Re: [ccp4bb] isopeptide bond and shelx topology file
On 28/04/2023 08:41, StrBio wrote: CAUTION: This email originated from outside of the LMB. Do not click links or open attachments unless you recognize the sender and know the content is safe. *.-owner-ccp...@jiscmail.ac.uk-.* Hello, Can you suggest how to make isopeptide bond in coot and generate .cif file to refine the structure in phenix? Well, for the Coot part I would use Acedrg in Link mode: https://www.youtube.com/watch?v=p4oTJ0bjD3M (first part) https://journals.iucr.org/d/issues/2021/06/00/ir5021/index.html I image that there would be some interest in how useful you find that link description when refining using phenix. Also need suggestions to create shelxl topology file for non standard amino acids. If you build your Coot, coot-make-shelx-restraints converts cif dictionaries to shelx input. Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] isopeptide bond and shelx topology file
Hi Amit, If you are interested in generating restraints for SHELX then Grade2 supports this (apply the cosine rule like Jon suggests) and producing ‘dfix’ files for SHELXL (is this what you mean by a “shelxl” topology file)? The Grade Web Server: https://grade.globalphasing.org can be used for any non-confidential ligand. Please note that --shelx is an option that you must turn on. Hope this helps, Oliver P.S. a general tip for posting any question or softwate bug report anywhere is to never say “ALSO NEED” If you are asking for help ask one question at a time. This makes replying and following threads much easier. > On 29 Apr 2023, at 09:58, Jon Cooper > <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > > 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. jon.b.coo...@protonmail.com > > Sent from Proton Mail mobile > > > > Original Message > On 28 Apr 2023, 08:41, StrBio < biophysics.w...@gmail.com> 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=1 > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] isopeptide bond and shelx topology file
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. jon.b.coo...@protonmail.com 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=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
[ccp4bb] isopeptide bond and shelx topology file
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=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/
