saxs input data normalization and plot for input pdb

[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 b667f4a..13154b4 100644 (file)
--- a/django_simple/todo/templates/input.html
+++ b/django_simple/todo/templates/input.html
@@ -13,6 +13,10 @@ 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.
+<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
@@ -21,10 +25,8 @@ 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. See example:
+protein proper chain records are necessary. See example:
 <pre>
-COMPND   3 CHAIN: A, B, C, D;
 SSBOND   1 CYS C  107    CYS C  138
 SSBOND   2 CYS C  124    CYS C  139
 SSBOND   3 CYS C  137    CYS C  149
@@ -38,8 +40,12 @@ which can crash calculations.
 <li>
 TER records in PDB file are read to recognize chain's ends.
 <li>
-Distance distribution (from SAXS experiment) cam be added for MREMD
-simulations in advanced mode. First column distance, second column
+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.
 </ol>
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