VMD-L Mailing List

From: Andrew Dalke (dalke_at_dalkescientific.com)
Date: Wed Jun 02 2004 - 23:21:30 CDT

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