[phenixbb] SA-omit maps for carbohydrates
jliu at nimr.mrc.ac.uk
Wed Jul 30 07:43:45 PDT 2008
Phenix can recognize the sugars automatically. It should be something
wrong in your cho2.pdb.
How can you get that? Using coot or vi? I made a mistake to edit a pdb
file in windows system last week. I think you'd better check your pdb
Enrico Girardi wrote:
> 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.
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