X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Ftemplates%2Ftutorial.html;h=5382ac7272b4b477d99725fdaab02856512377cc;hb=3fdf5468c153fa235f9e778a46cc2cd647555018;hp=9fd8fdf32fd0d98c7a09badb8c7e71eb9e7007ed;hpb=35ecdb6a53c194ab3f2809f3ad9e635a999feb01;p=django_unres.git diff --git a/django_simple/todo/templates/tutorial.html b/django_simple/todo/templates/tutorial.html index 9fd8fdf..5382ac7 100644 --- a/django_simple/todo/templates/tutorial.html +++ b/django_simple/todo/templates/tutorial.html @@ -8,30 +8,39 @@ In order to submit a job you need to provide its name:

-UNRES server allows three types of simulations: +The following three types of simulations can be run with the UNRES server: local minimization, molecular dynamics and replica exchange molecular dynamics:

-Use "Save & submit" button to start calculations. +Use the "Save & submit" button to start calculations.

-Use "Refresh" button to check the status of simulation: +Use the "Refresh" button to check the status of a simulation:

until

-The job status information will start from the "waiting in the queue to -start", then "running" and finally "postprocessing" before "done". -Autorefresh is active every 30 sec. +After the server job has been submitted the "waiting in the queue to +start" message will be displayed in the status field, which will subsequently change +to "running", "postprocessing", and "done". While the job has the "running" +status, the percentage of job accomplishment is displayed. +It should be noted that the "100%" accomplishment refers to the production +phase of a job, after which the postprocessing phase is triggered which also takes +some time (up to several minutes when making a movie from an MD trajectory is +requested) and whose progress is not monitored. The page is autorefreshed every 30 sec.

-Any single job can by accessed later using the adress of the web page -displayed after job submission: +Any single job can by accessed later (for at least 14 days) using the address of the web page +displayed after job submission: e.g. http://unres-server.chem.ug.edu.pl/details1/570cf15fc638493893ece1f011ea0182/984/
-Registered users can save all their jobs and access them after login. +Registered users can save all their jobs and access them later after logging in. +Note that the results will be available for a limited period of time, +depending on the storage space availability (at least 30 days). + +

You can use "Load example data" button before submitting calculations to try examples listed below:

@@ -45,25 +54,25 @@ to try examples listed below: -

  • Molecular dynamics of IGG-binding domain from streptococcal protein G -(PDB code:1IGD) starting from the native structure

    • +(PDB code:1IGD) starting from the experimental structure

    -The results of md simulations show temperature histogram, -potential energy changes, evolution of radius of gyration, -RMSD, fraction of native contacts, and CA fluctuations: +After the MD simulation is accomplished temperature histogram, +plots of UNRES energy, RMSD from the experimental structure, fraction of native +contacts, and radius of gyration vs. time, a movie of the trajectory, and +CA-atom fluctuations are displayed.

    @@ -89,12 +99,11 @@ RMSD, fraction of native contacts, and CA fluctuations:

    Evolution of RMSD, fraction of native contacts and comparison of CA fluctuations to Bfactor is presented -only when reference structure is provided as in this example. +only when the reference structure is provided, as in this example.

    -

  • -Replica exchange molecular dynamics of Trp-Cage miniprotein (PDB +Replica exchange molecular dynamics of the Trp-Cage miniprotein (PDB code:1L2Y) starting from the extended chain

    • @@ -104,26 +113,37 @@ code:1L2Y) starting from the extended chain
    +
    -Advanced mode allows for changes of more parameters of each type of -simulation. Separate examples are provided: minimization of 1EI0 with -dissulfide bonds, MD simulations of 1L2Y starting from extended chain -and replica exchange simulations of 1E0G starting form extended chain -using new UNRES force field and Berendsen thermostat. +Advanced mode enables the user to change more parameters for each type of +simulation. Separate examples are provided (use the Load example data button as +in the Basic mode): +
      +

    1. +Minimization of the P8MTCP1 disulfide-bonded helical hairpin miniprotein +(PDB code: 1EI0).

      2. +
      +
      + Show + + +
      + +

    2. +Canonical MD simulations of the Trp-Cage miniprotein (PDB code:1L2Y) +starting from the extended chain.

      3. +
      +
      + Show + + +
      + + +

    3. +MREMD simulations of 5G3Q:B (CASP12 target T0882)

      4. + +
      +
      + Show + + +
      +

    4. @@ -145,7 +292,7 @@ Distance distribution restrained (simulated SAXS data) replica exchange molecular dynamics of Bacteriocin CbnXY (PDB code:5UJQ) starting from the extended chain.
      -(Use Load example SAXS data button in advanced mode) +(Use Load SAXS 1 example button in advanced mode)

      5. @@ -160,36 +307,91 @@ Bacteriocin CbnXY (PDB code:5UJQ) starting from the extended chain.

      -Plots of histograms of UNRES energy for each temperature, and -energy vs temperature are presented. -The weighted histogram analysis (WHAM) is applied to compute the -probabilities of the obtained conformations to occur at particular -temperatures, plots of heat capacity and average RMSD as a functions -of temperature are shown. Replica exchanges are analyzed. +The output items are the same as those displayed with the Basic mode example 3. +Additionaly the input reference distance distribution and +distance distributions for 5 final models are plotted.

      - - + +

      -Finally cluster analysis is performed to select 5 families of conformations, -and representative model from each family is converted to all-atom -and refined. +Finally models.

      -

      -Additionaly the input reference distance distribution and -distance distributions for 5 final models are plotted. +Comparison of the input distance distributions with those calculated from the 5 models.

      +

      + + +

    5. +Distance distribution restrained (real SAXS data) +replica exchange molecular dynamics of +the central portion of Factor H (PDB code:2KMS). +
      +(Use Load SAXS 2 example button in advanced mode) +

      6. +
      +
      + Show + + +
      @@ -207,4 +409,4 @@ $('.majorpointslegend').click(function(){ -{% endblock %} \ No newline at end of file +{% endblock %}