From 6a2764586c4c00b5c0cba0c27385b5531795b376 Mon Sep 17 00:00:00 2001 From: Cezary Czaplewski Date: Thu, 12 Apr 2018 15:02:55 +0200 Subject: [PATCH] text corrections (CA rms, input/output description) --- django_simple/todo/forms.py | 2 +- django_simple/todo/templates/details.html | 9 +++++---- django_simple/todo/templates/details1.html | 9 +++++---- django_simple/todo/templates/input.html | 9 ++++++++- django_simple/todo/templates/outputs.html | 17 ++++++++++------- django_simple/todo/templates/tutorial.html | 3 ++- 6 files changed, 31 insertions(+), 18 deletions(-) diff --git a/django_simple/todo/forms.py b/django_simple/todo/forms.py index 45e78bf..f73212b 100644 --- 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 --- 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 %}
  • -
    RMSD
    +
    Cα RMSD
    @@ -564,21 +564,22 @@ Created {{ task.created_date }} {% if task.md_pdbref %}
  • -
    Average RMSD vs. temperature
    +
    Average Cα RMSD vs. temperature
  • -
    potential energy vs. RMSD
    +
    potential energy vs. + Cα RMSD
  • -
    RMSD vs. step*replica +
    Cα RMSD vs. step*replica colored by bath temperature
    -
    RMSD
    +
    Cα RMSD
    @@ -553,21 +553,22 @@ Created {{ task.created_date }} {% if task.md_pdbref %}
  • -
    Average RMSD vs. temperature
    +
    Average Cα RMSD vs. temperature
  • -
    potential energy vs. RMSD
    +
    potential energy vs. + Cα RMSD
  • -
    RMSD vs. step*replica +
    Cα RMSD vs. step*replica colored by bath temperature
    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.
  • 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. +
  • +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. {% endblock %} diff --git a/django_simple/todo/templates/outputs.html b/django_simple/todo/templates/outputs.html index 806afc4..1399dda 100644 --- a/django_simple/todo/templates/outputs.html +++ b/django_simple/todo/templates/outputs.html @@ -38,15 +38,15 @@ Contents
  • Summary of the files
  • The structure of the main output file (out) + HREF="outputs.html#SECTION00042000000000000000">The structure of the main output file
  • The thermodynamic quantity and ensemble average (thermal) files
  • The conformation summary with classification (stat) files -
  • The histogram files
  • The rmsd-radius of gyration potential of mean force files + HREF="outputs.html#SECTION00046000000000000000">The rmsd-radius of gyration potential of mean force files -->
  • The PDB files
  • These files are written in PDB standard (see. e.g., -ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdfftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions). The REMARK, ATOM, SSBOND, HELIX, SHEET, CONECT, TER, and ENDMDL are used. +ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions). The REMARK, ATOM, SSBOND, HELIX, SHEET, CONECT, TER, and ENDMDL are used. The Cα (marked CA) and SC (marked CB) coordinates are output. The CONECT records specify the Cα - Cα and Cα - SC virtual bonds. Secondary @@ -444,6 +444,7 @@ Summary of the files
    file.cx - the compressed UNRES coordinate file with information to compute the probability of a given conformation at any temperature. +

    @@ -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


    -The structure of the main output file (out) +The structure of the main output file

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

    +


    @@ -911,7 +914,7 @@ The PDB files

    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.pdfftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions. +by probabilities in descending order. The PDB files follow the standard format; see ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions. For single-chain proteins, an example is as follows:

    diff --git a/django_simple/todo/templates/tutorial.html b/django_simple/todo/templates/tutorial.html index 6fd03ad..eb28a67 100644 --- 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