[phenixbb] SA-omit maps for carbohydrates

Enrico Girardi enrico.girardi at kcl.ac.uk
Wed Jul 30 07:23:21 PDT 2008

Dear All,

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.


Enrico Girardi
Randall Division of Cell and Molecular Biophysics
King's College London
New Hunt's House	
Guy's Campus
London SE1 1UL

Tel  +44 (0)20 7848 6419
Fax  +44 (0)20 7848 6435 

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