Dear CCP4 Users,
Thank you very much for all suggestions. Special thanks to Oliver for
the ready-to-use files. Great job :) Hopefully it will solve my
problems...
Best wishes,
Rafal
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|Rafal Dolot, Ph.D.|
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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
Dear Rafal,
Acedrg could not handle with ligands containing metal elements at the
moment. When your input file was a mol file, acedrg gave that information.
For other kind of input format, acedrg should give the same information.
We are checking why it produced those confusing info.
The
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)
Hi,
as previously suggested you can use AceDRG to generate a cif file for your
ligand by input different type of files (SMILES, mmCIF, SDF/MOL, and SYBYL
MOL2 files).
You can use the AceDRG command line:
https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/acedrg/acedrg.html
or via ccp4i2,
Although it may not be apparent, there has been a lot of work going on
in Acedrg development regarding Boron.
One cannot say the same for Coot though and I can reproduce the
behaviour reported by Rafa Dolot. If/when I can fix it, it will be
available in 0.9.8.4.
Paul.
On 06/06/2022
Hi,
In case you don't have a cif file for the ligand, I would load the SMILES
expression into acedrg (or use any other input option) to create a cif file
which you can then read into Coot.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel
On Jun
Dear CCP4 Users,
I am working with data containing a possible complex of protein with
FESAN (iron bis(1,2-dicarbollide)). Unfortunately, to my knowledge, this
ligand is not available in PDB. The closest molecule is COSAN (cobalt
bis(1,2-dicarbollide)), which is labelled as CB5 and is
