On 27/05/2023 03:46, Nicholas Clark wrote:
Paul,
Yes, it appears that the upper level group is "NON-POLYMER". However,
there is an alias at the bottom that does state polymer.
Hi Nick,
In Coot: Edit -> Restraints... -> CSO -> OK -> Change "Non-POLYMER" to
"peptide" and press enter in the entry, then "Apply"
Now you can refine your CSO in Coot.
Paul.
Best,
Nick Clark
On Fri, May 26, 2023 at 10:37 PM Paul Emsley
<pems...@mrc-lmb.cam.ac.uk> wrote:
On 27/05/2023 03:23, Nicholas Clark wrote:
Hey Paul,
I found the dictionary entry for CSO, it appears to be in the
"peptide" group (under CCP4-8.0->lib->data->monomers->c->CSO.cif):
"loop_
_chem_comp_alias.comp_id
_chem_comp_alias.group
_chem_comp_alias.atom_id
_chem_comp_alias.atom_id_standard
CSO *peptide* HN2 H2"
I've attached the file I have for your reference, as I may not
be looking in the correct place. Also, if I'm looking in the
wrong file location, please let me know.
Due to other priorities, Coot is not up to speed with the
developments of my colleagues:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10167671/
<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC10167671%2F&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7C1c2231bcf96a46de05d008db5e5b425c%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638207518308847137%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=YnWTARiMSbo8MRMK8ScjTOuVlwN4MQ6GXFag6iRdnxI%3D&reserved=0>
(Section 2)
What is the value of _chem_comp.group ? That is (for the moment)
what Coot cares about.
Paul.
--
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203
Cell: 716-830-1908
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