VMD-L Mailing List

From: Ludovic (ludomer_at_gmail.com)
Date: Wed Jun 12 2013 - 19:14:35 CDT

Hi everyone!

I'm trying to visualize the movement of atoms using a system with 8000
frames.
I'm using a Tcl script to load each frame (each in a single PDB file)
and make a screenshot with VMD.
The problem is that it stops at the 1000-ish frame giving me the error:
"couldn't read file XXX: too many open files"
(it works well if I use less than a 1000 frames)
(I'm using Ubuntu 10.4 64-bit and VMD 1.9.1)

You can find the script I was using at the end of this post (version 1).

I guess it's a memory problem so I tried modifying the script (version
2) so it is creating a molecule, adding to it the first 1000 frames,
make the screenshots then delete the molecule, creating a second
molecule, adding to it the next 1000 frames...
But it gives me the same error.

I also tried using the command "animate delete" at the end end of each
loop, but still the same error.
I really have no idea what to do. Maybe the problem is in the "readBF" part?

I'd be really glad if someone could help me on this...

I also have another question while I'm at it.
For the time being I'm using the user-field to save data for each atom,
so that, each frame, VMD checks if this value is higher than a value
"$thresh" for each atom and modify the color using a color scale.
What I would like (and couldn't manage) to do is, when an atom get a
higher value of $thresh, modify its color but keep this color for all
subsequent frames (and still modify its position).
I tried using "mol colupdate 1 top off" but it doesn't work, and the
colors go weird.
I can't use "mol drawframes" either since the position of the atoms will
not be updated.

If you have an idea of some kind...

Thank you very much!

Regards,
Ludovic Mercier

##########################################################
##########################################################
###
### VERSION 1
###

## Name:
## makeanimallpdbwBF.tcl
##

proc readBF { fname } {
   set all [atomselect top all]
   set in [open $fname r]
   set beta {}
   set numat 0
   while { [gets $in line] != -1 } {
     switch -- [string range $line 0 3] {
      ATOM -
       HETA {
         incr numat
         lappend beta [expr [string range $line 61 66]]
       }
      }
   }
   return $beta
}

#start is 1
#end is the total number of frames
proc makeanimallpdbwBF {start end fileformat thresh threshmax} {

   for {set i [expr $start]} {$i <= $end} {incr i 1} {
     set filename [format $fileformat [expr $i]]
     mol addfile $filename type pdb waitfor all
   }

   for {set i $start} {$i <= $end} {incr i 1} {
     set filename [format $fileformat [expr $i]]
     set all [atomselect top all frame [expr $i-1]]
     set beta [readBF $filename]
     $all set user $beta
     $all delete
   }

   mol modselect 0 top user < $thresh and not protein
   mol modcolor 0 top ColorID 2
   mol modstyle 0 top CPK 1.800000 0.300000 10.000000 2.000000
   mol modmaterial 0 top AOEdgy
   #mol showperiodic top 0 xyXY
   #mol numperiodic top 0 1
   mol addrep top

   mol modselect 1 top user >= $thresh
   mol modcolor 1 top user
   mol modstyle 1 top CPK 2.600000 0.300000 10.000000 2.000000
   mol modmaterial 1 top Opaque
   #mol showperiodic top 1 xyXY
   #mol numperiodic top 1 1
   mol addrep top

   mol modselect 2 top protein
   mol modcolor 2 top Name
   mol modstyle 2 top CPK 1.500000 1.2000000 10.000000 2.000000
   mol modmaterial 2 top BrushedMetal
   #mol showperiodic top 2 xyXY
   #mol numperiodic top 2 1
   mol addrep top

   mol selupdate 0 top on
   mol selupdate 1 top on
   mol selupdate 2 top on
   mol colupdate 0 top on
   mol colupdate 1 top on
   mol colupdate 2 top on

   #pbc set {41.259 41.259 41.259 90.0 90.0 90.0} -molid top -all
   #pbc box -centersel protein -center com -color magenta

   color scale method BGR
   color scale midpoint 0.2
   mol scaleminmax top 1 $thresh $threshmax

   scale by 1.6

   for {set i [expr $start]} {$i <= $end} {incr i 1} {

     animate goto [expr $i-1]
     set filename [format $fileformat [expr $i]]
     set filename $filename.rgb
     render snapshot $filename
   }
   #atomselect list
}

############################################
############################################
###
### VERSION 2
###

## Name:
## makeanimallpdbwBF.tcl
##

proc readBF { fname } {
   set all [atomselect top all]
   set in [open $fname r]
   set beta {}
   set numat 0
   while { [gets $in line] != -1 } {
     switch -- [string range $line 0 3] {
      ATOM -
       HETA {
         incr numat
         lappend beta [expr [string range $line 61 66]]
       }
      }
   }
   return $beta
}

proc makeanimallpdbwBF {start end fileformat thresh threshmax} {

   set filename [format $fileformat [expr $start]]
   mol new $filename type pdb waitfor all

   mol modselect 0 top user < $thresh and not protein
   mol modcolor 0 top ColorID 2
   mol modstyle 0 top CPK 1.800000 0.300000 10.000000 2.000000
   mol modmaterial 0 top AOEdgy

   mol addrep top
   mol modselect 1 top user >= $thresh
   mol modcolor 1 top user
   mol modstyle 1 top CPK 2.600000 0.300000 10.000000 2.000000
   mol modmaterial 1 top Opaque

   mol addrep top
   mol modselect 2 top protein
   mol modcolor 2 top Name
   mol modstyle 2 top CPK 1.500000 1.2000000 10.000000 2.000000
   mol modmaterial 2 top BrushedMetal

   color scale method BGR
   color scale midpoint 0.2
   mol scaleminmax top 1 $thresh $threshmax

   scale by 1.7

   for {set i $start} {$i <= 1000} {incr i 1} {

     set filename [format $fileformat [expr $i]]
     animate read pdb $filename
     set all [atomselect top all]
     set beta [readBF $filename]
     $all set user $beta

     set filename $filename.rgb
     render snapshot $filename

     $all delete
   }
   animate delete all top

   mol delete top

   set filename [format $fileformat 1001]
   mol new $filename type pdb waitfor all

   mol modselect 0 top user < $thresh and not protein
   mol modcolor 0 top ColorID 2
   mol modstyle 0 top CPK 1.800000 0.300000 10.000000 2.000000
   mol modmaterial 0 top AOEdgy

   mol addrep top
   mol modselect 1 top user >= $thresh
   mol modcolor 1 top user
   mol modstyle 1 top CPK 2.600000 0.300000 10.000000 2.000000
   mol modmaterial 1 top Opaque

   mol addrep top
   mol modselect 2 top protein
   mol modcolor 2 top Name
   mol modstyle 2 top CPK 1.500000 1.2000000 10.000000 2.000000
   mol modmaterial 2 top BrushedMetal

   color scale method BGR
   color scale midpoint 0.2
   mol scaleminmax top 1 $thresh $threshmax

   scale by 1.7

   for {set i 1001} {$i <= 2000} {incr i 1} {

     set filename [format $fileformat [expr $i]]
     animate read pdb $filename
     set all [atomselect top all]
     set beta [readBF $filename]
     $all set user $beta

     set filename $filename.rgb
     render snapshot $filename

     $all delete
   }
   animate delete all top

#atomselect list
#mol list
}