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
Hi,
On 11/20/13, 4:17 PM, Zhijie Li wrote:
If you need to refine the structure with phenix.refine then you need
to make an edit file to specify that the mannose C1 is linked to the
ser OG by a covalent bond.
I am not sure if this is what was meant, but you don't need to define
bonds
the LINK line and make sure the residue numbers are
right).
Zhijie
-Original Message-
From: Dmitry Rodionov
Sent: Thursday, November 21, 2013 4:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Dealnig with O-linked mannose
Thank you all for helpful suggestions.
My question
Message-
From: Dmitry Rodionov
Sent: Thursday, November 21, 2013 4:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: 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
Hi Dmitry,
I think the best way is not to make a new monomer. MAN-SER and MAN-THR
linkages do exist in the ccp4 monomer lib. If you simply build a mannose
with its O1 removed and put the C1 ~1.4 Angstrom to the OG of the serine I
think refmac should be able to detect the linkage. When this
