Dear Angel:
Thanks for all your help.
If one does a search on "pdb format segid" there will be hundreds of
hits. Here is one:
http://bmerc-www.bu.edu/needle-doc/latest/atom-format.html
Admittedly, it is older but does mention a field for* segid*.
The most current pdb format description does not mention segid:
http://www.wwpdb.org/documentation/format33/sect9.html
but leaves the fields for the segid keyword blank. This discussion has
been going back and forth for a while now.
The situation is this.
Much application software today incorporates the use of the *segid *keyword
which was adopted from the earlier pdb format designation.
Consider the following snippet of a simple pdb (with nothing but
coordinates) file:
----- snip --- snip --- snip ---
ATOM 1 N MET 1 10.796 -0.039 -2.050 1.00 0.00
PROA
ATOM 2 HT1 MET 1 10.025 -0.285 -1.397 1.00 0.00
PROA
ATOM 3 HT2 MET 1 10.293 0.599 -2.699 1.00 0.00
PROA
ATOM 4 HT3 MET 1 11.518 0.486 -1.516 1.00 0.00
PROA
ATOM 5 CA MET 1 11.292 -1.242 -2.741 1.00 0.00
PROA
ATOM 6 HA MET 1 10.478 -1.776 -3.208 1.00 0.00
PROA
ATOM 7 CB MET 1 12.149 -0.821 -3.954 1.00 0.00
PROA
ATOM 8 HB1 MET 1 11.673 0.074 -4.409 1.00 0.00
PROA
ATOM 9 HB2 MET 1 13.202 -0.634 -3.654 1.00 0.00
PROA
ATOM 10 CG MET 1 12.231 -2.026 -4.935 1.00 0.00
PROA
ATOM 11 HG1 MET 1 12.814 -2.838 -4.450 1.00 0.00 PROA
ATOM 12 HG2 MET 1 11.193 -2.392 -5.086 1.00 0.00 PROA
---- snip ---- snip --- snip ---
If this is read into charmm, then I can manipulate the PROA segment, i.e.
one of the protein chains making up a transmembrane connexin channel like
this:
*if (segid PROA .and. .not. segid PROB ) *then do something
if it is read into VMD, I can do the following
*segid PROA and type HT2
*If it is read into PyMol, I can do something like,
# Create objects
create ptrna, startmodel and segid PROA
# Color objects
color ptrna, ptrna
The point is that these other programs, charmm (md program), VMD and
PyMol (visualization programs) can read columns 72-75 of the
PDB file as a segid and allow the user to manipulate a part of the
protein, if the segid keyword is there.
For example, as mentioned above. A connexin protein has six different
transmembrane chains segid PROA through segid PROF,
and I can manipulate them separately through the segid keyword in
other applications.
Again thanks for all your help.
Regards,
Angelo
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