OK, I will look into this.
Frieda
On Sep 10, 2008, at 2:10 PM, Robert Hanson wrote:
We could set up the mol2 reader to do this. BUT I have to be
convinced first that it's a real standard. What programs write
these? Is it just totally arbitrary what these IDs are? Are the
names standard? Try some more unusual structures, like DNA, RNA,
nonstandard amino acids, 1BLU with its FeS4 sites. Hemoglobin.
On Wed, Sep 10, 2008 at 8:51 AM, Angel Herraez
<[EMAIL PROTECTED]> wrote:
Dear Frieda
I've never tried that. From the doc
http://www.tripos.com/data/support/mol2.pdf
it seems that atoms can have IDs and residue IDs; they quote an
example:
1 CA -0.149 0.299 0.000 C.3 1 ALA1 0.000
BACKBONE|DICT|DIRECT
1 CA -0.149 0.299 0.000 C.3
[...] the atom is named CA and is [...] It belongs to the
substructure with ID 1 which is named ALA1.
So, Jmol should be able to interpret that, but maybe the file reader
has not been set for that.
As far as I know, the "protein" is determined based on bonding and
key atom names (N, CA, C) within the same residue.
Similarly for residue names.
A quick test with a pdb file read into Accelrys DS Viewer 1.7 and
saved into mol2 shows that the atom IDs are read in Jmol (example:
select *.CA works), but not recognized as protein. "select ala"
doesn't work either.
So maybe it's just the residue ID part that is not being interpreted.
Notably, that goes after the coordinates, rather than before them as
in pdb.
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Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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