VMD-L Mailing List

From: Philipp Schoen1 (SCH_at_zurich.ibm.com)
Date: Wed Apr 18 2007 - 11:55:03 CDT

Dear Users
I use 'set sel [atomselect top {water and same residue as {20 <= z}]' to
get a selection of water molecules in a certain domain. However, as you can
see this command selects also "parts" of the residue (here 5 and 15) only.
Any suggestions for a nice program to remove the partly loaded molecules or
to "weaken" the spatial restrictions?
I checked the mailing list but could find the hack for the H-bonds only

ATOM 1 OH2 TIP3W 5 7.316 20.975 20.297 1.00 0.00 WT2
ATOM 2 H2 TIP3W 5 6.932 20.103 20.509 1.00 0.00 WT2
ATOM 3 OH2 TIP3W 8 29.611 33.598 21.107 1.00 0.00 WT2
ATOM 4 H1 TIP3W 8 29.912 33.013 20.369 1.00 0.00 WT2
ATOM 5 H2 TIP3W 8 28.653 33.598 20.983 1.00 0.00 WT2
ATOM 6 H2 TIP3W 15 23.787 5.321 29.209 1.00 0.00 WT2
ATOM 7 OH2 TIP3W 17 20.392 9.414 22.948 1.00 0.00 WT2
ATOM 8 H1 TIP3W 17 19.854 9.886 22.277 1.00 0.00 WT2
ATOM 9 H2 TIP3W 17 20.383 8.504 22.591 1.00 0.00 WT2