VMD-L Mailing List

From: Magnus Andersson (magnus.andersson_at_scilifelab.se)
Date: Fri Feb 15 2013 - 07:12:04 CST

Hi all,

I have tried to write a script that calculates residence times of a certain selection as per Alex Kohlmeyers suggestion earlier in the VMD mailiing list (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/7697.html). However, I'm stuck. Basically, I want to end up with an output of indices as a fuction of number of hits (present in the selection). Here's an excerpt from my script - note that curly brackets might not be paired and parameters not defined (since this is part of a bigger script). I basically need help with how to structure the script to get the output I want (indeces and how many times these indices occur)

# initialize an array (i.e. fill it with zeroes) - one entry for each atom in the system
set atom [atomselect top all]
set allres [$atom num]
for {set i 0} {$i < $allres} {incr i} {
  set hist($i) 0
}

# Build the required selection
set sel [atomselect top "name OH2 and same residue as within 10 of protein"]

# Create list of indices
set water [$sel list]

# Compare this list to the list of the previous frame (initialized to {} )
set restime 0
foreach object $water {

# If an index is new or present in the previous list increment the entry in the array: incr $hist($object)
# Else if an entry from the previous list is missing in the new the water has left
# so you store the info via: lappend restime $hist($object) in a list and reset the counter via. set hist($object) 0

if {$hist($object)==0} {
             incr $hist($object)
             lappend restime $hist($object)

                       } else {
              set hist($object) 0

               }

       }

#now with the list in $restime, you can build a histogram or compute the average. voila.

# write out indices & number of hits

puts $idf "[$hist] [$restime num]"

Cheers /

Magnus