[Chimera-users] DMS output format

Conrad Huang conrad at cgl.ucsf.edu
Wed Jul 13 12:03:36 PDT 2011

DMS documentation may be found at 
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/dms1.html.  The 
(brief) section on the file format says:

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 

Hope this helps.


On Wed Jul 13 11:43:26 2011, Efrat Kligun wrote:
> Hello,
> I am a Phd student at the Technion, I use the program- DMS and I would 
> like to know what is the numeration of the columns of the first six 
> fields in the output format of the dms.
> Thanks in advance,
> Efrat
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