VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_vitae.cmm.upenn.edu)
Date: Fri Nov 18 2005 - 08:54:02 CST
- Next message: John Stone: "Re: STRIDE doesnt recognize unusual protein residue"
- Previous message: andrea spitaleri: "Re: calculate rmsd in a loop:feedback [sorry if you get it twice]"
- In reply to: andrea spitaleri: "Re: calculate rmsd in a loop:feedback [sorry if you get it twice]"
- Next in thread: andrea spitaleri: "Re: calculate rmsd in a loop:feedback [sorry if you get it twice]"
- Reply: andrea spitaleri: "Re: calculate rmsd in a loop:feedback [sorry if you get it twice]"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
On Fri, 18 Nov 2005, andrea spitaleri wrote:
hi,
sorry to beat a dead horse one more time, but even
though the script may now work for you, there is a
way to improve the script, which makes no assumptions
about the molecule ids and selections etc. and puts
the some of the 'expensive' operations outside the
measurement loop by using arrays for molecule
ids and selections. note that the mol load command
returns the (unique) mol id that vmd assigns to
a molecule.
please consider the following variation of the script
(untested, but you should get the general idea).
# set up molecules and selections
set nrmols 100
for {set i 1} {$i < $nrmols} {incr i} {
set mid($i) [mol load pdb "pro_$i.pdb" waitfor all]
set sel($i) [atomselect $mid($i) "protein and backbone"]
set lig($i) [atomselect $mid($i) "segid B"]
set all($i) [atomselect $mid($i) "all"]
}
# now loop and compare
for {set i 1} {$i < $nrmols} {incr i} {
for {set j [expr $i +1]} {$j < $nrmols} {incr j} {
$all($i) move [measure fit $sel($j) $sel($i)]
set rmsd [measure rmsd $lig($j) $lig($i)]
puts "RMSD of $i and $j is $rmsd"
puts $outfile "RMSD of $i and $j is $rmsd"
}
}
# clean up
for {set i 1} {$i < $nrmols} {incr i} {
set sel($i) delete
set lig($i) delete
set all($i) delete
mol delete mid($i)
}
ciao,
axel.
[...]
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
- Next message: John Stone: "Re: STRIDE doesnt recognize unusual protein residue"
- Previous message: andrea spitaleri: "Re: calculate rmsd in a loop:feedback [sorry if you get it twice]"
- In reply to: andrea spitaleri: "Re: calculate rmsd in a loop:feedback [sorry if you get it twice]"
- Next in thread: andrea spitaleri: "Re: calculate rmsd in a loop:feedback [sorry if you get it twice]"
- Reply: andrea spitaleri: "Re: calculate rmsd in a loop:feedback [sorry if you get it twice]"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]