[phenixbb] SA-omit maps for carbohydrates

[Enrico Girardi]

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.
Regards

Enrico



-- 
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