Hi,
What is the proper way of generating 3-letter code for a new ligand? As of now,
I insert my ligand in Coot using smiles string and for the 3-letter code I
picked a non-existent code by trial and error (not very efficient). A cif file
with corresponding name which I generated using Phenix
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Hi Emilio,
for publication purposes you can get something similar to carving by
setting the map radius in Coot, creating a Raster3D output file and
adjusting front and back clip. Not perfect and difficult for fine
tuning, but it's a step in the right
I use your method - trial error..
It would be nice if at least there was a list somewhere of unassigned codes!
On 5 June 2015 at 09:16, Lau Sze Yi (SIgN) lau_sze...@immunol.a-star.edu.sg
wrote:
Hi,
What is the proper way of generating 3-letter code for a new ligand? As of
now, I insert my
Emilia:
It appears to me that based on discussion on the CCP4BB by Thomas Holder and
James Holton that you should do the following:
· Run MAPMASK twice, first on an asymmetric unit to normalize, and a
second time to extend the map over your molecule
· Issue the command
All:
Why the concern for unassigned three-letter codes? The wwPDB isn’t going to let
you assign a three-letter code, it will choose its own code.
At BMS (a pharmaceutical company), we do many hundreds of structures a year
with ligands and we assign the same, already assigned, three-letter code
