Refmacat/Gemmi cannot use 4TI restraints from AceDRG

[drlemmus]

The restraint file for 4TI (Titanium(IV) ion) isn't in the monomer library. When I make one with AceDRG, refmacat cannot use it, but a restraint file from Grade2 works fine.

[GaribMurshudov]

I do not think you acedrg for this. (acedrg will not work on this). It is just a single atom. Something like S.cif should be added.

It raises another question: We should add all single atoms to the monomer library. How should we deal with various ions? I do not think various ions should be in the monomer library. One single atom entry for each element should be sufficient. Charges should be in the pdb/mmcif file

[keitaroyam]

I tried Acedrg 277 from CCP4 8.0.017. It apparently failed (as expected)

Output dictionary file: AcedrgOut.cif
Output coordinate file: AcedrgOut.pdb
Number of atoms in the cif file  1
The input ligands/molecules contains metal or other heavier atoms 
Acedrg currently deals with ligands/molecules with following elements only 
As, B, Br, C, Cl, F, Ge, H, I, N, O, P, S, Si
Your molecule contains atoms of elements of the following type_symbol:
TI
The job finishes without the output cif file.
workMode is  11

but the output cif file was actually produced:

data_comp_list
loop
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
4TI     4TI     "TITANIUM ION"      NON-POLYMER      1     0     .   
data_comp_4TI
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
4TI     TI      TI      TI      4     0.000     0.000     0.000     
loop_
_pdbx_chem_comp_description_generator.comp_id
_pdbx_chem_comp_description_generator.program_name
_pdbx_chem_comp_description_generator.program_version
_pdbx_chem_comp_description_generator.descriptor
4TI   acedrg               277         "dictionary generator"                  
4TI   acedrg_database      12          "data source"                           
4TI refmac5              5.8.0425    "optimization tool"                     

This cif file is broken: '_' is missing after loop (line 2) and 'loop_' is missing (line 12). @flong-mrc could you look into this?

[drlemmus]

There are different residue names for different charges of the same atom (e.g. CU and CU1). If you want a single file for all versions this has to be mapped somehow. I think it is better to just follow the CCD here.

[GaribMurshudov]

Ok. Bu I think CCD needs to be changed, many unnecessary and repeated entries. @flong-mrc could you please fix this problem. It seems that intermediate file or something like this has wrong cif.

[keitaroyam]

OK, I will add missing single-atom entries into #44, and also fix some inconsistencies (for example, a Be atom is BE in the monomer library, but it's called 0BE in the CCD).

[flong-mrc]

Hi,

The bug in missing single-atom entries #44 [1] is fixed. Two things were changed. (1) The output information "The input ligands/molecules contains metal or other heavier atoms Acedrg currently deals with ligands/molecules with following elements only As, B, Br, C, Cl, F, Ge, H, I, N, O, P, S, Si" is taken out, as from version 280 or something, metal elements could be dealt with and the output cif contain some information on metal atoms. (2) the bug on the output single atom cif.

The version is updated already on LMB network (hex/hal/max). It should be CCP4 brz soon.

Thanks,

Fei

On 2024-03-09 12:07, keitaroyam wrote:

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OK, I will add missing single-atom entries into #44 [1], and also fix some inconsistencies (for example, a Be atom is BE in the monomer library, but it's called 0BE in the CCD).

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Links:

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[keitaroyam]

This has been fixed in the latest Acedrg (thank you @flong-mrc), and now the single-atom entries are available from master.