Jaim, I think ths may be what you need, picking up the older definition of
ligand:
http://wiki.jmol.org/index.php/AtomSets
ligand:
The new definition (Jmol 12.2) includes atoms that do not belong to
protein, nucleic or solvent. That includes water, other solvent, ions and
select hetero
?
On Wed, Jan 22, 2014 at 12:16 PM, Jaime Prilusky
jaime.prilu...@weizmann.ac.il wrote:
Thank you Angel for the explanation. Still looking for a solution.
Jaim
On Jan 22, 2014, at 5:00 PM, Angel Herráez angel.herr...@uah.es wrote:
I'm guessing, but ATP may be recognized as
definitely:
boolean isHetero = line.startsWith(HETATM);
On Fri, Jan 24, 2014 at 6:16 PM, Robert Hanson hans...@stolaf.edu wrote:
select hetero
?
On Wed, Jan 22, 2014 at 12:16 PM, Jaime Prilusky
jaime.prilu...@weizmann.ac.il wrote:
Thank you Angel for the explanation. Still
I'm looking for the equivalent to getProperty ligandInfo that will return the
complete list of names in HET or HETAM
definitely:
boolean isHetero = line.startsWith(HETATM);
On Fri, Jan 24, 2014 at 6:16 PM, Robert Hanson
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
select hetero
?
getProperty ligandInfo returns a nice list of elements in the HET record of the
PDB file, with some exceptions, like ATP and ADP.
Those are not included in the ligandInfo report. Tested on Jmol 14.0.7 (both
Java and HTML5) on several structures, including 1s22 and 1php
Is there other
I'm guessing, but ATP may be recognized as nucleic by Jmol
algorithm and hence excluded from the ligand set, which is not
protein, not nucleic, not solvent if I remember correctly
Sorry, ligand used to be hetero and not solvent, but the problem may
be along those lines.
Thank you Angel for the explanation. Still looking for a solution.
Jaim
On Jan 22, 2014, at 5:00 PM, Angel Herráez angel.herr...@uah.es wrote:
I'm guessing, but ATP may be recognized as nucleic by Jmol
algorithm and hence excluded from the ligand set, which is not
protein, not nucleic, not
7 matches
Mail list logo
