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=35b8dba122f2b7e659b0220d8529f1785835ef1b;hpb=0f5d683edc824468ab5da53d015b39e91fe2766d;p=django_unres.git diff --git a/django_simple/todo/templates/tutorial.html b/django_simple/todo/templates/tutorial.html index 35b8dba..5382ac7 100644 --- a/django_simple/todo/templates/tutorial.html +++ b/django_simple/todo/templates/tutorial.html @@ -7,25 +7,43 @@ In order to submit a job you need to provide its name:

- -UNRES server allows three types of simulations: -local minimization, molecular dynamics, replica exchange molecular dynamics: +

+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

+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 (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 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). -

Use "Load example data" button before submitting calculations -to try all examples listed below:

+

+

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

  1. Local minimization of protein A (PDB code:1BDD) structure

    2. @@ -36,20 +54,25 @@ to try all examples listed below: -

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

    3. +(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.

    @@ -75,12 +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 case. +only when the reference structure is provided, as in this example.

    -

  3. -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

    4. @@ -90,26 +113,37 @@ code:1L2Y) starting from the extended chain
    +
+
+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 + + +
    + +
    -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. +

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

    5. +
    +
    + Show + + +
    + +

  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 + + + +
    + -{% endblock %} \ No newline at end of file +{% endblock %}