Hi Dan,
Wow, this command is amazing! Thank you so much for making my life an order
of magnitude easier!
My only remaining question is whether subsequent calls to filter are
stackable or resettable? For example:
dihedral d1 <args>
dihedral d2 <args>
filter d1 min max
<process actions>
filter d2 min max
<process other actions>
Will the second filter act on already filtered dataset, or will it reset to
filtering out the original dataset?
Thank you,
Eugene Yedvabny
On Tue, May 6, 2014 at 1:54 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> You can do this in cpptraj with the 'filter' command, which filters
> frames for subsequent actions based on given data sets and ranges. For
> example, say you only want to look at frames that fall within 0-90
> degrees for a certain dihedral:
>
> dihedral d1 <dihedral args>
> filter d1 min 0 max 90 out FilteredFrames.dat
> <more actions>
>
> In this case, only frames that are between 0 and 90 for dihedral d1
> will continue to be processed, otherwise all subsequent
> actions/trajectory output will be skipped. FilteredFrames.dat will
> contain a 1 for frames that were processed and 0 for frames that were
> filtered. Note that you can filter on multiple data sets (e.g. an
> angle and a distance etc). See the manual for more details.
>
> Hope this helps,
>
> -Dan
>
>
> On Tue, May 6, 2014 at 2:34 PM, Eugene Yedvabny <eyedvabny.berkeley.edu>
> wrote:
> > Hello Amber community,
> >
> > Is it possible in cpptraj to do processing on only a subset of mdcrd
> > frames, with that subset determined by the output of a previous command?
> > For example, I would like to load an mdcrd, calculate the phi or chi
> > dihedral and then perform secstruct and hbond analysis on a subset of
> > frames that fall within a certain dihedral range. Another option would be
> > to just create a new 'sub-trajectory' with frames that fit the dihedral
> > range, but per Amber manual I can only specify the start/end frames to
> > trajout, not an array of frame numbers.
> >
> > Presently I am doing such post-processing by printing out the entire
> series
> > data and then running the statistics in python, but that is proving to be
> > cumbersome and lacks the full information that gets printed out in the
> > summary files for the whole trajectory.
> >
> > Thank you,
> > Eugene Yedvabny
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue May 06 2014 - 15:30:03 PDT
