Jan Abendroth wrote:
does anyone have any hints on how to real space refine cyclic peptides
with unusual amino acids in Coot? A good example are DNA-sliding clamp
proteins in complex with the cyclic peptide Griselimycin, eg. PDB code
6PTV.
In Coot I load the ligand description cif files for the unusual amino
acids.
Generated by Acedrg, I presume. This makes NZC-acedrg.cif:
$ acedrg -c coot-download/PDBe-NZC.cif -p -o NZC-acedrg
When I then real space refine with 't' i.e. the current and flanking
amino acids, the refinement blows up as if the peptide bond is not
known and coot wants to minimize the 'steric clash';
Yes.
though it realizes that these are adjacent residues, since shortcut
't' works.
You want "Sphere Refine" or the plus version.
When I specify 'make link' for the peptide bonds, the refinement is
the same, coot just draws a long line, see attached screenshot.
That is not the way, if you want to refine rather than just annotate the
model.
The tutorial on my blog is a good place to start
https://pemsley.github.io/coot/blog/2020/06/30/make-a-link.html
Also, see Rob Nicholls link paper which, I understand, has recently been
accepted (btw, I thought the referees did a particularly good job on
this manuscript - thanks, if that was you)
So, in most link cases, it's click, click, click, done. But not here.
There is a bug in Coot sadly, as this was an untested case. So run
acedrg like this:
$ echo LINK: RES-NAME-1 GLY ATOM-NAME-1 C RES-NAME-2 NZC ATOM-NAME-2
OG1 FILE-2 NZC-acedrg.cif DELETE ATOM OXT 1 >
acedrg-link-from-coot-GLY-NZC-link-instructions.txt
$ acedrg -L acedrg-link-from-coot-GLY-NZC-link-instructions.txt
Now edit AcedrgOut_link.cif
change "L-PEPTIDE LINKING" to "L-peptide"
change the _chem_link.group_comp_1 from . to peptide
change the _chem_link.group_comp_2 from . to peptide
Now read AcedrgOut_link.cif into Coot and you should be good to go.
This is a bit of a palaver, no doubt and my understanding is that the
changes needed in Acedrg for improved communication between in Acedrg
and Coot have been made and are making their way into CCP4 binaries.
Paul.
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