I have recently been trying to find my way around Sybyl5.5 running on a
Silicon Graphics and using it to examine a Brookhaven PDB file. I could
get the protein up on the screen with no problem and manipulate it etc.,
but it seemed unable to recognise the connectivities between heterologous
sugar atoms (the protein has several N and O-linked glycosylation sites).
The atoms appeared simply as individual dots. It made no difference whether
the biopolymer protein or carbohydrate dictionaries were open.
Does anyone out there know how to solve this problem ? I have previously
used Frodo on an Evans and Sutherland, which manages better - the sugar
structures appear but are not linked to the polypeptide. In contrast simple
display programs running on a Mac seem to be able to get it absolutely
Alternatively, does anyone know of any software that has specific features
allowing the construction, modelling etc of glycopeptides ? I once asked a
rep how is program coped with glycoproteins or proteoglycans and just got
a blank look and standard answer about the wonders of the package.
Looking forward to your replies,
c.pook at ic.ac.uk