VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 29 2006 - 10:24:32 CST

Hi,
  You can swap out the selection text "all" that I gave in that example
for something like this (pick a rectangular sub-region):
  "x > 0 and x < 2 and y > -1 and y < 3 and z > 1 and z < 42"

Or, something like:
  "same residue as within 5 of (residue 0 to 5)"

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 29, 2006 at 05:18:30PM +0100, Naser, Md Abu wrote:
> Hi John,
>
> Thanks for our email. I want to select atoms from a particular region in the box and write them in atomlist.txt. My question was how to define the selection domain in vmd.
>
> With regards,
>
> Abu Naser
>
> School Of Life Sciences
> Heriot-Watt University
> Edinburgh EH14 4AS
> Email: mn2_at_hw.ac.uk
> Phone: +44(0)1314518265
> Fax : +44(0) 131 451 3009
>
>
>
>
>
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Wed 29/03/2006 4:48 PM
> To: Naser, Md Abu
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: script for cutting box
>
>
> Hi,
> I'm not entirely sure what you're looking for, but if you're just
> trying to create a file containing a list of atom indices, you can do
> that with:
> set sel [atomselect top "all"]
> set atomlist [$sel list]
> set f [open "atomlist.txt" w]
> puts $f $atomlist
> close $f
>
> Enjoy,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Mar 29, 2006 at 10:27:19AM +0100, Naser, Md Abu wrote:
> > Hi All,
> >
> > I have been wondering whether it is possible to make an atom index file using vmd. Can anyone give some idea of the selection criteria in vmd?
> >
> > With best regards,
> >
> > Abu Naser
> >
> > School Of Life Sciences
> > Heriot-Watt University
> > Edinburgh EH14 4AS
> > Email: mn2_at_hw.ac.uk
> > Phone: +44(0)1314518265
> > Fax : +44(0) 131 451 3009
> >
> >
> >
> >
> >
> >
> > -----Original Message-----
> > From: John Stone [mailto:johns_at_ks.uiuc.edu]
> > Sent: Thu 23/03/2006 5:45 PM
> > To: Naser, Md Abu
> > Cc: vmd_at_ks.uiuc.edu
> > Subject: Re: script for cutting box
> >
> >
> > Yes, that should be right, as VMD uses coordinates in Angstroms.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Thu, Mar 23, 2006 at 05:39:45PM -0000, Naser, Md Abu wrote:
> > > Thanks john. Its working now.
> > >
> > > One more question though. If I write :
> > > set xmin 0
> > > set xmax 100 , is the length in x direction 10 nm?
> > >
> > >
> > > With best regards,
> > >
> > > Abu Naser
> > >
> > > School Of Life Sciences
> > > Heriot-Watt University
> > > Edinburgh EH14 4AS
> > > Email: mn2_at_hw.ac.uk
> > > Phone: +44(0)1314518265
> > > Fax : +44(0) 131 451 3009
> > >
> > >
> > >
> > >
> > >
> > >
> > > -----Original Message-----
> > > From: John Stone [mailto:johns_at_ks.uiuc.edu]
> > > Sent: Thu 23/03/2006 2:52 PM
> > > To: Naser, Md Abu
> > > Subject: Re: script for cutting box
> > >
> > >
> > > The "same residue as" should be added to the atom selection text, not
> > > used as a separate command. If you still have trouble, show me the
> > > sequence of commands you're typing.
> > >
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > > On Thu, Mar 23, 2006 at 01:26:09PM -0000, Naser, Md Abu wrote:
> > > > Hi John,
> > > >
> > > > I having trying to use same residue as command and it giving me :
> > > >
> > > > invalid command name "same"
> > > >
> > > > Do I have to do anything before using this command?
> > > >
> > > > With regards,
> > > >
> > > > Abu Naser
> > > >
> > > > School Of Life Sciences
> > > > Heriot-Watt University
> > > > Edinburgh EH14 4AS
> > > > Email: mn2_at_hw.ac.uk
> > > > Phone: +44(0)1314518265
> > > > Fax : +44(0) 131 451 3009
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > -----Original Message-----
> > > > From: John Stone [mailto:johns_at_ks.uiuc.edu]
> > > > Sent: Wed 15/03/2006 9:35 PM
> > > > To: Naser, Md Abu
> > > > Cc: vmd_at_ks.uiuc.edu
> > > > Subject: Re: script for cutting box
> > > >
> > > >
> > > > Hi,
> > > > If you need to keep whole residues intact (including atoms outside the
> > > > box) you can see "same residue as ( ... )" around the examples I sent so
> > > > that whole residues are kept rather than just the atoms.
> > > >
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > > On Wed, Mar 15, 2006 at 08:59:20AM -0000, Naser, Md Abu wrote:
> > > > > Hi John Stone,
> > > > >
> > > > > Thanks you very much for your advise. I have been wondering these commands would keep the molecule intact, I dont want broken molecule inside the box.
> > > > >
> > > > >
> > > > > Regards,
> > > > >
> > > > > Abu Naser
> > > > >
> > > > > School Of Life Sciences
> > > > > Heriot-Watt University
> > > > > Edinburgh EH14 4AS
> > > > > Email: mn2_at_hw.ac.uk
> > > > > Phone: +44(0)1314518265
> > > > > Fax : +44(0) 131 451 3009
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > -----Original Message-----
> > > > > From: John Stone [mailto:johns_at_ks.uiuc.edu]
> > > > > Sent: Tue 14/03/2006 9:57 PM
> > > > > To: Naser, Md Abu
> > > > > Cc: vmd_at_ks.uiuc.edu
> > > > > Subject: Re: script for cutting box
> > > > >
> > > > >
> > > > > Hi,
> > > > > This should be a simple task actually.
> > > > > If you know the dimensions of your box with xmin/xmax ymin/ymax zmin/zmax,
> > > > > you can use a single VMD atom selection to chop off atoms outside the box:
> > > > > set xmin 0
> > > > > set xmax 100
> > > > > set ymin 0
> > > > > set ymax 100
> > > > > set zmin 0
> > > > > set zmax 100
> > > > > set sel [atomselect top "x >= $xmin and x <= $xmax and \
> > > > > y >= $ymin and y <= $ymax and \
> > > > > z >= $zmin and z <= $zmax"]
> > > > >
> > > > > $sel writepdb chopped.pdb
> > > > >
> > > > > Enjoy,
> > > > > John Stone
> > > > > vmd_at_ks.uiuc.edu
> > > > >
> > > > > On Tue, Mar 14, 2006 at 09:28:53AM -0000, Naser, Md Abu wrote:
> > > > > > Hi All vmd user,
> > > > > >
> > > > > > I have a big box of decane molecules with an appropiate density and wondering whether there is any script available so that
> > > > > > I can cut the box into a smaller size.
> > > > > >
> > > > > > With regards,
> > > > > >
> > > > > > Abu Naser
> > > > > >
> > > > > > School Of Life Sciences
> > > > > > Heriot-Watt University
> > > > > > Edinburgh EH14 4AS
> > > > > > Email: mn2_at_hw.ac.uk
> > > > > > Phone: +44(0)1314518265
> > > > > > Fax : +44(0) 131 451 3009
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > -----Original Message-----
> > > > > > From: John Stone [mailto:johns_at_ks.uiuc.edu]
> > > > > > Sent: Wed 01/03/2006 8:56 PM
> > > > > > To: Naser, Md Abu
> > > > > > Cc: vmd-l_at_ks.uiuc.edu
> > > > > > Subject: Re: vmd-l:
> > > > > >
> > > > > >
> > > > > > Hi,
> > > > > > Did you compile the plugins before building VMD?
> > > > > > http://www.ks.uiuc.edu/Research/vmd/doxygen/compiling.html#compiling
> > > > > >
> > > > > > John Stone
> > > > > > vmd_at_ks.uiuc.edu
> > > > > >
> > > > > > On Wed, Mar 01, 2006 at 08:17:10PM -0000, Naser, Md Abu wrote:
> > > > > > > Hi All,
> > > > > > >
> > > > > > > I have been trying to compile vmd from the source. I am having the following error message during compilation :
> > > > > > > Linking vmd_LINUX ...
> > > > > > > /usr/bin/ld: cannot find -lmolfile_plugin
> > > > > > > collect2: ld returned 1 exit status
> > > > > > > make: *** [vmd_LINUX] Error 1
> > > > > > >
> > > > > > > Can anyone give some clue to overcome this problem.
> > > > > > >
> > > > > > > Best regards,
> > > > > > >
> > > > > > >
> > > > > > > Abu Naser
> > > > > > >
> > > > > > > School Of Life Sciences
> > > > > > > Heriot-Watt University
> > > > > > > Edinburgh EH14 4AS
> > > > > > > Email: mn2_at_hw.ac.uk
> > > > > > > Phone: +44(0)1314518265
> > > > > > > Fax : +44(0) 131 451 3009
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > > > --
> > > > > > 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
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > > --
> > > > > 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
> > > > >
> > > > >
> > > > >
> > > >
> > > > --
> > > > 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
> > > >
> > > >
> > > >
> > >
> > > --
> > > 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
> > >
> > >
> > >
> >
> > --
> > 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
> >
> >
> >
>
> --
> 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
>
>
> 

-- 
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