Hi Dimetry,
The difference between LINK and LINKR can't be explained better:
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11865.html
Older versions of COOT used to not display the LINKR record, but now the
newer versions display both LINK and LINKR records as dotted bonds. I assume
that means COOT will now treat LINKR as LINK, otherwise there is no point
displaying a bond but not taking its meanings. However outside the
refmac-COOT universe, LINKR is not a legitimate record.
Zhijie
-----Original Message-----
From: Dmitry Rodionov
Sent: Friday, November 22, 2013 11:11 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Dealnig with O-linked mannose
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
-----Urspr�ngliche 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
