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sphereical cuttoff-water residues
#27669 06/17/11 07:33 PM
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prakash Offline OP
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I have 30 angs protein-solvent system and I want to extract s small cluster consists only protein, and water molecules of 3 angs from the surface of the protein.

while using this command,

define sol1 sele (segid PROA .around. 3.0 ) end

Although the command prints water molecules from 3 angs from surface of the protein, It has some of the water residues with only single atoms H1 , H2, OH2, and some of them prints double atoms "a) H1,H2 2)H1,OH2 3)H2,OH2 combinations.

How to avoid such "single and double atoms of water residues".
thank you

Re: sphereical cuttoff-water residues
prakash #27670 06/17/11 07:48 PM
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define sol1 sele .byres. ( type OH2 .and. ( segid PROA .around. 3.0 ) ) end

The above will select whole water molecules within 3 exclusively.


Rick Venable
computational chemist

Re: sphereical cuttoff-water residues
rmv #27671 06/17/11 08:03 PM
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The define command in itself does not print anything.
How do you define "water molecules of 3 angs from the surface of the protein"? Is it sufficient if one atom in a water molecule is within 3 of the protein surface? Should all three atoms be within 3, or perhaps is it the oxygen that is important?

define sol1 sele type oh2 .and. (.byres. ( segid PROA .around. 3.0 ) ) end
may give a slightly different result, but still valid.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: sphereical cuttoff-water residues
lennart #27672 06/17/11 09:48 PM
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If the SHOW option of SELECT is included, any command (incl. DEFINE) will print a list of selected atoms.

The first case gives whole molecules, based on OH2 atoms within 3 of the solute; the second case gives OH2 atoms only, based on any atom of the water molecule being within 3 of the solute. Both are valid selections, but clearly different, due to the scope of the .BYRES. operator.


Rick Venable
computational chemist

Re: sphereical cuttoff-water residues
rmv #27673 06/18/11 01:07 AM
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prakash Offline OP
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thank you very much,
after define command (yes, it does not print print anything) , to look the coordinates, I use "print coor sel sol1 end- command.


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