text corrections (CA rms, input/output description)

diff --git a/django_simple/todo/forms.py b/django_simple/todo/forms.py
index 45e78bf..f73212b 100644 (file)
--- a/django_simple/todo/forms.py
+++ b/django_simple/todo/forms.py
@@ -287,7 +287,7 @@ class TaskForm_md_a(forms.Form):
      md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
                   help_text='scaling of the friction coefficients (Langevin)')
      md_respa = forms.BooleanField(required=False,initial=True,label='RESPA')
-     md_mdpdb = forms.BooleanField(required=False,label='trajectory as PDB')
+     md_mdpdb = forms.BooleanField(required=True,label='trajectory as PDB')
 
      boxx = forms.FloatField(label='Box X',initial=1000.0,
                        help_text='box x dimension')

diff --git a/django_simple/todo/templates/details.html b/django_simple/todo/templates/details.html
index ba9425c..28e640e 100644 (file)
--- a/django_simple/todo/templates/details.html
+++ b/django_simple/todo/templates/details.html
@@ -488,7 +488,7 @@ Created {{ task.created_date  }}
                
                           {% if task.md_pdbref %}
                        <li class="list-group-item task-item">
-                         <div class="col-md-2"> RMSD </div>
+                         <div class="col-md-2"> C<sup>&alpha;</sup> RMSD </div>
                          <div class="col-md-10"> <img 
                          src="/myfiles/download-file/{{task.jobdirname}}/md_rms.png"
                          width="500"> </div>
@@ -564,21 +564,22 @@ Created {{ task.created_date  }}
                           {% if task.md_pdbref %}
 
                        <li class="list-group-item task-item">
-                         <div class="col-md-2"> Average RMSD vs. temperature </div>
+                         <div class="col-md-2"> Average C<sup>&alpha;</sup> RMSD vs. temperature </div>
                          <div class="col-md-10"> <img 
                          src="/myfiles/download-file/{{task.jobdirname}}/remd_rmsd.png"
                          width="500"> </div>
                        </li>
 
                        <li class="list-group-item task-item">
-                         <div class="col-md-2"> potential energy vs. RMSD</div>
+                         <div class="col-md-2"> potential energy vs.
+                         C<sup>&alpha;</sup> RMSD</div>
                          <div class="col-md-10"> <img 
                          src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_rms.png"
                          width="500"> </div>
                        </li>
 
                         <li class="list-group-item task-item">
-                         <div class="col-md-2"> RMSD vs. step*replica
+                         <div class="col-md-2"> C<sup>&alpha;</sup> RMSD vs. step*replica
                          colored by bath temperature</div>
                          <div class="col-md-10"> <img 
                          src="/myfiles/download-file/{{task.jobdirname}}/remd_step_rms.png"

diff --git a/django_simple/todo/templates/details1.html b/django_simple/todo/templates/details1.html
index 4abd64d..e3135c8 100644 (file)
--- a/django_simple/todo/templates/details1.html
+++ b/django_simple/todo/templates/details1.html
@@ -477,7 +477,7 @@ Created {{ task.created_date  }}
                
                           {% if task.md_pdbref %}
                        <li class="list-group-item task-item">
-                         <div class="col-md-2"> RMSD </div>
+                         <div class="col-md-2"> C<sup>&alpha;</sup> RMSD </div>
                          <div class="col-md-10"> <img 
                          src="/myfiles/download-file/{{task.jobdirname}}/md_rms.png"
                          width="500"> </div>
@@ -553,21 +553,22 @@ Created {{ task.created_date  }}
                           {% if task.md_pdbref %}
 
                        <li class="list-group-item task-item">
-                         <div class="col-md-2"> Average RMSD vs. temperature </div>
+                         <div class="col-md-2"> Average C<sup>&alpha;</sup> RMSD vs. temperature </div>
                          <div class="col-md-10"> <img 
                          src="/myfiles/download-file/{{task.jobdirname}}/remd_rmsd.png"
                          width="500"> </div>
                        </li>
 
                        <li class="list-group-item task-item">
-                         <div class="col-md-2"> potential energy vs. RMSD</div>
+                         <div class="col-md-2"> potential energy vs.
+                         C<sup>&alpha;</sup> RMSD</div>
                          <div class="col-md-10"> <img 
                          src="/myfiles/download-file/{{task.jobdirname}}/remd_ene_rms.png"
                          width="500"> </div>
                        </li>
 
                         <li class="list-group-item task-item">
-                         <div class="col-md-2"> RMSD vs. step*replica
+                         <div class="col-md-2"> C<sup>&alpha;</sup> RMSD vs. step*replica
                          colored by bath temperature</div>
                          <div class="col-md-10"> <img 
                          src="/myfiles/download-file/{{task.jobdirname}}/remd_step_rms.png"

diff --git a/django_simple/todo/templates/input.html b/django_simple/todo/templates/input.html
index 13154b4..01a33c8 100644 (file)
--- a/django_simple/todo/templates/input.html
+++ b/django_simple/todo/templates/input.html
@@ -15,7 +15,8 @@ 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.
+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
@@ -47,5 +48,11 @@ distribution function value (separated by space).
 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 %}

diff --git a/django_simple/todo/templates/outputs.html b/django_simple/todo/templates/outputs.html
index 806afc4..1399dda 100644 (file)
--- a/django_simple/todo/templates/outputs.html
+++ b/django_simple/todo/templates/outputs.html
@@ -38,15 +38,15 @@ Contents</A>
 <LI><A NAME="tex2html36"
   HREF="outputs.html#SECTION00041000000000000000">Summary of the files</A>
 <LI><A NAME="tex2html37"
-  HREF="outputs.html#SECTION00042000000000000000">The structure of the main output file (out)</A>
+  HREF="outputs.html#SECTION00042000000000000000">The structure of the main output file</A>
 <LI><A NAME="tex2html38"
   HREF="outputs.html#SECTION00043000000000000000">The thermodynamic quantity and ensemble average (thermal) files</A>
 <LI><A NAME="tex2html39"
   HREF="outputs.html#SECTION00044000000000000000">The conformation summary with classification (stat) files</A>
-<LI><A NAME="tex2html40"
+<!--<LI><A NAME="tex2html40"
   HREF="outputs.html#SECTION00045000000000000000">The histogram files</A>
 <LI><A NAME="tex2html41"
-  HREF="outputs.html#SECTION00046000000000000000">The rmsd-radius of gyration potential of mean force files</A>
+  HREF="outputs.html#SECTION00046000000000000000">The rmsd-radius of gyration potential of mean force files</A> -->
 <LI><A NAME="tex2html42"
   HREF="outputs.html#SECTION00047000000000000000">The PDB files</A>
 <LI><A NAME="tex2html43"
@@ -287,7 +287,7 @@ The Brookhaven Protein Data Bank format (PDB) files
 
 <P>
 These files are written in PDB standard (see. e.g., 
-ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf<FONT COLOR="#0000ff">ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions</FONT>). The REMARK, ATOM, SSBOND, HELIX, SHEET, CONECT, TER, and ENDMDL are used.
+<a href="ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf">ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions</a>). The REMARK, ATOM, SSBOND, HELIX, SHEET, CONECT, TER, and ENDMDL are used.
 The C&alpha;
  (marked CA) and SC (marked CB) coordinates are output. The CONECT
 records specify the C&alpha; - C&alpha; and C&alpha; - SC virtual bonds. Secondary
@@ -444,6 +444,7 @@ Summary of the files
 <DT></DT>
 <DD>file.cx - the compressed UNRES coordinate file with information to compute the probability of a given conformation at any temperature.
 
+<!--
 <P>
 </DD>
 <DT></DT>
@@ -459,6 +460,7 @@ Summary of the files
 <DT></DT>
 <DD>file.rmsrgy, file_par_yy.rmsrgy, file_slice_xx.rmsrgy or file_par_yy_slice_xx.rmsrgy - the 2D histogram(s) of rmsd from the experimental structure and radius of gyration.
 
+-->
 <P>
 </DD>
 </DL>
@@ -544,7 +546,7 @@ Bits s, c, and h of level 1 are explained in point 2; bits c and h of level 2 pe
 <H2><A NAME="SECTION00042000000000000000"></A>
 <A NAME="sect:whamoutfiles:output:main"></A>
 <BR>
-The structure of the main output file (out)
+The structure of the main output file
 </H2>
 
 <P>
@@ -850,6 +852,7 @@ The octal/quaternary/binary numbers denoting the class for a fragment at level 1
 
 <P>
 
+<!--
 <H2><A NAME="SECTION00045000000000000000"></A>
 <A NAME="sect:whamoutfiles:histograms"></A>
 <BR>
@@ -902,7 +905,7 @@ A line contains the left boundaries of the radius of gyration - rmsd bin (radius
 With SEPARATE_PARSET, the PMFs corresponding to different parameter sets are printed to separate files.
 
 <P>
-
+-->
 <H2><A NAME="SECTION00047000000000000000"></A>
 <A NAME="sect:whamoutfiles:PDB"></A>
 <BR>
@@ -911,7 +914,7 @@ The PDB files
 
 <P>
 The PDB files with names file_[slice_xx_]Tyyy.pdb, where Tyyy specifies a given replica temperature contain the conformations whose probabilities at replica temperature T sum to 0.99, after sorting the conformations 
-by probabilities in descending order. The PDB files follow the standard format; see ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf<FONT COLOR="#0000ff">ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions</FONT>.
+by probabilities in descending order. The PDB files follow the standard format; see <a href="ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf">ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions</a>.
 For single-chain proteins, an example is as follows:
 
 <P>

diff --git a/django_simple/todo/templates/tutorial.html b/django_simple/todo/templates/tutorial.html
index 6fd03ad..eb28a67 100644 (file)
--- a/django_simple/todo/templates/tutorial.html
+++ b/django_simple/todo/templates/tutorial.html
@@ -340,7 +340,8 @@ the central portion of Factor H (PDB code:2KMS).
             style="background-color:#d3d3d3;cursor: pointer;">Show</legend>
     
     <div class="hiders" style="display:none" >
-REMD simulation starts from the experimental NMR structure. Secondary
+REMD simulation starts from the experimental NMR structure (the first model
+is taken as the input structure). Secondary
 structure restraints are used. Only a short (50 energy evaluations)
 initial minimization is requested.
 The distance distribution has been downloaded from the SASBDB database (the SASDA25 entry).