If you download a starting nucleotide from the PDB it will have the
chemical types attached.
And have you tried submitting the coordinate fragment to PRODRG? I
think it makes inspired guesses..
Eleanor
Garib Murshudov wrote:
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If there are element names on the columns 77-78 then refmac deals
with them otherwise
dictionary should be available and then refmac takes element name
from dictionary. If dictionary is not available
then it is tough. refmac tries to extract element name from atom
names (have you ever tried to do this. code becomes
very very very long if you want to have a general solution that does
not exist)
Garib
On 13 Jun 2006, at 19:09, [EMAIL PROTECTED] wrote:
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[EMAIL PROTECTED] wrote on 06/13/2006 11:54:45 AM:
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Hi,
I am looking desperately for a program that can generate proper
chemical element symbols (column 77-78) for nucleotides etc. (i.e.
those with funny atom names like AC2*). MOST WANTED: A program like
pdbset or pdbcur which reads a pdb and writes the processed pdb and
in addition "knows" all monomers in the monomer library.
Thanks a lot for your help,
Dirk
--
Doesn't Refmac's output have the elements in cols 77-78? You could
run a
mock refinement with 0 cycles of rigid body minimization or some
such...
Actually, you might try this script:
http://www.ccp4.ac.uk/dist/html/refmac5/usage/examples.html#exam3
If you set NCYC to zero, you shouldn't get any shifts in atomic
positions
or B factors, but you ought to get the output formatted as you want it.
- Matt
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