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[FEATURE REQUEST] initial data_comp_list section in ChemComp output #269
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Dear all,
On Wed, Jun 14, 2023 at 08:18:20AM -0700, rimmartin wrote:
Buster is asking for more to run with our cif
```
data_comp_list
```
Busrer error message without the comp_list
```
[E003] First block in file is comp_CLR not comp_list
```
The mmCIF restraints file are less well defined (compared to
PDBx/mmCIF files) and we therefore work on the assumptions that files
from the main restraint generators atm (Grade/Grade2, AceDrg, eLBOW)
have a similar structure. So far, they all had a data_comp_list
datablock at the top - and BUSTER checks for that to ensure the file
given is not "something else".
Other refinement programs might have less stringent checks, but I'd
highly recommend trying to stick with the structure/format of existing
restraint dictionary files as much as possible: we are lucky to
(currently) have very good interchangeability between very different
refinement programs /even/ allowing for the fact that those files are
poorly documented in mmCIF dictionaries. Let's try and avoid any
divergence if at all possible - even if allowed by the mmCIF format.
For CLR we have
(1) $CCP4/lib/data/monomers/c/CLR.cif
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
CLR CLR CHOLESTEROL NON-POLYMER 74 28 .
#
data_comp_CLR
...
(2) Grade2
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
_chem_comp.type
CLR CLR CHOLESTEROL NON-POLYMER 74 28 . NON-POLYMER
#
data_comp_CLR
...
Cheers
Clemens
|
I don't know what's the minimal content of the comp_list block that will satisfy all programs. Perhaps 2-3 lines would do, for example:
_chem_comp.group is used for finding links that can be automatically applied to the residue (for example, if it's L-peptide, CIS and TRANS links can be applied). |
If I write minimally:
at the top of the cif, buster will run with it; Grade2 style |
Hi
We have made a chemcomp style cif via
gemmi::make_chemcomp_with_restraints
,gemmi::add_chemcomp_to_block
andgemmi::cif::write_cif_block_to_stream
which restrains a phenix run.Buster is asking for more to run with our cif
Busrer error message without the comp_list
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