-users at cgl.ucsf.edu
Asunto: 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 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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