VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 03 2004 - 17:00:32 CDT

Hi guys,
  As Andrew helpfully pointed out, there's a way to get the list of
supported atom selection keywords. The built-in VMD $sel command help
is quite ambiguous however, and so its easy to misinterpret what the
intent of this help text is:
  get <attributes> {for parameter list, use 'atomselect list'

If you just type 'atomselect', you get a more understandable help
suggestion:
vmd > atomselect
usage: atomselect <command> [args...]

Creating an Atom Selection:
  <molId> <selection string> [frame <n>] -- creates an atom selection

(type the resulting atom selection to see a list of commands for it)

Dealing with Atom Selections:
  list -- lists atom selections previously created
  keywords -- keywords for selection's get/set commands
  symboltable
[....]

You get the idea.
So, the right command to get the keyword list is:
  atomselect keywords

This will list all of the valid atom selection keywords which
are the same you'd use with get/set.

If you want more detail, you can use this command to dump not only the
names of the keywords but what argument types they expect/return etc:
  atomselect symboltable
  
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 02, 2004 at 10:21:30PM -0600, Andrew Dalke wrote:
> Vani Krishna
> >is there a command to write the VDW radius of common
> >atoms like carbon/oxygen? some key word that can be
> >used with 'get' command?
>
> Should be able to say "get radius". Like this
>
> vmd > set sel [atomselect top "resid 100 and chain 1"]
> atomselect0
> vmd > $sel num
> 8
> vmd > $sel get radius
> 1.39999997616 1.5 1.5 1.29999995232 1.5 1.5 1.29999995232 1.39999997616
> vmd > $sel get {radius name}
> {1.39999997616 N} {1.5 CA} {1.5 C} {1.29999995232 O} {1.5 CB} {1.5 CG}
> {1.29999995232 OD1} {1.39999997616 ND2}
> vmd >
>
> Once upon a time you could ask for a list of all the property
> names that could be retrieved from an atom selection. There's
> a note about it still in the error message
>
> vmd > $sel count
> atomselection: improper method: count
> [num|list|molid|text|type|delete|global|frame|writepdb]
> get <attributes> {for parameter list, use 'atomselect list'
> set <attributes> <list in the same form as returned from get>
> getbonds
> setbonds <bondlists>
> frame <new frame value>
> [moveto|moveby] <3 vector>
> [lmoveto|lmoveby] <x> <y> <z>
> move <4x4 transforamtion matrix>
> writepdb <filename>
> vmd >
>
> But it doesn't seem to work any more
> vmd > atomselect list
> atomselect0
> vmd >
>
> Looks like it's a list of the available atom selections.
>
> (And btw, it's "transformation" not "transforamtion". Wonder
> if I did that typo. :)
>
> Andrew
> dalke_at_dalkescientific.com 

-- 
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