Thanks, Herman. Zhijie, what is the difference between LINK and LINKR?
Maybe this will help somebody (though phenix-related):
phenix.link_edits parses the pdb for LINK records and outputs the pdb.edits
file.
Alternatively, phenix.ligand_linking can guess what should be bonded in the
absence of LINK records and produce apply_link.def
Best rgards,
Dmitry
On 2013-11-22, at 3:18 AM, herman.schreu...@sanofi.com wrote:
> Using your favorite editor, you can copy the LINK record from the pdb file
> generated by Coot and paste it into the pdb file produced by Phenix. You can
> also make a script to do this. This is what I did during the time LINK
> records were not properly handled by coot, refmac and buster.
>
> Best regards,
> Herman
>
>
>
> -----Ursprüngliche Nachricht-----
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Dmitry
> Rodionov
> Gesendet: Donnerstag, 21. November 2013 22:09
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] Dealnig with O-linked mannose
>
> Thank you all for helpful suggestions.
>
> My question was how to properly connect a mannose to a serine and real-space
> refine the result. My apologies for not being clear enough.
>
> Coot can't find MAN-SER or SER-MAN in it's library (Coot 0.7.1, mon_lib 5.41)
> It does not automatically make the bond between MAN C1 and OG of SER either.
>
> Here is the way I finally made the connection followed by refinement it in
> Coot:
>
> 1) Get monomer... MAN
> 2) real-space refine MAN into reasonable position
> 3) Delete hydrogens and reducing hydroxyl
> Bond is not detected
> 4) Extensions->Modelling ...->make Link (Click 2 atoms) ... Click on C1 of
> MAN and OG of SER
> dashed bond appears
> 5) Sphere refine
>
> A whole different issue that was touched in the replies is how this model
> will be handled by refinement programs.
> For the sake of a record, I am using Phenix and it seems to not respect the
> described link without massaging by means of either pdb.edits or
> apply_link.def.
> Also, phenix.refine does not produce LINK records in the output PDB, so step
> 4 might have to be repeated.
>
> Best regards,
> Dmitry
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