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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