[Blends-commit] r3555 - /projects/pan/trunk/debian-pan/tasks/mx
picca at users.alioth.debian.org
picca at users.alioth.debian.org
Thu Aug 9 07:03:06 UTC 2012
Author: picca
Date: Thu Aug 9 07:03:06 2012
New Revision: 3555
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3555
Log:
more homepage and description added to mx task
Modified:
projects/pan/trunk/debian-pan/tasks/mx
Modified: projects/pan/trunk/debian-pan/tasks/mx
URL: http://svn.debian.org/wsvn/blends/projects/pan/trunk/debian-pan/tasks/mx?rev=3555&op=diff
==============================================================================
--- projects/pan/trunk/debian-pan/tasks/mx (original)
+++ projects/pan/trunk/debian-pan/tasks/mx Thu Aug 9 07:03:06 2012
@@ -520,29 +520,101 @@
Homepage: http://ucxray.berkeley.edu/~jamesh/elves/
License: non-free
Pkg-Description: ?
-Comment: ?
Suggests: epmr
-Homepage: ?
-License: ?
-Pkg-Description: ?
-Comment: ?
+Homepage: http://www.epmr.info/
+License: GPL2
+Pkg-Description: EPMR is a general-purpose molecular replacement
+ program. Unlike most molecular replacement programs, it does not
+ divide the problem into separate rotation and translation
+ searches. Instead, it uses an evolutionary search algorithm to
+ simultaneously optimize the orientation and position of a search
+ model (1,2). The program operates as follows:
+ .
+ * An initial set of random solutions (random orientations and
+ positions for the search model) is generated.
+ * The correlation coefficient is alculated for each trial solution.
+ * A fraction of the highest scoring solutions are retained and used
+ to regenerate a complete set of new trial solutions. This is done
+ by applying random alterations to the orientation angles and
+ translations for each “surviving†solution. The correlation
+ coefficients for the new population are calculated, the
+ population is again regenerated from the top scoring solutions,
+ and this procedure is repeated for a specified number of cycles.
+ .
+ The algorithm provides broad, stochastic, initial sampling of the
+ search space while gradually focusing in on the most promising
+ regions. It allows for efficient searching of the six-dimensional (or
+ higher) space. In general, it is several orders of magnitude faster
+ than a brute-force, systematic, 6-D search. At the end of the
+ evolutionary optimization, a local minimization is performed on the
+ best solution. This is simply a rigid-body refinement of the search
+ molecule.
+ .
+ The program calculates structure factors rapidly by indexing into a
+ molecular transform using the method of Huber and Schneider (3). A
+ traditional structure factor calculation is done only once - for the
+ search model set at the origin of a P1 cell. Subsequent structure
+ factor calculations are done by transforming reflection indices
+ according to the rotations and translations applied to the model and
+ the relationship between the P1 and real cells, interpolating into
+ the grid of P1 structure factors and summing over the symmetry
+ operators of the crystal. This is much faster than an FFT
+ calculation. A simple Babinet-type solvent correction is applied to
+ the calculated structure factors. The values of the solvent
+ correction parameters (k, B) are optimized during the search.
+ .
+ Because of the stochastic nature of the evolutionary optimization
+ process, the correct solution will not be obtained on every run, even
+ with a very good search model. The success rate is dependent on the
+ quality of the model (2). By default, 20 optimization attempts are
+ done, and more may be required if you have a difficult problem. For
+ search models that are poor and at the limit of detection, the search
+ efficiency can be quite low. If you have a molecular replacement
+ problem that has not yielded a solution by any other means, a
+ reasonable last resort is to set up EPMR to do as many runs as your
+ patience and computing resources will allow. As long as the true
+ solution represents the global maximum in the correlation coefficient
+ between Fo and Fc, even if by the slimmest of margins, the algorithm
+ will eventually find it.
+ .
+ EPMR includes the following features:
+ * the ability to automatically search for multiple copies of a
+ molecule in the asymmetric unit, either sequentially or
+ concurrently
+ * the ability to search with multiple models, either sequentially
+ or simultaneously (i.e., in competition with each other)
+ * the ability to use multiple coordinate sets as parts of an
+ “assembly†that comprises the complete search model
+ * an option to search over all related space groups, either
+ sequentially or simultaneously
+ * rotation-only and translation-only search modes
+ * an option to provide static, partial structure
+ * independent optimization of each segment of a search model during
+ the final rigid-body refinement step
+ * an option to bypass the evolutionary search and do only local,
+ rigid-body optimization of the model
+Published-Authors: Charles R. Kissinger, Daniel K. Gehlhaar & David B. Fogel
+Published-Title: “Rapid automated molecular replacement by evolutionary searchâ€
+Published-In: Acta Crystallographica, D55, 484-491 (1999).
+Comment: contact the upstream for packaging.
Suggests: escet
-Homepage: ?
-License: ?
-Pkg-Description: ?
-Comment: ?
+Homepage: http://www.ifom-ieo-campus.it/escet/
+License: non-free
+Pkg-Description: ?
+Remark: ESRF, still used ?, the homepage is dead
Suggests: evrouter
-Homepage: ?
-License: ?
-Pkg-Description: ?
-Comment: ?
+Homepage: http://www.bedroomlan.org/projects/evrouter
+License: GPL
+Pkg-Description: ?
+Pkg-URL: http://debian.bedroomlan.org/debian/pool/main/e/evrouter/
+Remark: ESRF, still used ?
Suggests: fit2d
-Homepage: ?
-License: ?
+Homepage: http://www.esrf.eu/computing/scientific/FIT2D/
+License: non-free
Pkg-Description: ?
Comment: ?
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