VMD-L Mailing List

From: Lubos Vrbka (shnek_at_tiscali.cz)
Date: Wed Dec 01 2004 - 09:25:53 CST

good afternoon to everybody,

i've used vmd for long time, but i've just started using it for more
than only display... i tried to find a solution to my problem described
below, but i didn't have luck :(

i want to do analysis of distribution of given species around the
protein in solution,e.g. i want to know how many hexanol molecules (HEX)
are located within 5A of protein. so i use
        resname HEX and within 5 of protein
(i tried another forms like (resname HEX) within 5 of protein, but these
didn't work for me). this works fine, however the result is based on the
frame that was displayed when this selection was entered... how can i
force vmd (can i?) to recalculate the selection for every frame?
interactively i click on "Apply" button in Graphical Representations
dialog...

vmd (correctly) displays only that parts of HEX residues that lie within
the limit. from this it seems to me that the selection is based on
atoms. i display the whole residues using
        same residue as (resname HEX and within 5 of protein)
so vmd displays all residues that at least partially fulfill the
distance constraint. however can i get somehow number of these residues?

how can i do this analysis for the whole trajectory? i.e. i need vmd to
print out to some text file nuber of residues satisfying the distance
limit for each frame.

i guess that this must have been asked and answered before... so any
hints or pointers to the relevant information are greatly acknowledged.

best regards, 

-- 
Lubos
_@_"