[ccp4bb] Postdoctoral position in Manchester

[Harshwardhan Poddar]

Hi everyone,
There is a PostDoc position available in the laboratory of Prof Nigel Scrutton 
based at Manchester Institute of Biotechnology. This is an exciting opportunity 
to characterise some newly discovered light-sensitive proteins using 
time-resolved structural techniques. 
More details can be found here-
Research Associate in Structural Biology : Manchester Institute of 
Biotechnology (MIB) 
  
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Research Associate in Structural Biology : Manchester Institute of 
Biotechnology (MIB)
 

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Best
Harshwardhan 



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Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Oliver Smart]

Dear Rafal,

Apologies my email client rather scrambled the text from my previous message, 
so I will send again here

Please find attached (in the previous message!) a restraint CIF file and a 
corresponding PDB file for your FESAN ligand.

Details:

Your ligand FESAN is a difficult test case for all restraint generation and 
refinement programs. It combines two carborane groups with a charged iron atom. 
Carborane groups have unusual chemistry that does not conform to normal valence 
models (they have carbon atoms bonded to six other atoms). Combining these 
groups with an iron atom that is bonded to 12 other atoms makes things even 
more complicated. Starting from a SMILES string is not wise for such a molecule.

Fortunately, such chemistry can be handled by the Grade2 restraint generator, 
that is supplied with BUSTER:

https://gphl.gitlab.io/grade2_docs/ 
Starting from the PDB file you supplied I converted to MOL2 format using CSD 
Mercury. Grade2 can read the MOL2 file and produce restraints (despite RDKit 
not being able to handle carboranes). All bond restraints are based on Mogul 
searches of CSD small molecule structures.

I manually edited the restraint CIF because there were too many bond angles to 
be useful. In the carborane cluster, each non-hydrogen atom is bonded to 5 
others to form an icosahedral shell, so that the bond length restraints alone 
are sufficient to fully define the geometry since all angles are implied. 
Additional bond angle restraints both within the cluster and for the 
12-coordinated FE atom are unnecessary and likely to be counter-productive.

It appears from CSD entries that FESAN is a cation carrying an overall charge 
of +1. But I did not correct this.

Please note that the atom names are slightly different from your PDB file as 
the FE atom has an uppercase atom name.

Unfortunately, the current CCP4 distribution of Coot 0.8.9.2-pre EL (revision 
count 7766) cannot cope this molecule as 'Send in the bond angels! Ahem I mean 
"Regularize Zone (Click two atoms)' produces a lock-up using all the CPU that 
has to be terminated by a kill. But you should be able to do a manual fit in 
Coot. BUSTER has no difficulty refining a structure with such restraints, as 
shown in this test using PDB entry 3I8W with FESAN replacing the CB5 ligand:

(Picture attached to previous message)
I hope that the restraint dictionary works for you.

All the best,

Oliver Smart, Andrew Sharff for BUSTER Developers.


> On 7 Jun 2022, at 08:35, Rafal Dolot  wrote:
> 
> Dear all,
> 
> Thank you very much for all your messages. Unfortunately, I'm still on the 
> same place, as yesterday...
> 
> First of all, I prepared a pdb/cif file of the ligand based on CCDC entry 
> 1176355 containing FESAN molecule. Also, I prepared SMILES file based on 
> SMILES of CB5 ligand (COSAN) available on PDB, where I simply switched Co 
> into Fe atom.
> 
> -> When I tried use acedrg with SMILES, I received an error info:
> 
> Input file: FSM.smi
> Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.cif
> Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.pdb
> workMode :  12
> Can not generate a molecule from the input SMILES string!
> Check your SMILES or report the bug
> Can not get the element symbols of atoms. Check input file format
> Error : The job stops because of errors
> 
> -> When I tried use acedrg with *pdb/*cif files I received no output files:
> 
> Input file: fsm.cif
> Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.cif
> Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.pdb
> workMode :  11
> Number of atoms in the cif file  0
> 
> -> When I tried use acedrg with *.mol file I received no output files:
> 
> Input file: fsm.mol
> Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.cif
> Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.pdb
> workMode :  13
> The system contains atoms of the following elements
> C B   Fe  H
> The input ligands/molecules contains metal or other heavier atoms
> Acedrg currently deals with ligands/molecules with following elements only
> C, N, O, S, P, B, F, Cl, Br, I, H
> The job finishes succesfully
> 
> 
> -> When I tried use prodrg, the program has been crashed:
> 
> The program run with command: cprodrg XYZIN 
> "C:/data_cryst/hsa_fesan_04/fsm.pdb" LIBOUT 
> "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.cif" XYZOUT 
> "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.pdb" MOLOUT 
> "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.mol"
> has failed with error message
> forrtl: severe (157): Program Exception - access violation
> Image  PCRoutineLineSource
> cprodrg.exe7FF623CB058F  Unknown   Unknown  Unknown
> cprodrg.exe7FF623CB05E0  Unknown   Unknown  Unknown
> cprodrg.exe7FF623CAFB4F  Unknown   Unknown  Unknown
>