To add CRYST and SCALE cards.
Run
pdbset xyzin cns.pdb xyzout cns+header.pdb
CELL ........ (a b c alpha beta gamma )
end
Fred. Vellieux wrote:
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On Wed, 20 Sep 2006, Robert Immormino wrote:
Fred,
In my experience there are two major places where CNS standard format
needs to be changed when switching to CCP4. As Anastassis points out,
the first is in the header. CNS format files don't necessarily have
the SCALE card or the CRYST1 card both of which will be needed by
CCP4.
An easy way to get this is to run Molecular replacment with Molrep
looking for 1 rotation and 1 translation peak. Molrep doesn't require
these headers.
The second is throughout the ATOM records, nucleic acids follow
different naming conventions, for ILE the delta carbon is either CD or
CD1, and the chain terminating carboylate also has a different name.
As for heterogens CCP4 tends to follow exactly the names in ligand
depot.
I hope this proves helpful,
-bob
Indeed it was the absence of CRYST1 and SCALE cards that caused the
problems.
The rest (naming conventions) I can sort out easily.
I must admit that reading this cryptic message (in red, with REFMAC in
bold) meant to me stop reading further and fix the problem.
Whereas the cause for the crash was probably within the log files
indicated further.
But since I had stopped reading and was trying to figure out what was
wrong... Looking for some refmac log files... Which I did not find...
Fred.
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