Difference between revisions of "Conserved Waters"

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(3 examples of how to find conserved waters)
 
m (→‎Finding Consereved Waters: (Fixed link to rasmol))
 
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If you have two similar or maybe identical structures, you may want to investigate which waters are conserved between the two PDB-files. There are a few options:
 
If you have two similar or maybe identical structures, you may want to investigate which waters are conserved between the two PDB-files. There are a few options:
# [[RasMol]]: Assuming the waters from one file are all in chain 'W' and those from the other file are in chain 'X', the following command writes the conserved waters to the file 'conserved.pdb':
+
# [[Rasmol]]: Assuming the waters from one file are all in chain 'W' and those from the other file are in chain 'X', the following command writes the conserved waters to the file 'conserved.pdb':
 
  select (water and *:W) and within (0.7, (water and *:X))
 
  select (water and *:W) and within (0.7, (water and *:X))
 
  write pdb conserved.pdb
 
  write pdb conserved.pdb

Latest revision as of 22:48, 2 July 2009

Finding Consereved Waters[edit | edit source]

(This is a summary from a posting on the CCP4 Bulleting Board, Sep. 2008)

If you have two similar or maybe identical structures, you may want to investigate which waters are conserved between the two PDB-files. There are a few options:

  1. Rasmol: Assuming the waters from one file are all in chain 'W' and those from the other file are in chain 'X', the following command writes the conserved waters to the file 'conserved.pdb':
select (water and *:W) and within (0.7, (water and *:X))
write pdb conserved.pdb

(Thanks to J. T. Kaiser)

  1. lsqman The linked section of the lsqman manual describes the same problem. (Thanks to G. Kleywegt)
  2. in case you are familiar with the program 'xp', commonly used in small molecule crystallography, you can also use the 'envi' command. (Thanks to G. M. Sheldrick)