On Tue, May 6, 2014 at 4:19 PM, Eugene Yedvabny <eyedvabny.berkeley.edu> wrote:
> 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?
The second filter will act on the already filtered dataset, i.e. you
can only get to the 2nd filter if you pass the 1st one.
-Dan
>
> 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
>>
> _______________________________________________
> 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
Received on Tue May 06 2014 - 21:00:03 PDT
