VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun May 29 2011 - 03:17:08 CDT

On Sun, May 29, 2011 at 12:26 AM, BRAULIO VALDEBENITO MATURANA
<bvaldebenito09_at_alumnos.utalca.cl> wrote:
> Thanks for the answers, but what we really want to know is  (or if you could
> pinpoint us to a site where this is explained) how exactly are those density
> values in the .dx file related to the atoms in the pdf file, I mean, if
> there are some zeros on the first file, how could I be able to tell which
> x,y,z coordinates do they match?

the correlation of the gridpoint values and the coordinates can be
optained from the header of the respective files. for DX files, see:
http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html

this is just a regular 3d grid.

> We have already looked into tools like CASTp, CSPro, McVol, etc., and they
> all use some geometrial approach to solve this problem, like "Delaunay
> Triangulation" or using probe spheres. We would like to develop a script
> that let us to get a "crude" estimate, like you said. We're in college, and
> this is the main task for one of our courses, you could think of this as
> something "binary", in the way that the output of the script should say if
> there are cavities, where they are, and a rough estimate of their volume.

things are not as easy as you might think. you have to be able to
tell whether you are inside of a protein or on the surface and that
can be _really_ difficult. think of having a molecule with a "deep"
pocket. when would it belong to the surface, and when inside?

cheers,
     axel.

> Cheers,
> Braulio.
>
>> --------------------------------------------------
>> From: "John Stone" <johns_at_ks.uiuc.edu>
>> Sent: Friday, May 27, 2011 3:47 PM
>> To: "BRAULIOFAVIÁNVALDEBENITO MATURANA" <bvaldebenito09_at_alumnos.utalca.cl>
>> Cc: <vmd-l_at_ks.uiuc.edu>
>> Subject: Re: vmd-l: Protein cavities
>>
>>>
>>> Hi,
>>>  The DX files are a visualization file format that can also be used to
>>> store
>>> uniform grids of scalar data, which is what the 'volmap' commands do.
>>> If you compute a density map from your structure, you'll get density
>>> values
>>> of zero at the points associated with empty space, so that is a very
>>> simple
>>> way to determine where you have pockets or cavities of empty space.
>>> You could get a crude estimate of empty volume from this kind of
>>> approach,
>>> but I should also point out that with a little google searching, that
>>> I think that there are tools available that are specifically designed to
>>> find cavity volumes.  So, before you implement it yourself in a VMD
>>> script, I would suggest googling for 15 or 20 minutes and see if you can
>>> find one of those tools.  I seem to remember I've heard of a couple such
>>> programs in the past, but I don't remember them anymore.
>>>
>>> Cheers,
>>>  John Stone
>>>  vmd_at_ks.uiuc.edu
>>>
>>>
>>>
>>> On Thu, May 26, 2011 at 05:41:48PM +0000, BRAULIO FAVIÁN VALDEBENITO
>>> MATURANA wrote:
>>>>
>>>>   Dear all,
>>>>
>>>>   We're working on a Tcl/Tk script whose function is to determine both
>>>>   surface and internal cavities of a given protein. In order to achieve
>>>>   that, we've been thinking in the "volmap" function as stated by John
>>>> Stone
>>>>   in reply to "cavity/pocket representation" on May 2nd, 2006 (it can be
>>>>   seen here:
>>>>   http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/6885.html), but
>>>>   instead of a graphical output, we need the analytical data too.
>>>>
>>>>   Well, regarding the output of the "volmap" command, which is a file
>>>> with
>>>>   .dx extension, we would like to know if there is any way to use the
>>>>   information on that file so that we can "substract" from the entire
>>>> map
>>>>   the volume occupied by the actual molecule, thus letting the volume of
>>>> any
>>>>   possible cavities.
>>>>
>>>>   Thanks in advance!
>>>>   Braulio.
>>>
>>> --
>>> NIH Resource for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
>>> http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078
>>>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.