other people recently asked about the ligand surface, and Jason gave the following answer on 02 Apr. Hope it is also helpful to your glycan case.

-----------------------------

Hi Peter,

In order to do this you either need to extract the ligand to its own
object or unset the ignore flag on "rep surface".  That is,

# fetch the protein

fetch 1rg7, async=0

# show surface
show surface, resn MTX

# do not ignore surfacing of ligands

flag ignore, not rep surface

# force PyMOL to rebuild the surface

rebuild

Cheers,

-- Jason
On 05.05.2011 9:22, Yamei Yu wrote:
Hi all, 

  I want to display the surface of my structure with pymol. The problem is that it automatically excludes all the glycans. Does anybody know the method to solve this problem?
Thank you very much!
yamei
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