On 01/11/2023 18:02, Xuewu Zhang wrote:
Hi Paul,
Thanks so much for the quick response.
Using the cifs from the new CCPEM library did the trick. Cifs from
Phenix or an older version of CCP4 failed. I am not sure why (is there
a flag in the cifs to tell Coot whether the molecule is a polymer or
individual units?)
For others who may also face this issue: Cifs files from Phenix and
Coot use different atom names in the SGN and IDS units. The chain I
copied from 3IRI works with Phenix (after running phenix.ready_set and
phenix_reduce), but not with the Coot Cifs. 1HPN works with Coot
perfectly when the new CCPEM Cifs were imported. However, Phenix
doesn't recognize it, only it worked when the CCPEM cifs were included
in the inputs.
OK, I feel from that that the ball is not in my court.
Two related questions, can we (1) add disaccharide units to the
existing chain?;
Yes (long-hand) and no (quick and clever). My intention was that the
dehydration should occur upon real space refinement.
(2) Delete monomers from the existing chain (I tried it, Coot removed
the last monomer, but also the oxygen atom linking the last and the
second to the last unit, which should remain and become a OH group)?
"Delete Residue" only deletes atoms of the specified residue. It won't
delete the O4 (say) of the upstream residue.
What it also won't do is restore the O1 atom of the downstream residue -
I suspect that that is what you want and would be a useful features to have.
Ctrl-D is the hot-key for delete-residue btw.
Regards,
Paul.
On Wed, Nov 1, 2023 at 12:22 PM Paul Emsley
<pems...@mrc-lmb.cam.ac.uk> wrote:
On 01/11/2023 16:34, Xuewu Zhang wrote:
>
> Dear Paul,
> Can Coot handle heparin chains (not attached to protein) now? I was
> able to read a heparin chain in the PDB format, and import the cif
> restraints for the two sugar units (named IDS and SGN, from the
phenix
> monomer library; Coot would recognize the molecule without them).
> However, it appears that the bonds between the sugar units are not
> recognized by Coot, and the units were pushed apart whenever I
tried
> to do realspace refinement or regularize zone. I am not sure how to
> fix this, is there a way to tell Coot these units belong to a
polymer
> and should be linked together?
>
Dear Xuewu,
I used PDB code 1hpn as and example.
I used the monomer library that comes with CCP4 and Coot.
I selected one of the models (MODEL 1).
I chose regularize fragment.
Everything is connected as it should be and I could yank stuff
around [1].
How can I reproduce what you are seeing?
Regards,
Paul.
[1] this is the technical term.
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