VMD-L Mailing List

From: Bernardo Sosa Padilla Araujo (bernardospa_at_gmail.com)
Date: Thu Dec 10 2009 - 18:48:20 CST

Thanks a lot for all the comments. That was really helpful. I'm gonna try
those commands.

2009/12/9 Andrew Dalke <dalke_at_dalkescientific.com>

> On Dec 9, 2009, at 11:30 PM, Bernardo Sosa Padilla Araujo wrote:
> > I was wondering if any of you had a script or at least any idea about how
> to write one, that can count the number of water molecules around a specific
> part of an enzyme.
> > Any suggestions would be greatly appreciated.
>
> In general you can do this on the interactive window using the 'atomselect'
> command
>
> http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.7/ug/node118.html
>
> For example,
>
> set sel [atomselect top "water within 5 of resid 28"]
>
> will find all the atoms in all the water molecules within 5A of residue 28
> and put the result into the variable "sel", which is the variable name I
> most often use because it's short for "selection'.
>
> You can then get information about how many atoms are in the selection like
> this:
>
> $sel num
>
> However, bear in mind that the selection includes hydrogens, if they are
> present in your waters. (Most structure files omit hydrogens, but not all.)
> If that happens then you'll want to restrict the selection to just the
> oxygens
>
> set sel [atomselect top "element O and water within 5 of resid 28"]
>
> Now, VMD knows that a residue is a water if the residue name is H2O, HHO,
> OHH, or HOH. This may not be true for all input structures. If you have
> something else then you'll have to know more about how your file defines
> what a water is.
>
>
> Also, your definition of "specific part" might not be a residue. You can
> select a single atom, or multiple residues, or anything in between by using
> a different atom selection than "resid 28". Or, your active site might be a
> region, like inside a bounded box, or within a certain distance of a point
> in space. For those you can construct queries based on the x, y, z
> coordinates of each atom.
>
> The easiest way to test out a selection is with the selection window. Once
> you've figured it out then you can use it in your script.
>
>
> Andrew
> dalke_at_dalkescientific.com
>
> (Felt like answering this one for old time's sake. I wrote the selection
> language in VMD a long time ago and I'm still rather proud about it.)
>
>
>