VMD-L Mailing List

From: BRAULIO VALDEBENITO MATURANA (bvaldebenito09_at_alumnos.utalca.cl)
Date: Sat May 28 2011 - 23:26:02 CDT

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?

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.

Cheers,
Braulio.

> --------------------------------------------------
> From: "John Stone" <johns_at_ks.uiuc.edu>
> Sent: Friday, May 27, 2011 3:47 PM
> To: "BRAULIOFAVINVALDEBENITO 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 FAVIN 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
>>