[phenixbb] SA-omit maps for carbohydrates

[junfeng liu]

Dear Enrico,
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 
file first.
Good luck!
leo
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.
> Regards
>
> Enrico
>
>
>
>