From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Apr 28 2007 - 16:15:06 CDT

On Sat, 28 Apr 2007, Charles Cleveland wrote:

CC> I observe that 'pdb' does not show up in a search of the VMD 1.8.6

well, pdb should show up quite a few times. ;)

but 'pbc' is part of the pbctools plugin and those are
generally less strictly tied to the VMD version and
the documentation is currently only available online under:
http://www.ks.uiuc.edu/Research/vmd/plugins/

CC> manual. Where is one supposed to learn about the existence of such
CC> useful facilities? Perhaps there are others that should be publicized.

the are a number of issues with the plugins for VMD altogether and
their documentation in particular. the fact that VMD has these excellent
scripting capabilities make it easy to write plugins, but they tend
to be written in a less general fashion (people usually write what
solves _their_ problem). so we now have a large library of plugins
that have a sometimes inconsistent interface, are in different stages
of maintenance, and have different quality of documentation.

having the whole library consolidated and (frequent) redundancies
eliminated has been discussed amongst VMD developers a number of times.

in fact, olaf's latest version of the pbctools a very good example of
such consolidation as it combines multiple approaches and interfaces
to similar problems in a clean an maintainable fashion.

sadly, this is all a _lot_ of work, so every little effort from the
community of users would be highly welcome (it is my conviction that
real users generally are in the better position to write documentation,
as they know much better what is important in a package. a developer
usually considers what is complicated to implement...).

thank you for your understanding,
    axel.

CC>
CC> Olaf Lenz wrote:
CC> > -----BEGIN PGP SIGNED MESSAGE-----
CC> > Hash: RIPEMD160
CC> >
CC> > Hi!
CC> >
CC> > Jianhui Tian wrote:
CC> >
CC> >> I am simulating a box of water using periodic condition with constant NPT.
CC> >> Here I want to get all the residue LIST of molecules within "x" of resid
CC> >> "b"
CC> >> by using "[atomselect top "within x of resid b"] get resid". If this
CC> >> molecule with resid "b" is on the edge of the unitcell, whether the LIST
CC> >> will contain the molecules whose periodic images are within the
CC> >> distance. If
CC> >> not? How can I do this? Thanks a lot.
CC> >>
CC> >
CC> > Another simple approach would be to use the function "pbc wrap" like
CC> >
CC> > pbc wrap -center "resid b"
CC> >
CC> > to wrap all atoms into a box centered around resid b, and use your
CC> > expression afterwards to select the residues.
CC> >
CC> > Best regards
CC> >
CC> > Olaf
CC> > -----BEGIN PGP SIGNATURE-----
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CC> > Comment: Using GnuPG with SUSE - http://enigmail.mozdev.org
CC> >
CC> > iD8DBQFGM494tQ3riQ3oo/oRA+h8AJsHm0QsanBe34N141gg5GhSu1aPPACgh7p5
CC> > vqj/DBePKp7hMh75vGGUP+g=
CC> > =718h
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CC> >
CC> >
CC>
CC>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.