VMD-L Mailing List

From: Andrew Dalke (dalke_at_ks.uiuc.edu)
Date: Fri Dec 20 1996 - 04:01:38 CST

Hello,

  I am leaving for vacation today, but I thought you all might be
interested in getting the most recent internal version of the VMD
binary. It has a few new features: a C-alpha trace and a (simplistic
but fast) solvent accessible surface, more rendering styles (including
VRML and POV 3) and a few more atom selection commands (selections of
the form 'asp38', 'cys3', etc.).

  Most the changes are internal. We fixed about a half-dozen core
dump level bugs, and a lot of smaller bugs that didn't meet the
documentation or didn't quite work (quoted selection commands in the
log files). The Tcl scripting language fits together much better now,
and more of the commands have at least somewhat helpful error
messages. For example, calling animate without parameters does:

vmd > animate

ERROR) animate styles
ERROR) animate style [once|rock|loop]
ERROR) animate dup [|frame <number>] <molecule id>
ERROR) animate [reverse|rev|forward|for|prev|next|pause]
ERROR) animate [speed|skip] [|<value>]
ERROR) animate delete all
ERROR) animate delete [|beg <num>] [|end <num>] [|skip <num>] <molecule id>
ERROR) animate [read|write|readdel] <file type> <filename>
ERROR) [|beg <num>] [|end <num>] [|skip <num>] <molecule id>

A few new commands were added to make it easier to generate animations
on the fly, as with 'animate dup ...'. Alas, the documentation has
yet to be updated.

  I have been working on the OpenGL port, and decided at the same time
that the VMD GUI should run under Tk. Not only will those make VMD
more portable, but by using Tk, it should be easy for you or others to
add new menus for whatever you want.

  There are a couple of minor bugs in this binary release (which is
one reason why I'm not yet releasing the full source): you can't pick
atoms of the solvent surface, the VRML lines have material properties,
and the alpha shape drawing method is compiled into the code.
Otherwise there is no reason to try out this code.

To get the binary:
  ftp ftp.ks.uiuc.edu
  cd /pub/group/dalke
  binary
  get vmd_IRIX5.Z
  quit
  uncompress vmd_IRIX5.Z
  chmod +x vmd_IRIX5

Go to where you installed vmd (/usr/local/lib/vmd/, by default)
  mv vmd_IRIX5 vmd_IRIX5.old
  mv /where/ever/it/was/vmd_IRIX5 .

And if there are any problems that weren't in the old version, just go
back to vmd_IRIX.old, and send us mail at vmd_at_ks.uiuc.edu describing
what happened.

  Consider this our holiday gift to you,

                                                Andrew
                                                dalke_at_ks.uiuc.edu
P.S.
  I will be on vacation and then at a conference until the middle of
Jan. If you have a question, post it to this list or to
vmd_at_ks.uiuc.edu and one of the other people here should be able to
answer it.

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