VMD-L Mailing List

From: Cesar Millan (pachequin_at_gmail.com)
Date: Sun Jun 10 2007 - 22:09:27 CDT

Hi Axel, thanks for your response and sorry for not including more
information about my problem. I have some pdbs that are the transition from
state A to state B of a protein and I want to create a movie of the change
on the potential map along the transition. The electrostatic map was done
using apbs (command line program). I have a few pdbs called frame0.pdb to
frame20.pdb and each one have a dx potential map frame0.dx to frame20.dx.

I tried the untested option that you gave me, but the archives were loaded
as on a terminal, I have to modify the script to load them sequentially and
after I think that MultiMolAnim plugin could do the rest.

What do you think? Is this the less painful way to do this?

thanks for your help.

On 6/10/07, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
>
> On Sat, 9 Jun 2007, Cesar Millan wrote:
>
> hi cesar,
>
> CM> Hi everyone! I would like to use the animatepdbs.tcl to load multiple
> pdb
> CM> files with their corresponding dx potential map at the same time. Does
> any
> CM> one knows how to do this?
>
> yes. i would expect that is quite a few people out here,
> that know how to do this. however, with the information you
> provide, it is very difficult to help you, since you didn't
> tell us what you want to achieve.
>
> CM>
> CM> I was trying at the following manner but I got some errors:
>
> please tell us, what _were_ the error messages.
>
> there are a number of subtleties involved here:
>
> - the use of 'mol load' is now deprecated, you should
> use 'mol new', 'mol addfile' instead
>
> - from the perspective of VMD, coordinate frames and
> volumetric data sets are not correlated (yet).
>
> so if you want to do an animation of your system with the
> potential maps included (my guess), you have essentially
> two options. load everything into one (VMD) molecule and
> use a script like the one at:
>
> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part5.html#chap7_sect6
>
> or load every frame and density pair into a different molecule
> and try out the (new) MultiMolAnim plugin
> http://www.ks.uiuc.edu/Research/vmd/plugins/multimolanim/
>
> synchronize the visualization of all the molecules, you
> could use the CloneReps plugin:
> http://www.ks.uiuc.edu/Research/vmd/plugins/clonerep/
>
>
> to load all files you can try something like this (untested):
>
> set pdblist [lsort [glob -type f "my*.pdb"]]
> set dxlist [lsort [glob -type f "my*.dx"]]
>
> mol new [lindex $pdblist 0] type pdb waitfor all
> mol addfile [lindex $dxlist 0] type dx waitfor all
>
> for {set i 1} {$i <= [llength $pdblist]} {incr i} {
>
> mol new [lindex $pdblist $i] type pdb waitfor all
> mol addfile [lindex $dxlist $i] type dx waitfor all
>
> }
>
> in case you want to load everything into one (VMD) molecule,
> you can replace the second 'mol new' with 'mol addfile'.
> for more details, please check out the scripting section
> of the VMD user's guide and/or a good text book or (online)
> reference on TCL.
>
> please let us know, if this works and/or if you need more help.
>
> cheers,
> axel.
>
> CM> proc animatepdbs {start end fileformat fileformat2} {
> CM> set filename [format $fileformat [expr $start]]
> CM> set filedx [format $fileformat2 [expr $start]]
> CM> incr start
> CM> puts "Reading initial frame in PDB sequence $filename"
> CM> mol load pdb $filename -dx $filedx
> CM>
> CM> puts "Reading PDB files as an animation..."
> CM> for {set i $start} {$i <= $end} {incr i 1} {
> CM> set filename [format $fileformat [expr $i]]
> CM> set filedx [format $fileformat2 [expr $start]]
> CM> animate read pdb $filename -dx $filedx
> CM> }
> CM> }
> CM>
> CM> thank you for any help.
> CM>
> CM>
>
> --
> =======================================================================
> 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.
>
> 

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