Re: [ccp4bb] LSQKAB

[Paul Emsley]

On 30/12/13 04:10, Doeke Hekstra wrote:

Hi All,

I would like to superimpose a query chain (moving frame) from a rather large 
PDB file (~50 chains) to a target frame specified by a chain in a reference PDB 
file.

  echo FIT RESIDUE CA 2 TO 63 CHAIN $CHAIN  lsqkab.conf
  echo MATCH RESIDUE CA 2 TO 63 CHAIN A  lsqkab.conf
  echo OUTPUT XYZ  lsqkab.conf
  echo end  lsqkab.conf
  lsqkab XYZINM ${f} XYZINF 1AHO.pdb XYZout ${fileout} lsqkab.conf

Rotates/translates all chains in the moving frame to the target frame and 
outputs all of them up to 40,000 atom records. Would it be possible to output 
only the chain of interest (preferred) OR to output all atom records?



This doesn't answer your question, but if you have Coot you can use the 
attached script as a work-around (you will have to do some editing).


Paul.



(let ((imol-1 (read-pdb reference.pdb))
  (imol-2 (read-pdb moving.pdb))
  (c-ids (list A B C ))) ;; or perhaps (chain-ids imol-2)
  
  (for-each (lambda (chain-id)
	  (let ((imol-moving-copy (copy-molecule imol-2)))
		(clear-lsq-matches)
		(add-lsq-match 2 63 A 2 63 chain-id 0)
		(apply-lsq-matches imol-1 imol-moving-copy)
		(let*  ((selection (string-append // chain-id))
			(frag-mol (new-molecule-by-atom-selection imol-moving-copy selection))
			(frag-mol-file-name (string-append fragment- chain-id .pdb)))
			   
		  (write-pdb-file frag-mol frag-mol-file-name
	c-ids))

Re: [ccp4bb] structural homologs as cross seeds

[Patrick Shaw Stewart]

There are many examples where cross-seeding with homologous proteins has
worked, both in classical and recent work.  You should add seed-stocks from
any crystals with significant homology to your routine screening
experiments in the first place.

The important thing is to use *random *screens at first.  This has the
effect of giving you new leads and also optimizing the ones that you have
(plus you can control the number of crystals per drop).

See http://hamptonresearch.com/documents/ramc/RAMC2011_T11_Obmolova.pdf
(Omolova and colleagues have examples where complexes were seeded with
crystals of one of the components and vice versa.)

The excellent review by Stura and co covers most of the theoretical points.
 (1999). Epitaxial jumps. *J. crystal growth*, *196*(2), 250-260.

For practical details see the original paper by D'Arcy (Acta Cryst D:
63.4 (2007):
550-554) and also our paper Random microseeding: a theoretical and
practical exploration   *Crystal Growth  Design* 11.8 (2011):
3432-3441.

also http://www.douglas.co.uk/MMS_proc.htm

Acoot, this is also the approach to use with your cubic crystals.  Don't
think about it too much, just try it!

The only thing that I can't explain is why this random seeding method,
including cross-seeding, is not more well-known.

Hope it works

Patrick



On 27 December 2013 21:03, Mark van Raaij mjvanra...@cnb.csic.es wrote:

 the differences are likely to be on the protein surface, and these would
 make the crystal contacts, i.e. it would be unlikely the protein could
 crystallise in the same crystal habit.
 Never say never in crystallisation (i.e. try anything), but I would go for
 other things first like additives, different crystallisation techniques,
 temperatures, concentrations etc.

 On 27 Dec 2013, at 20:29, Mahesh Lingaraju wrote:

  Dear all,
 
  I was wondering if it sounds logical to use the crystals from a possible
 structural homolog as seeds to induce nucleation ? (in terms of overall
 sequence, the proteins are considerably different but based on sequence
 alignment and structures from other related proteins, it is highly likely
 the protein would have the same structure.)
 
  Please comment if any of you had experience with this.
 
  Thank you
 
  Happy holidays :)
 
  Mahesh




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