VMD-L Mailing List

From: Philipp Schoen1 (SCH_at_zurich.ibm.com)
Date: Tue Apr 17 2007 - 07:03:46 CDT

Dear Alex
thanks for your answer. I could perefctly usae your hints. However, there
is still some issue:
If I do something like set bin [atomselect top {2 <= x and x < 5}] I get
all the wanted atoms of the water molecules (tested by writepdb test.pdb).
But, if I chekc it by list $bin I see that the labeling (the integers of
the index) is not correct. E.g.
ATOM 9568 H2 TIP3 9250 4.264 10.733 -48.677 1.00 0.00 WT1
H
ATOM 9569 OH2 TIP3 5 3.668 10.176 13.191 1.00 0.00 WT2
O
ATOM 9570 H1 TIP3 5 3.224 10.545 12.387 1.00 0.00 WT2
H
ATOM 9571 H2 TIP3 5 3.092 10.473 13.913 1.00 0.00 WT2
H
The correct ones are index 9569, 9570 and 9571 (also shown in the test.pdb
file). Calling the list $bin command, however results in 9568, 9569 and
9570. That is, all indices are reduced by one. Is it a bug?

Gruezi Wohl!
Philipp