Hi Gary,
Sounds painful. The TCL version is very fast. Take a look at
xplor/tcl/noe_reporting.tcl There's a proc called
summarizeMarvinResults.
Inside it are calls to TCL procs called meanStruct,
compareToReference, and structPrecision.
You'd use it something like this:
set allFiles [grabPDBFiles -fileNames [glob *.pdb]]
set backboneSel [AtomSel -args "(name ca or name c or name n)"]
set heavyatomSel [AtomSel -args "(not name h*)"]
meanStruct -files $allFiles -selection $backboneSel
set bbnRMSD [compareToReference -referenceFileName "answer.pdb" -
selection $backboneSel]
set heavyRMSD [compareToReference -referenceFileName "answer.pdb" -
selection $heavyatomSel]
set precisionReport [structPrecision -files $allFiles \
-backboneSelection $backboneSel \
-heavyatomSelection $heavyatomSel \
-verbose]
puts [format "Accuracy of the mean structure is %f A backbone, %f A
heavyatoms" $bbnRMSD $heavyRMSD]
puts [format "Precision of the individual ensemble members to the
mean is %s" $precisionReport]
Hope this helps.
--JK
On Sep 27, 2007, at 9:27 AM, Gary Thompson wrote:
> Hi
> I am using the Fit and RMSD objects to fit structures to a starting
> structure as shown in the example python/tests/fitTest.py .
> However, it
> seems to be incredibly slow (it takes minutes to fit 50 structures
> with
> CA overlay and 150 residues...) is this expected
>
> regards
> gary
>
> --
> -------------------------------------------------------------------
> Dr Gary Thompson
> Astbury Centre for Structural Molecular Biology,
> University of Leeds, Astbury Building,
> Leeds, LS2 9JT, West-Yorkshire, UK Tel. +44-113-3433024
> email: garyt at bmb.leeds.ac.uk Fax +44-113-2331407
> -------------------------------------------------------------------
>
>
> _______________________________________________
> Xplor-nih mailing list
> Xplor-nih at nmr.cit.nih.gov
> http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
