[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 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 file, and also edited .edits file for phenix.refine. In both conditions, phenix.refine works except that it wouldn't add covalent bonds between the residues as I expected. I have used .edits file for covalent binding between residues before, and it worked well. So there must be something wrong with my input files. But I couldn't fighure out where the problem is. Thanks a lot and best regards! Xiaoming
Re: [ccp4bb] Problem with making covalent bonds in phenix by LINK or edits file
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 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 file, and > also edited .edits file for phenix.refine. In both conditions, > phenix.refine works except that it wouldn't add covalent bonds between the > residues as I expected. > > I have used .edits file for covalent binding between residues before, and > it worked well. > > So there must be something wrong with my input files. But I couldn't > fighure out where the problem is. > > Thanks a lot and best regards! > Xiaoming > -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov
Re: [ccp4bb] Problem with making covalent bonds in phenix by LINK or edits file
Dear Xiaoming, I would try using the graphical interface within phenix refine to add in the bond length/angle constraints for your link. This seemed to work fine with our system without actually needing a link record. J -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@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 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 file, and also edited .edits file for phenix.refine. In both conditions, phenix.refine works except that it wouldn't add covalent bonds between the residues as I expected. I have used .edits file for covalent binding between residues before, and it worked well. So there must be something wrong with my input files. But I couldn't fighure out where the problem is. Thanks a lot and best regards! Xiaoming
