dock DockQ

[django_unres.git] / django_simple / todo / templates / input.html

diff --git a/django_simple/todo/templates/input.html b/django_simple/todo/templates/input.html
index 9189f6b..01a33c8 100644 (file)
--- a/django_simple/todo/templates/input.html
+++ b/django_simple/todo/templates/input.html
@@ -13,6 +13,11 @@ As input Unres server can use protein sequence given using one letter code
 <li>
 Only standard codes of aminoacids are recognized in PDB files.
 <li>
+PDB files can be downloaded from the PDB database based on given PDB code.
+To select only a single chain use PDB_code:chain_id notation (for example 
+5G3Q:B), chain_id is case sensitive. For the PDB files containing multiple
+models, only the first models is taken.
+<li>
 Unres server requires input PDB files with continuous (without breaks)
 protein chains. PDB files with gaps in the structure have to be first prepared
 by filling up all missing residues. There is a plan to add such service to
@@ -21,12 +26,33 @@ external software or online servers (for example Modeller software, Modloop
 server).
 <li>
 Disulfide bonds are read from PDB based on SSBOND records and for multichain
-protein COMPND record with propers CHAIN: tokens listing all chains in the
-PDB file.
+protein proper chain records are necessary. See example:
+<pre>
+SSBOND   1 CYS C  107    CYS C  138
+SSBOND   2 CYS C  124    CYS C  139
+SSBOND   3 CYS C  137    CYS C  149
+SSBOND   4 CYS D  107    CYS D  138
+SSBOND   5 CYS D  124    CYS D  139
+SSBOND   6 CYS D  137    CYS D  149
+</pre>
 <li> A protein structure with disulfide bonds and no corresponding 
 SSBOND records will result in clashes and a very high energy 
 which can crash calculations.
 <li>
 TER records in PDB file are read to recognize chain's ends.
+<li>
+Distance distribution (from SAXS experiment) can be added for MREMD
+simulation in advanced mode. First column distance in  Angstroms, second column
+distribution function value (separated by space).
+<li>
+Secondary structure restraints can be added to MD and MREMD
+simulation in advanced mode. Sequence of letters H,E and C or - for each
+residue is used to input helical, extended and no restraints, respectively.
+<li>
+For MD simulations by default the snapshots are written in PDB format to be
+displayed by NGLViewer. In advanced mode, the user can request the compressed
+cx format, which is recommended for larger jobs. In this case, the movie 
+in mp4 and ogv formats are rendered and displayed. The movie files can also
+be downloaded for further use.
 </ol>
 {% endblock %}