[phenixbb] SA-omit maps for carbohydrates
enrico.girardi at kcl.ac.uk
Wed Jul 30 07:23:21 PDT 2008
I would like to create a SA-omit map for two carbohydrate chains present
in my structure.
My attempts using the command
phenix.autobuild data=data.mtz model=final.pdb omit_box_pdb=cho2.pdb composite_omit_type=sa_omit
lead to a message in the log file saying:
Failed to carry out AutoBuild_set_up_build:
Sorry, unable to define an omit region with cho2.pdb
res_start = None
res end = None
chain = ''
? Possibly no atoms?
The procedure works fine with protein residues so I am assuming that
phenix.autobuild is ignoring the sugars in the original pdb file (as it
says in the log file..).
Is this correct? How can I fix the problem?
I am running Phenix 1.3b.
Many thanks in advance for your help.
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