VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Jan 05 2007 - 00:13:53 CST

Just an additional note, make sure to put it like this (or some
variation):

not (water and same residue as (x > 5) and (x < 10))

so you don't get fractional water molecules left over.

On Jan 4, 2007, at 4:38 PM, John Stone wrote:

>
> Hi,
> You can select a boxes, spheres, and other shapes with
> the position based selection operators such as:
> not (water and (x > 5) and (x < 10)))
>
> John
>
> On Thu, Jan 04, 2007 at 07:13:49PM -0300, Cesar Luis Avila wrote:
>> No. I have an equilibrated membrane/water/ions system which I want to
>> combine with an equilibrated protein/water/ion system. I do not
>> want to
>> lose all the water from both systems. So I want to make a hole to
>> accomodate the protein box. I know this may sound a little strange
>> but I
>> think it is the best way for my system.
>> Regards
>> Cesar
>>
>> nunolf_at_ci.uc.pt escribió:
>>> Hi Cesar
>>>
>>> Quoting Cesar Luis Avila <cavila_at_fbqf.unt.edu.ar>:
>>>
>>>> Dear all,
>>>> I would like to remove water molecules in a box. The number of
>>>> water
>>>> molecules is huge and they are spread among several segments which
>>>> may also contain ions. Does anyone have an efficient tcl script for
>>>> doing this under vmd /psfgen ?
>>>> Thanks in advance
>>>> Cesar
>>>>
>>>>
>>>
>>> Supposing that your box has protein+water+ions.
>>> On the VMD console, if you type:
>>>
>>> set sel [atomselect top protein]
>>> $sel writepdb only_protein.pdb
>>>
>>> You will get a pdb file with only protein atoms.
>>> Is this what you want?
>>>
>>> Cheers,
>>> Nuno
>>>
>>>
>>>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078