Re: MDFF for huge trajectories

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed May 16 2012 - 16:36:41 CDT

The line should be:

set crosscoefficient [mdff ccc $sel0 -i pre2.situs -res 5] ;
puts "Cross Correlation Coefficient (CCC) = $crosscoefficient";

And this should probably go to the VMD mailing list...

On 16 May 2012 21:31, Samuel Flores <samuelfloresc_at_gmail.com> wrote:

> Hi Guys,
>
> I have a trajectory of the ribosome with 16S, 23S, two tRNAs, L5, and L1.
> I have a few hundred frames of this, in a .pdb formatted trajectory. I
> also have a few density maps that this trajectory needs to be compared
> against (trjectory should gradually fit into map). I am using this TCL
> script:
>
>
> package require mdff;
> for {set i 3} {$i < 102} {incr i } {
> set sel0 [atomselect 0 " chain V or chain Y or chain A or chain a or
> chain c or chain g " frame i ];
> mdff ccc $sel0 -i pre2.situs -res 5
> }
>
>
> I have two questions:
>
> 1. Isn't there a more efficient way to do this? It looks to me like it's
> loading the density map at every single frame. Surely the map could be
> loaded once and then referred to at each step $i?
> 2. How can I print out the cross-correlation coefficient? if I put the
> commands in through the TK console I get a printout, but if I run in
> batchmode (-dispdev text -e .. etc) then I try:
>
> package require mdff;
> puts "howdy!";
> # load starting from frame *** (default 0):
> mol new temp.pdb first 0 step 1 ;
> for {set i 3} {$i <= 102} {incr i } {set sel0 [atomselect 0 " chain V or
> chain Y or chain A or chain a or chain c or chain g " frame i ];
> set $crosscoefficient [mdff ccc $sel0 -i pre2.situs -res 5] ;
> puts "Cross Correlation Coefficient (CCC) = ", $crosscoefficient;
> }
>
> but while this appears to still be doing the ccc calculation, it doesn't
> output the answer as expected. That second puts command appears to be
> doing nothing, though the first puts command works as expected.
>
> Thanks
>
> Sam
>

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