VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Mar 25 2011 - 13:04:44 CDT

fred,

rather than overloading the coordinate writing code with many
options to select and write out frames, i would suggest a
different strategy.

load the file(s) you want to read in full. then selectively _delete_
the frames that you don't want to save and then write it out in one go.
the deleting can be easily scripted, if you are careful to delete "backwards"
(i.e. from large frame numbers to small ones), it should be easy to
write a logic that compacts a data set from the frame numbers that
you want to keep.

cheers,
    axel.

On Fri, Mar 25, 2011 at 1:22 PM, Phelan Jr., Frederick R. Dr.
<frederick.phelan_at_nist.gov> wrote:
> I have a LAMMPS trajectory file that I would like to save individual frames
> from at various points in time, so I can then read them all back in
> eventually as a sequential overlay (the trajectory is for an individual
> molecule).
>
>
>
> The manual says:
>
> Saving Trajectory Frames
>
> Using the Save Coordinates... menu item, you can write trajectory frames to
> a file in one of several file formats including PDB, DCD, Amber CRD, etc.
> This feature may be used to write out a new trajectory in a single file
> after assembling many frames from different sources (such as PDB CRD, DCD or
> Gromacs files, or even from a remote simulation). You can also use this, in
> combination with the molecule file browser as a way to make PDB files from a
> DCD/CRD trajectory.
>
>
>
> However, the File > Save Coordinates … menu option is always grayed out when
> you read in a trajectory file.
>
>
>
> Is there a reason I am getting this options grayed out … is there a
> scripting workaround?
>
>
>
> Thanks,
>
> Fred Phelan
>
>
>
>
>
>
>
>
>
>
>
> ________________________________
>
> Frederick R. Phelan Jr., Ph.D.
> Complex Fluids Group
> Polymers Division
> National Institute of Standards and Technology
>
> ________________________________
>
> NIST, Bldg. 224/Rm. A209
> 100 Bureau Dr., STOP 8542
> Gaithersburg, MD 20899-8542
> 301.975.6761 (VOX)
> 301.975.4924 (FAX)
> Frederick.Phelan_at_nist.gov
>
> My Polymers Home Page
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.