Hello Amit, without PRODRG I don't know of another way to make the SHELX dictionary restraints but it can be done by hand with a small-molecule structure to measure the bond lengths and 1-3 atom distances from. You can also use general values for the ideal bond lengths and angles and the cosine rule will give you the 1-3 distances, if things get really desperate. It would be worth looking at pdb2ins. I remember Ian Tickle wrote a program to make distance restraints for Restrain from a ligand pub file and I have a copy somewhere. The restrain dictionary was similar to the shelx one.
Best wishes, Jon Cooper. [email protected] Sent from Proton Mail mobile -------- Original Message -------- On 28 Apr 2023, 08:41, StrBio wrote: > Hello, > > Can you suggest how to make isopeptide bond in coot and generate .cif file to > refine the structure in phenix? > > Also need suggestions to create shelxl topology file for non standard amino > acids. > I used PRODGR before but seems like the sever is down last couple of months. > Any alternatives? > > Thank you > Amit > > --------------------------------------------------------------- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
