On 8/23/24 11:35 AM, Kelvin Lau wrote:
Hello
Hello Kelvin.
Here we go at last...
With Coot 0.9.8.94 EL or Coot 1.1.08, I am wondering if this is a known issue
or not.
I have generated ligand restraints with the GRADE2 server. I named it RU4SE
With no issues I can import the CIF and generate my ligand using this file
within Coot using Get Monomer, even though its a 5-letter code.
So far so good - that is the expected behaviour.
However, when I refine in phenix, I noticed it says my ligand within the PDB is
now called RU4.
Yes. Writing a 5-letter ligand to a PDB file will truncate the name to
3-chars.
I double checked within Coot and the imported ligand is RU4SE. However the
moment I save, it becomes RU4
Is this a known issue? Easy solution?
It is indeed a know issue and the solution (from your point of view) is
to use mmCIF as the output format for your molecule.
From my point of view, actually getting Coot is write a modern mmCIF
file is tricky (somewhere between a week and 10 months work). You can of
course use the current mmCIF output style but that is long in the tooth
and not well tested.
Paul.
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