Hi Dan!
I've finally managed to obtain the Project.dat file and run the 'filter'
command. Thank you very much for help.
How to properly interpret the Project.dat file? Are they just a collection
of eigenvectors in each simulation frame?
And second question: are those structures in filtered.pc.nc comes from the
original trajectories? If so, can I somehow extract their numbers from the
trajectory?
Best regards,
Karolina
2018-07-20 16:23 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
> On Fri, Jul 20, 2018 at 10:20 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >>
> >> And if I finally get the "distribution of components" plot, how would I
> >> know, which conformation is represented by which part of the plot?
>
> This can be done using the 'filter' command and your 'projection'
> data. After reading in your trajectory and projection data:
>
> trajin MyTraj.nc
> readdata Project.dat
>
> the 'filter' command can be used to select regions of interest. Note
> that when reading the projections back in, the data set index will
> refer to the column (eigenvector 1 is in column 2):
>
> # Select regions between -30 to -25 for PC1 and 10 to 15 for PC2
> filter Project.dat:2 min -30 max -25 Project.dat:3 min 10 max 15
> trajout filtered.pc.nc
>
> -Dan
>
> >>
> >> Thanks for your help!
> >> Karolina Mitusińska
> >> PhD student
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 26 2018 - 06:30:03 PDT
