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_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')
 
      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">
                
                           {% 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>
                          <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">
                           {% 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-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-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"
                          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">
                
                           {% 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>
                          <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">
                           {% 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-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-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"
                          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 
 <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
 <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.
 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 %}
 </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"
 <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="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#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"
 <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., 
 
 <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
 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.
 
 <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>
 <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.
 
 <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>
 <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>
 <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>
 </H2>
 
 <P>

@@ -850,6 +852,7 @@ The octal/quaternary/binary numbers denoting the class for a fragment at level 1
 
 <P>
 
 
 <P>
 

+<!--

 <H2><A NAME="SECTION00045000000000000000"></A>
 <A NAME="sect:whamoutfiles:histograms"></A>
 <BR>
 <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>
 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>
 <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 
 
 <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>
 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" >
             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).
 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).