Re: [ccp4bb] Problem with making covalent bonds in phenix by LINK or edits file

2014-04-03 Thread Joel Tyndall
@JISCMAIL.AC.UK] On Behalf Of Xiaoming Ren Sent: Friday, 4 April 2014 9:17 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Problem with making covalent bonds in phenix by LINK or edits file Dear all: I am encountering a problem. I built a monomer model which is a modified nucleotide with Sketcher in

Re: [ccp4bb] Problem with making covalent bonds in phenix by LINK or edits file

2014-04-03 Thread Nigel Moriarty
Xiaoming Can you send me the three residues in question (or the whole model) and the files you have so I can point you in the right direction. Cheers Nigel On Thu, Apr 3, 2014 at 1:17 PM, Xiaoming Ren wrote: > Dear all: > > I am encountering a problem. I built a monomer model which is a modif

[ccp4bb] Problem with making covalent bonds in phenix by LINK or edits file

2014-04-03 Thread Xiaoming Ren
Dear all: I am encountering a problem. I built a monomer model which is a modified nucleotide with Sketcher in ccp4 suite and generated the .cif file of this monomer. However, I could not make it bind with other nucleotides in the nucleic acid chain. I have tried to write LINK lines into PDB fi