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