Hello Eleanor,
We tried to follow your suggestion. The atoms to be linked were 1.46A apart in the input pdb model and we ran 10 cycles of refinement in Refmac with the "make link between" option chosen in either "defined in the file or residues are close". After the refinement we saw the linkage as dotted line and the distance between the atoms was 2.2A (in other words they moved apart instead of forming a covalent bond). Thanks in advance for any further suggestions, Pavel ---------- Původní e-mail ---------- Od: Eleanor Dodson <[email protected]> Komu: [email protected] Datum: 4. 11. 2019 12:16:38 Předmět: Re: [ccp4bb] why does Coot ignore CONECT? " What does refmac do if you feed it the coordinates with side chains close enough to bond? In some cases it makes a full link dictionary with bonds angles planes etc. But can coot read such a dictionary entry? On Mon, 4 Nov 2019 at 17:06, Pavel Mader <[email protected] (mailto:[email protected])> wrote: " Hi Paul, thank you for your answer. My problem is that I am building a cyclic peptide with non-standard amino acids, the side chains of which are linked by click chemistry... I know how to make modified amino acids that will make peptide bonds with their neighbors in the polypeptide chain, but I don't know how to make a covalent link between side chains of amino acids say No. 3 and 12 for example (of a 15 AA long chain). I was trying to solve the issue by making a CONECT record in the pdb file, but Coot ignored it. LINK "sort of" worked, but it was not possible to control the geometry (bond length and angles), often the real space refinement simply "explodes" probably in a attempt to avoid clashes. My current workaround is to make a cif file for the whole 15 AA long polypeptide (the bonds and angles now behave more or less as expected), but I don't consider this as a good general practice for building long polypeptide chains... Thanks in advance for any hints guiding me in the right direction. Pavel ---------- Původní e-mail ---------- Od: Paul Emsley <[email protected](mailto:[email protected]) > Komu: [email protected](mailto:[email protected]) Datum: 1. 11. 2019 21:16:11 Předmět: Re: [ccp4bb] why does Coot ignore CONECT? "On 01/11/2019 20:17, Pavel Mader wrote: > Hello, Hello. > > I have a question, can anyone explain, why does Coot not display a covalent bond manually specified by > CONECT line in a pdb file? Because I have never thought them necessary. Using SSBOND, LINK and residue dictionaries seemed to me to cover the bases for which CONECT would be used. Paul. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 (https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1) " ---------------------------------------------------------------------------- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 (https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1) " ---------------------------------------------------------------------------- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 (https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1) " ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
