Re: Writing out common waters from multiple files

[Raji Edayathumangalam]

Thanks a bunch.
Raji


Kumar, Abhinav wrote:

Raji,

Here is a perl script to do it.

The cut-off distance to flag two waters identical is set to 0.3. You can change 
it as you wish.

Also, water residues are named HOH.

Thanks Abhinav

-----Original Message-----
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Raji 
Edayathumangalam
Sent: Friday, January 19, 2007 11:17 AM
To: [EMAIL PROTECTED]
Subject: Writing out common waters from multiple files

Hi Everyone,

I think there might be a very simple way to do this but I don't know the easy way out.

I have superimposed one structure on top of another. Now, I am interested in only displaying the water molecules that are identical between the two structures. MolA has ~3000 waters and molB has ~900 waters. There are ~330 water molecules identical between the two structures.

I don't want to manually sit and delete 100s of lines or do something cumbersome like that, if I can be avoid it.

The water numbering is different between the two PDB files. Is there any easy way to write out the common waters?

Thanks for your suggestion.
Raji

--
Raji Edayathumangalam
Postdoctoral Fellow
The Rockefeller University
Box 224. 1230 York Avenue
New York, NY 10021