fix insufficient restraints to define hydrogen geometry

[keitaroyam]

During a test of gemmi, found several link restraints were insufficient to define hydrogen positions (as gemmi failed). Following links have been updated using Acedrg 269.

link	instruction	pdb
CYS-MPR	LINK: RES-NAME-1 CYS ATOM-NAME-1 SG RES-NAME-2 MPR ATOM-NAME-2 S3	3d1l
FOR_C-N	LINK: RES-NAME-1 FOR ATOM-NAME-1 C RES-NAME-2 ALA ATOM-NAME-2 N	1jlx
IVA_C-N	LINK: RES-NAME-1 IVA ATOM-NAME-1 C RES-NAME-2 ALA ATOM-NAME-2 N DELETE ATOM OXT 1	1apt
BOC_C-N	LINK: RES-NAME-1 BOC ATOM-NAME-1 C RES-NAME-2 ALA ATOM-NAME-2 N DELETE ATOM O3 1	7agb
NME_N-C	LINK: RES-NAME-1 ALA ATOM-NAME-1 C RES-NAME-2 NME ATOM-NAME-2 N DELETE ATOM OXT 1	4bea
ACYSNN	LINK: RES-NAME-1 ACY ATOM-NAME-1 CH3 RES-NAME-2 SNN ATOM-NAME-2 N1	7aby
ALASNN	LINK: RES-NAME-1 ALA ATOM-NAME-1 C RES-NAME-2 SNN ATOM-NAME-2 N3 DELETE ATOM OXT 1	6a56

ALASNN was renamed to pept-SNN. Regarding ACYSNN, I think ACE should be used instead of ACY, but it's already used in several PDB models.

[GaribMurshudov]

Good. It would be good to add a file of instructions. I need to check these and other links. All links need to be updated (perhaps not all, at least older ones)

[keitaroyam]

Thanks. I think overhaul of all links will be a separate PR.

[GaribMurshudov]

Would running refmac only be sufficient for tests? should I run servalcat and anlyse the results?

[keitaroyam]

I already tested them with servalcat. I thought they would be ok for Refmac (even with old ones), but it's good to check.

[GaribMurshudov]

Double checking is not bad idea. One of them already looked fine. At the moment I am only running refmac geometry idealisation with hydrogens in the output file. then I am trying to check them on coot to see if they look reasonable. I have done one of them now (MPR-CYS). I should finish the rest today.

[GaribMurshudov]

Do we need to add MBN-A2G? It is in 1jlx. Link betwen benzene ring and a sugar?

[keitaroyam]

I think we can have it. Just out of curiosity, any particular interest in this link (among many others we don't have)?

[GaribMurshudov]

I just saw that link in the pdb I tested

[keitaroyam]

I updated BFD, which had NH2 terminal (not NH3).

First replaced Be with C, used Acedrg, edited, and used Servalcat (without Refmac!) to update idealised structure. We used Be-O distance of 1.63 and Be-F of 1.54 A from Garib.

[GaribMurshudov]

I am trying to go over these links. With 1apt.pdb refmac had a problem. Link is defined between IVA and peptide in the monomer library. In the pdb file it was given between VAL and IVA. Order had a problem. Now refmac should be able to deal with this also. So far, new links look fine.

[GaribMurshudov]

I do not know if it is a problem but NME in 4bea has only two atoms. NME in our monomer library has hydrogne names HN1, HN2 on N. It is not consistent with other H atom names on peptides. But it should cause any problem (I hope)

[GaribMurshudov]

ACYSNN link loks fine. However, refmac again has an order problem. I need to fix this. This and other pdb files have many peptide like links. Are they going to be dealt with using aliase mechanism?

[GaribMurshudov]

6a56: is this pdb file correct entry for ALASNN? There many links to SNN but ALASNN does not seem to be one of them

[GaribMurshudov]

It seems that all links are fine (apart from ALASNN which i have not been able to test)

[keitaroyam]

ALASNN is surely in 6a56: atom1= A/ARG 64/C atom2= A/SNN 65/N3 (but it's not ALA, so I renamed it to pept-SNN)

[keitaroyam]

This and other pdb files have many peptide like links. Are they going to be dealt with using aliase mechanism?

Which pdb? At least in 7aby there is no monomer with alias.

[keitaroyam]

Checked these links with Acedrg 271, and found no significant differences. I think they are ok as they are.

[GaribMurshudov]

I think they look fine.