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MonomerLibrary / monomers

dictionary of monomers and links
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fix PJE-CYS and CYS-HEMB #15

Closed keitaroyam closed 1 year ago

keitaroyam commented 1 year ago

Original title: missing new_atom_id.

They are needed for gemmi, while Refmac seems to already take care of this kind of error. Anyway that was an error of the dictionary. Will need to test.

keitaroyam commented 1 year ago

Testing it, I found several problems with these links and fixed them.

PJE-CYS: PJEmod2 was insufficient and caused a "Unhandled topology of 2 hydrogens bonded to C21" problem in gemmi. So I updated this link using Acedrg 269:

LINK: RES-NAME-1 PJE ATOM-NAME-1 C20 RES-NAME-2 CYS ATOM-NAME-2 SG CHANGE BOND C20 C21 SINGLE 1

HEMmod2: it was deleting wrong plane (plan-10), which was now corrected to plan-8.

CYS-HEMC: added for completeness (CAC side version of CYS-HEMB). Created by replacing atoms

sed -e "s/CAB/CAC/; s/HAB/HAC/; s/CBB/CBC/; s/HBBA/HBCA/; s/HBB/HBC/; s/C3B/C3C/; s/C2B/C2C/; s/H33/H34/; s/plan-8/plan-10/; s/HEMmod2/HEMmod3/; s/CYS-HEMB/CYS-HEMC/" CYS-HEMB.cif

I used PDB 2amq and 2e84 for the test.

keitaroyam commented 1 year ago

HEMmod2 and HEMmod3 had unupdated angle restraints, as pointed out by Garib. Fixed.

GaribMurshudov commented 1 year ago

I think for PJEmod2 the following modifications (related to H4 of PJE) should be added. they were missing in my copy (I may have mixed up things again):

PJEmod2 change C22 C21 H4 108.416 1.50 PJEmod2 change C20 C21 H4 108.757 1.50

I have added in my local branch. I am worried that I may mix things up if i commit this.

keitaroyam commented 1 year ago

You can check changes in the "Files changed" tab above. There is

PJEmod2 change C20 C21 H4 108.891 1.50

but that for C22-C21-H4 is missing.

GaribMurshudov commented 1 year ago

This should be fixed by acedrg. Let us discuss this today. If we are to use acedrg for link generation it should do things properly.

keitaroyam commented 1 year ago

PJE-CYS has been updated using Acedrg 271, and PJEmod2 has changed. Also manually updated _chem_mod_tor of HEMmod2 and HEMmod3, where id and new_period were missing.

Note that gemmi has ignored _chem_mod_tor having no id or new_period. Now it's also fixed https://github.com/project-gemmi/gemmi/commit/ed72fc2d7597748b712995f1ccf883179dc97a92

GaribMurshudov commented 1 year ago

Good. You could merge them.