[Chimera-users] Fields in dms format

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 12 10:19:44 PST 2009

Hi Yasser,

The detailed description is in
DMS file format:
The output consists of a series of atom and surface point records,  
with the same format for the first six fields. Each atom is followed  
by the surface points (if any) which belong to it. These first six  
fields are in the following format: residue name, sequence number,  
atom name, x coordinate, y coordinate, z coordinate. For an atom  
record, the seventh field is "A." For a surface point record, the  
seventh field begins with an "S," followed by a "C," "R," or "S"  
according to whether the point is part of contact, reentrant, or  
saddle surface (saddle is a type of reentrant surface where the probe  
is in contact with exactly two atoms). This is followed by a digit  
used for depicting different density levels. The eighth field is the  
molecular surface area associated with the point in square angstroms.  
If -n is specified, the next three fields are the unit normal vector  
pointing outward from the surface.

The "0" is described as "a digit used for depicting different density  
levels" -- I'm guessing this was something that was used by the  
original MS program by Mike Connolly... maybe the file could contain  
multiple surfaces and that number was used to distinguish them from  
each other.  In the files written by Chimera, I believe it is just  
there for compatibility with the original format and otherwise does  
not have a meaning.

The eighth field is the estimated surface area assigned to the dot, as  
if the surface were divided up into separate pieces for each dot.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 12, 2009, at 7:59 AM, Yasser Almeida Hernández wrote:

> Hi all...
> In the .dms format:
> 1 - What's the meaning of the digit (allways 0) after the SR (or SC,  
> SC)?
> 2 - What's the meaning of the number in the 8th field?
> I've read the help of this format, but i don't understand the  
> meaning of these numbers
> Thanks...

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