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 1509f69..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
@@ -39,5 +44,15 @@ TER records in PDB file are read to recognize chain's ends.
 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 %}