From: Axel Kohlmeyer (
Date: Tue Aug 07 2007 - 15:18:02 CDT

On Tue, 7 Aug 2007, [iso-8859-7] Θωμας [iso-8859-7] Ευαγγελιδης wrote:


TE> Axel,
TE> what you proposed was my first attempt and was extremely slow. Now I am working

this is only slow if you compute the distance matrix for all atoms.
if you do a first estimate with a selection and then improve it
from the resulting distance matrix. it also depends a _lot_ on how
you write the code. computing the matrix may be made significantly
faster with a dynamically loaded tcl-plugin written in c/c++ or as
a subcommand to measure.

TE> with successive "within $R of protein" commands and reduce $R in each step (or
TE> increase it if the number of atoms caught at first is higher that that of the
TE> first frame). When the number of selected atoms becomes lower than that of
TE> frame1 then I find the redundant atoms and calculate the distances for each of
TE> them.

if you just want to reduce the size of the file, why go through all
these lengths? you'll just have additional troubles reading the
resulting trajectory. just cut away what can be safely removed or
store/load only every second/third/tenth frame and you should be fine.

to have the exact n nearest atoms, makes most sense in visualization
and analysis and there you can easily live with the two step procedure
of first flagging the matching atoms with a user value and then use
that for selection.

this way everything is cleaner, simpler, and easier to maintain.


TE> In fact the original concept was to create smaller dcd files from bigger ones
TE> and facilitate their transfer, but at the moment the program produces pdb files
TE> ,one for each frame. I will check tommorow the plugins you indicated and come
TE> with an answer later.
TE> thanks for your help,
TE> Thomas

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.