Hi Robbie, That works!
If I call one C-alpha "CA", I can use the standard TRANS definition in mon_lib_list.cif for the LINKR record. To restrain the other, I duplicated the TRANS section in this file and called it TRANS2. Then I replaced the appropriate CA entries with the name of my second C-alpha (CA2) and used the TRANS2 definition for the LINKR record for this peptide linkage. Thanks very much, Dave ------------------------------- Dr. David M. Lawson Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Fax: +44-(0)1603-450018 Email: [email protected]<mailto:[email protected]> From: Robbie Joosten [mailto:[email protected]] On Behalf Of Robbie Joosten Sent: 27 September 2017 17:04 To: david lawson (JIC) <[email protected]>; [email protected] Subject: RE: [ccp4bb] restraints for pseudo-amino acids within a peptide chain Hi David, You can copy the TRANS definition from the CCP4 dictionary and hack it to match your atom names. It's in a file called mon_lib_list.cif Cheers, Robbie Sent from my Windows 10 phone From: david lawson (JIC)<mailto:[email protected]> Sent: woensdag 27 september 2017 17:44 To: [email protected]<mailto:[email protected]> Subject: [ccp4bb] restraints for pseudo-amino acids within a peptide chain Hi All, I am having issues with getting pseudo-amino acids to behave in refmac such that they correctly form peptide bonds with standard residues before and after them. The problem I have is that when naming atoms forming the peptide bonds, there are effectively two C-alpha atoms, as shown below, where the pseudo-amino acid is contained within the square brackets: standard_aminoacid-[N-CA-some_stuff-CA-CO]-standard_aminoacid (both CA atoms have R groups, but I have not shown them) I have inserted the "L-peptide" line into the cif dictionary for the pseudo-amino acid, but in order to get the correct geometry, in particular the planarity of the peptide bond, the C-alpha atoms need to be called "CA", but I can only use that label once per residue. I did wonder whether it's possible to create some special TRANS definitions to use in LINKR lines in the pdb header, but I can't figure out how to do that. Any suggestions? Many thanks Dave Lawson ------------------------------- Dr. David M. Lawson Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Fax: +44-(0)1603-450018 Email: [email protected]<mailto:[email protected]>
