[Chimera-users] Fields in dms format
meng at cgl.ucsf.edu
Thu Nov 12 10:19:44 PST 2009
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,
> 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
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