VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 05 2006 - 17:36:06 CDT

Hi,
  You can use the various atom selection commands such as
$sel move, $sel moveby, $sel lmoveby, etc... They are described
in the User's Guide here:
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.3/ug/node107.html

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 05, 2006 at 06:05:39PM -0400, xiaoqin huang wrote:
> Yes, that is good, I switch to 32-bit version of vmd-1.8.3, and now it can
> safely load membrane.
> the next question is to align the protein with membrane, is ther any good
> way to align them exactly by superimposing along X,Y,Z axes?
> in a tutorial saying "Hold down the shift-key to rotate them
> separately...". this is difficult to get a good alignment for the protein
> with the membrane.
>
> appreciate any good help!
>
> xiaoqin
>
> 04/05/2006
>
>
>
> >From: John Stone <johns_at_ks.uiuc.edu>
> >To: xiaoqin huang <xqhuang1018_at_msn.com>
> >CC: vmd-l_at_ks.uiuc.edu
> >Subject: Re: vmd-l: membrane loading
> >Date: Wed, 5 Apr 2006 14:32:38 -0500
> >
> >
> >Hi,
> > I believe this is caused by a dynamic loading problem with psfgen on
> >IRIX.
> >Can you try running the 32-bit version of VMD on your SGI and see if you
> >still
> >encounter the problem? This is a particularly odd problem that has
> >cropped up
> >as a result of a particular version of the SGI compilers used to build VMD.
> >Let me know if you still have this problem with the 32-bit version of VMD.
> >
> > John
> >
> >On Wed, Apr 05, 2006 at 03:25:12PM -0400, xiaoqin huang wrote:
> >> Can anyone help me to see what is the problem when loading membrane?
> >> I did it in ths way on Fuel workstation of SGI with IRIX64 system
> >>
> >-----------------------------------------------------------------------------------------
> >> #in the shell
> >> vmd
> >> # in vmd console
> >> package require membrane
> >> #comes out
> >> 1.0
> >> #command
> >> membrane -l POPC -x 60 -y 60
> >> #result in:
> >> the whole vmd process is killed, and all the windows disappeared,
> >produce a
> >> core
> >>
> >-----------------------------------------------------------------------------------------------------------------
> >>
> >> I installed vmd-1.8.4b11, and the membrane plugin should be ok as the
> >> membrane command works.
> >>
> >> thanks.
> >>
> >> xiaoqin
> >>
> >> 04/05/2006
> >>
> >
> >--
> >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