Merge branch 'release-0.1.9'

bdb_web/pages/about.md

@@ -12,13 +12,13 @@ bioinformaticians frequently analyze B-factors in PDB structures because
 B-factors are a measure of mobility. Normally full B-factors are stored in
 the [B-factor field in the ATOM records][1] of a PDB file. However, in about
 10% of the X-ray PDB files the B-factor field represents different quantities.
-For example, ["residual" B-factors][2] without the isotropic TLS contribution
-can be present, atomic [mean-square displacements][1] instead of B-factors
-have been deposited, or [sometimes][3] the anisotropic overall scale has not
-been included in the B-factors.
-In general, this leads to lower B-factors
-than the B-factors reported for the majority of the PDB files. Furthermore, the
-location of apparent (normalized) B-factor maxima in a chain might be different
+For example, ["residual" B-factors][2] without the
+[isotropic TLS contribution][3] can be present, atomic
+[mean-square displacements][1] instead of B-factors have been deposited,
+or sometimes the [anisotropic overall scale][3] has not been included in the
+B-factors. In general, this leads to lower B-factors than the B-factors
+reported for the majority of the PDB files. Furthermore, the location of
+apparent (normalized) B-factor maxima in a chain might be different
 and might even shift to a different secondary structure element of a different
 secondary structure type when full (estimates of) isotropic B-factors instead
 of residual B-factors are considered.
@@ -113,8 +113,7 @@ Wouter Touw &
 
 [1]: {{ url_for("pages", name="theory") }}  "Theory"
 [2]: http://dx.doi.org/10.1107/S0907444900014736 "Winn, Isupov & Murshudov"
-[3]: http://phenix-online.org/pipermail/phenixbb/2012-August/018927.html
-"overall anisotropic scale"
+[3]: {{ url_for("pages", name="tls_background") }} "TLS background"
 [4]: http://www.cmbi.ru.nl/WHY_NOT2/resources/list/BDB_PRESENT "List of all BDB
 entries"
 [5]: {{ url_for("static", filename="bdb-0.6.5.zip") }} "Source"

bdb_web/pages/tls_background.md

@@ -0,0 +1,79 @@
+title: TLS background
+
+Displacement of groups of atoms can be modeled by the TLS formalism presented
+in detail by Schomaker and Trueblood (1968). The TLS formalism describes a
+rigid-body displacement with three tensors T, L, and S for Translation,
+Libration, Screw. Useful qualitative and quantitative explanations of the TLS
+formalism summaries are presented by Winn, Isupov and Murshudov (2001),
+Painter and Merritt (2005, 2006). All of the papers above are references for
+this page.
+
+T and L are symmetric 3x3 tensors with units in Å^2^ and radians^2^,
+respectively. The
+translation tensor T describes the anisotropic translational displacement for
+the atoms in the rigid body and is analogous to the individual anisotropic
+mean-square displacement tensor [U][1]. The rotation of the rigid body is
+described by the libration tensor L. The screw tensor S describes the
+correlation between the rotation and translation of a rigid body undergoing
+rotation about three non-intersecting orthogonal axes.
+
+Here, we consider the total [ADP][1] to have 3 contributions:
+U = U~crystal~ + U~TLS~ + U~atom,residual~
+
+The overall anisotropy U~crystal~ is generally modeled using a single
+anisotropic scale factor. The isotropic component of the overall scale factor
+is usually included in the B-factors, but in [some][2] PDB files this is not
+the case. U~TLS~ can be related to the T, L, and S tensors, their origin,
+and an atom in the TLS group located at x, y, z as:
+
+U~TLS~^11^ = L^22^z^2^+ L^33^y^2^- 2L^23^yz+ 2S^21^z- 2S^31^y+ T^11^
+
+U~TLS~^22^ = L^11^z^2^+ L^33^x^2^- 2L^31^xz- 2S^12^z+ 2S^32^x+ T^22^
+
+U~TLS~^33^ = L^11^y^2^+ L^22^x^2^- 2L^12^xy- 2S^23^x+ 2S^13^y+ T^33^
+
+U~TLS~^12^ = -L^33^xy+ L^23^yxz- L^13^yz- L^12^z^2^- S^11^z+ S^22^z+ S^31^x- S^32^y+ T^12^
+
+U~TLS~^13^ = -L^22^xz+ L^23^yx- L^13^y^2^+ L^12^yz+ S^11^y- S^33^y+ S^23^z- S^21^x+ T^13^
+
+U~TLS~^23^ = -L^11^yz- L^23^x^2^+ L^13^xy+ L^12^xz- S^22^x+ S^33^x+ S^12^y- S^13^z+ T^23^
+
+A TLS model can be interpreted as a sum of 6 independent displacements:
+3 screw librations about non-intersecting axes and 3 translations. The program
+[TLSView][3] (Painter and Merrit, 2005) is very useful for visualizing the TLS
+motion.
+
+Modeling U~atom,residual~ is described [here][1]. The B-factor in PDB files is
+usually the sum of the isotropic components of U~crystal~, U~TLS~, and
+U~atom,residual~.
+
+
+### Additional analyses: PDB versus BDB
+Several analyses of the (differences between) PDB and BDB files are described
+in the [BDB paper][4].
+
+In the article we show that the global B-factor maximum smoothed in a
+5-residue window in a PDB chain is often tens of residues away from the
+maximum in the corresponding BDB chain.
+
+This figure shows correlation of the Cα-Cα distance between the
+maxima with the distance in primary structure.
+
+![][5]
+
+
+### References and Further Reading
+
+* Painter, J. and Merritt, E.A. (2005) Acta Crystallogr. D, 61, 465-471.
+* Painter, J. and Merritt, E.A. (2006) Acta Crystallogr. D, 62, 439-450.
+* Schomaker, V. and Trueblood, K.N. (1968) Acta Crystallogr. B, 24, 63-76.
+* Winn, M.D., Isupov, M.N. and Murshudov, G.N. (2001) Acta Crystallogr. D, 57, 122-133.
+* Zucker, F., Champ, P. and Merritt, E.A. (2010) Acta Crystallogr. D, 66, 889-900.
+
+[1]: {{ url_for("pages", name="theory") }} "U"
+[2]: http://phenix-online.org/pipermail/phenixbb/2012-August/018927.html
+"overall anisotropic scale"
+[3]: http://pymmlib.sourceforge.net/doc/tlsview/tlsview.html "TLSView"
+[4]: {{ url_for("pages", name="about") }} "About BDB"
+[5]: {{ url_for("static", filename="background/penta_caca_seq_dist.png") }}
+"maxima"

config/settings.example

@@ -1,4 +1,4 @@
-# Flask settings for version 0.1.8
+# Flask settings for version 0.1.9
 BDB_ROOT = "bdb"
 MAIL_SERVER = "127.0.0.1"
 MAIL_SMTP_PORT = 25