[phenixbb] LINK records, sugars, and a question in two parts
eozkan at stanford.edu
Sat Feb 14 11:51:34 PST 2009
I was wondering if phenix.refine does or does not write out LINK records
in the output pdb. Also, are carbohydrate groups written out as ATOM or
The reason I am asking is that I was trying to use a sugar group
geometry/naming validation tool called pdbcare (at glycosciences.de),
and the program is failing to read out the sugar groups from the pdb.
One reason I can see is that the sugars are written out with ATOM cards,
while the program possibly expects HETATM, and the other is that this
program might be looking for LINK cards (These pdb files were written
put by phenix 1.3rc6, so maybe if I rerefined them with 1.4.3, I might
get a different result). By the way, I can get these files to be read
properly by pdb2linucs at the same webpage (after telling it to use both
ATOM and HETATM, and telling it to calculate linkages itself).
If there is anyone out there who has used the pdbcare successfully on
phenix.refine pdb files, please let me know.
It would also be great to add carbohydrate validation tools to the army
of great modules in phenix (such as phenix.xtriage and phenix.ramalyze).
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