From: David Jiang (davidbjiang_at_gmail.com)
Date: Tue Jun 23 2009 - 14:02:48 CDT
Hi Peter,
I figured out what I was doing wrong. Thank you so much for your help. I
appreciate your patience.
David
On Tue, Jun 23, 2009 at 12:06 PM, Peter Freddolino <petefred_at_ks.uiuc.edu>wrote:
> Hi David,
> if I misunderstood your question, could you clarify it? The procedure
> that I gave you will (with a slight amendment; see below) load the same
> molecule twice (and thus give you two identical molecules), offset the
> coordinates of one of them, and then generate a psf/pdb that will
> simultaneously display both molecules. What else are you trying to do?
>
> # forgot to load psfs for the individual molecules the first time
> mol new myfile.psf
> mol addfile myfile.pdb
> mol new myfile.psf
> mol addfile myfile.pdb
> set sel [atomselect top all]
> $sel moveby {20 0 0 }
>
> (and then use the Merge Structures graphical interface as before)
>
> Peter
>
>
> David Jiang wrote:
> > Hi peter,
> >
> > Thanks for your help. I think you misunderstood my question. I was
> > wondering if there's a way I can create one psf/pdb file that will
> > display both the original molecule and the offset molecule. I appreciate
> > it.
> >
> > David
> >
> > On Tue, Jun 23, 2009 at 11:17 AM, Peter Freddolino <petefred_at_ks.uiuc.edu
> > <mailto:petefred_at_ks.uiuc.edu>> wrote:
> >
> > Hi David,
> > what you need to do is combine the two molecules after offsetting the
> > coordinates of one of them. So you could, for example, do the
> following
> > (using the command line):
> >
> > mol new myfile.pdb
> > mol new myfile.pdb
> > set sel [atomselect top all]
> > $sel moveby {20 0 0 }
> >
> > And then use the graphical interface to combine the two molecules,
> one
> > of which has been moved 20 angstroms along the x axis.
> >
> > Best,
> > Peter
> >
> > David Jiang wrote:
> > > Hi,
> > >
> > > Is there a way to combine two identical molecules with offset
> > > coordinates so that one psf file and one pdb file will display both
> > > molecules? I saw that there is a plug-in on VMD 1.8.7 Beta but it
> > > overlaps the two molecules. Is there a way to use this plug-in so
> that
> > > it is possible to show both molecules when combined. If not, how
> can I
> > > do this? Thank you for your help.
> > >
> > > David
> > >
> > > On Sat, Jun 20, 2009 at 12:21 PM, Joshua Adelman
> > <jadelman_at_berkeley.edu <mailto:jadelman_at_berkeley.edu>
> > > <mailto:jadelman_at_berkeley.edu <mailto:jadelman_at_berkeley.edu>>>
> wrote:
> > >
> > > Hi David,
> > >
> > > If both molecules have identical coordinates, then VMD won't
> > > separate them automatically. You can translate one of the
> > molecules
> > > a particular distance using the TCL command line. See:
> > >
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node183.html#14513
> > >
> > > While it is standard practice to solvate with a shape that
> > you can
> > > apply periodic boundary conditions to, I imagine that you
> > could use
> > > the solvate plugin and a little tcl scripting to create a
> sphere.
> > > What you'd want to do is to create a box around your protein
> > that is
> > > more than generous in size, such that it could contain the
> sphere
> > > that you want. Then you could select atoms that are within some
> > > distance (the radius of your sphere) from the center of the
> > box (or
> > > an atom that is approximately at the
> > > center), and write a new PDB just with those atoms.
> > Alternatively you could use the script supplied with the NAMD
> tutorial:
> > >
> >
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node26.html
> > >
> > > Best of luck.
> > >
> > > Josh
> > >
> > >
> > > On Jun 20, 2009, at 9:02 AM, David Jiang wrote:
> > >
> > >> Hi all,
> > >>
> > >> My name is David and I am a high school student interning at
> the
> > >> University of Houston. I'm trying to solvate two identical
> > >> molecules in a water sphere but I have been unsuccessful for a
> > >> number of reasons. I do not know how to make it so that VMD
> > >> doesn't overlap the two identical molecules and instead,
> allows
> > >> both molecules to be seen. In addition, is there a way to
> solvate
> > >> this two molecule structure in a water sphere using NAMD? I
> would
> > >> really appreciate any help and thank you all for your time.
> > >>
> > >> David
> > >>
> > >
> > >
> >
> ------------------------------------------------------------------------------------------------------
> > > Joshua L. Adelman
> > > Biophysics Graduate Group Lab: 510.643.2159
> > > 218 Wellman Hall Fax:
> 510.642.7428
> > > University of California, Berkeley
> > > http://nature.berkeley.edu/~jadelman
> > <http://nature.berkeley.edu/%7Ejadelman>
> > > <http://nature.berkeley.edu/%7Ejadelman>
> > > Berkeley, CA 94720 USA jadelman_at_berkeley.edu
> > <mailto:jadelman_at_berkeley.edu>
> > > <mailto:jadelman_at_berkeley.edu <mailto:jadelman_at_berkeley.edu>>
> > >
> >
> ------------------------------------------------------------------------------------------------------
> > >
> > >
> > >
> > >
> >
> >
>
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