[phenixbb] LINK records, sugars, and a question in two parts

Engin Ozkan eozkan at stanford.edu
Sat Feb 14 11:51:34 PST 2009

Hi everyone,

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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