Re: [ccp4bb] AW: [ccp4bb] insertion code problem
Last time I checked pdbset doesn't renumber the LINK, CISPEP, SSBOND records at the same time (but maybe it was fixed). -- Ian On 26 June 2013 07:41, Francois Berenger beren...@riken.jp wrote: I think pdbset from CCP4 can renumber a PDB and hence get rid of the uggly insertion codes. On 06/26/2013 03:33 PM, herman.schreu...@sanofi.com wrote: Dear Rain, Insertion codes are still a sore point for many CCP4 programs and one of the reasons I prefer Buster over Refmac. Refmac5 does not remove insertion codes so I suspect the problem was with autoMR. The easiest is to superimpose your search model with insertion codes onto the pdb file which came out of the autoMR procedure. You could use lsqkab, but I think you can also do it in Coot. Then you continue refinement with this superimposed model. However, when I refined some structure with insertion codes in Refmac last week, Refmac created LINKR gap records for the inserted residues, cutting all peptide links. With an editor I had to change the gap to TRANS and then it worked. Good luck! Herman --**--** *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von *MAGGIE *Gesendet:* Mittwoch, 26. Juni 2013 04:07 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* [ccp4bb] insertion code problem Dear group, I have a insertion code question. I used molecular replacement (CCP4, autoMR) to solve two structures: one is monomer, and another one is tetramer. The model I used is one chain of a dimer and the model has insertion code. After molecular replacement and refinement using refmac5 in CCP4, the new structures lost the insertion code, and the residues were numbered consecutively. Can anyone tell me how to keep the insertion code in the new structures? Thank you, Rain
Re: [ccp4bb] AW: [ccp4bb] insertion code problem
Thank you, guys. My problem has been solved. AutoMR in CCP4 removed the insertion code. But I used it before, and it did not mess up with the insertion code at those times. Rain On Thu, Jun 27, 2013 at 12:56 PM, Ian Tickle ianj...@gmail.com wrote: Last time I checked pdbset doesn't renumber the LINK, CISPEP, SSBOND records at the same time (but maybe it was fixed). -- Ian On 26 June 2013 07:41, Francois Berenger beren...@riken.jp wrote: I think pdbset from CCP4 can renumber a PDB and hence get rid of the uggly insertion codes. On 06/26/2013 03:33 PM, herman.schreu...@sanofi.com wrote: Dear Rain, Insertion codes are still a sore point for many CCP4 programs and one of the reasons I prefer Buster over Refmac. Refmac5 does not remove insertion codes so I suspect the problem was with autoMR. The easiest is to superimpose your search model with insertion codes onto the pdb file which came out of the autoMR procedure. You could use lsqkab, but I think you can also do it in Coot. Then you continue refinement with this superimposed model. However, when I refined some structure with insertion codes in Refmac last week, Refmac created LINKR gap records for the inserted residues, cutting all peptide links. With an editor I had to change the gap to TRANS and then it worked. Good luck! Herman --**--** *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von *MAGGIE *Gesendet:* Mittwoch, 26. Juni 2013 04:07 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* [ccp4bb] insertion code problem Dear group, I have a insertion code question. I used molecular replacement (CCP4, autoMR) to solve two structures: one is monomer, and another one is tetramer. The model I used is one chain of a dimer and the model has insertion code. After molecular replacement and refinement using refmac5 in CCP4, the new structures lost the insertion code, and the residues were numbered consecutively. Can anyone tell me how to keep the insertion code in the new structures? Thank you, Rain
[ccp4bb] AW: [ccp4bb] insertion code problem
Dear Rain, Insertion codes are still a sore point for many CCP4 programs and one of the reasons I prefer Buster over Refmac. Refmac5 does not remove insertion codes so I suspect the problem was with autoMR. The easiest is to superimpose your search model with insertion codes onto the pdb file which came out of the autoMR procedure. You could use lsqkab, but I think you can also do it in Coot. Then you continue refinement with this superimposed model. However, when I refined some structure with insertion codes in Refmac last week, Refmac created LINKR gap records for the inserted residues, cutting all peptide links. With an editor I had to change the gap to TRANS and then it worked. Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von MAGGIE Gesendet: Mittwoch, 26. Juni 2013 04:07 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] insertion code problem Dear group, I have a insertion code question. I used molecular replacement (CCP4, autoMR) to solve two structures: one is monomer, and another one is tetramer. The model I used is one chain of a dimer and the model has insertion code. After molecular replacement and refinement using refmac5 in CCP4, the new structures lost the insertion code, and the residues were numbered consecutively. Can anyone tell me how to keep the insertion code in the new structures? Thank you, Rain
Re: [ccp4bb] AW: [ccp4bb] insertion code problem
I think pdbset from CCP4 can renumber a PDB and hence get rid of the uggly insertion codes. On 06/26/2013 03:33 PM, herman.schreu...@sanofi.com wrote: Dear Rain, Insertion codes are still a sore point for many CCP4 programs and one of the reasons I prefer Buster over Refmac. Refmac5 does not remove insertion codes so I suspect the problem was with autoMR. The easiest is to superimpose your search model with insertion codes onto the pdb file which came out of the autoMR procedure. You could use lsqkab, but I think you can also do it in Coot. Then you continue refinement with this superimposed model. However, when I refined some structure with insertion codes in Refmac last week, Refmac created LINKR gap records for the inserted residues, cutting all peptide links. With an editor I had to change the gap to TRANS and then it worked. Good luck! Herman *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von *MAGGIE *Gesendet:* Mittwoch, 26. Juni 2013 04:07 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* [ccp4bb] insertion code problem Dear group, I have a insertion code question. I used molecular replacement (CCP4, autoMR) to solve two structures: one is monomer, and another one is tetramer. The model I used is one chain of a dimer and the model has insertion code. After molecular replacement and refinement using refmac5 in CCP4, the new structures lost the insertion code, and the residues were numbered consecutively. Can anyone tell me how to keep the insertion code in the new structures? Thank you, Rain
[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] insertion code problem
Dear Francois, I also prefer not to use insertion codes. However, for certain protein families (serine proteases, antibodies), vast amounts of literature exist using amino acid numbering schemes with insertion codes. By creating a new numbering scheme without insertion codes, one would create a lot of confusion. Also, nowhere in the PDB definitions it is mentioned that insertion codes are not allowed or that amino acids should be numbered consecutively. It is only due to poor programming that programs are not able to handle insertion codes correctly. Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Francois Berenger Gesendet: Mittwoch, 26. Juni 2013 08:42 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] AW: [ccp4bb] insertion code problem I think pdbset from CCP4 can renumber a PDB and hence get rid of the uggly insertion codes. On 06/26/2013 03:33 PM, herman.schreu...@sanofi.com wrote: Dear Rain, Insertion codes are still a sore point for many CCP4 programs and one of the reasons I prefer Buster over Refmac. Refmac5 does not remove insertion codes so I suspect the problem was with autoMR. The easiest is to superimpose your search model with insertion codes onto the pdb file which came out of the autoMR procedure. You could use lsqkab, but I think you can also do it in Coot. Then you continue refinement with this superimposed model. However, when I refined some structure with insertion codes in Refmac last week, Refmac created LINKR gap records for the inserted residues, cutting all peptide links. With an editor I had to change the gap to TRANS and then it worked. Good luck! Herman *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von *MAGGIE *Gesendet:* Mittwoch, 26. Juni 2013 04:07 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* [ccp4bb] insertion code problem Dear group, I have a insertion code question. I used molecular replacement (CCP4, autoMR) to solve two structures: one is monomer, and another one is tetramer. The model I used is one chain of a dimer and the model has insertion code. After molecular replacement and refinement using refmac5 in CCP4, the new structures lost the insertion code, and the residues were numbered consecutively. Can anyone tell me how to keep the insertion code in the new structures? Thank you, Rain
