From: Cezary Czaplewski Date: Mon, 29 Jan 2018 22:43:51 +0000 (+0100) Subject: tutorial update and other changes X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=commitdiff_plain;h=03c96699333f5c45ba11d3e1da84b4f471e52ace;p=django_unres.git tutorial update and other changes preminim=50 for saxs example 2 --- diff --git a/django_simple/todo/templates/changelog.html b/django_simple/todo/templates/changelog.html index 1c159b0..9507fc8 100644 --- a/django_simple/todo/templates/changelog.html +++ b/django_simple/todo/templates/changelog.html @@ -34,6 +34,14 @@ NGL Viewer added for 3D display of structures and trajectories. +
29.01.2018
+
+ Random initial SEED value.
+ Second SAXS example in advance mode for the central + portion of Factor H (PDB code: 2KMS).
+ Extension and update of the Tutorial. +
+ diff --git a/django_simple/todo/templates/tutorial.html b/django_simple/todo/templates/tutorial.html index e073eb7..e271941 100644 --- a/django_simple/todo/templates/tutorial.html +++ b/django_simple/todo/templates/tutorial.html @@ -25,7 +25,7 @@ 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. +Postprocessing do not count to 100%. Autorefresh is active every 30 sec.

Any single job can by accessed later using the adress of the web page displayed after job submission: @@ -61,7 +61,6 @@ can be viewed/download by clicking on "Directory" link. -

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

    • @@ -75,7 +74,8 @@ can be viewed/download by clicking on "Directory" link.

    The results of md simulations show temperature histogram, -potential energy changes, evolution of radius of gyration, +potential energy changes, movie generated from trajectory, +evolution of radius of gyration, RMSD, fraction of native contacts, and CA fluctuations:

    @@ -92,7 +92,6 @@ comparison of CA fluctuations to Bfactor is presented only when reference structure is provided as in this example.

    -

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

    • @@ -123,7 +122,8 @@ of temperature are shown. Replica exchanges are analyzed.

    Finally cluster analysis is performed to select 5 families of conformations, and representative model from each family is converted to all-atom -and refined. PDB files can be downloaded by clicking on the picture. +and refined. Models are shown using NGL Viewer. +PDB files can be downloaded by clicking on the Download button.

    @@ -132,14 +132,149 @@ and refined. PDB files can be downloaded by clicking on the picture. +

    Advanced mode allows for changes of more parameters of each type of simulation. Separate examples are provided (use Load example data button as -in Basic mode): minimization of 1EI0 with -dissulfide bonds, MD simulations of 1L2Y starting from extended chain -and multiplexed replica exchange simulations of 5G3Q:B (CASP12 target T0882) -starting form extended chain with secondary structure restraints predicted -by PSIPRED and Berendsen thermostat. +in Basic mode): +
      +

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

      2. +
      +
      + Show + + +
      + +

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

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

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

      4. + +
      +
      + Show + + +
      +

    4. @@ -147,7 +282,7 @@ 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 example SAXS 1 button in advanced mode)

      5. @@ -190,8 +325,81 @@ distance distributions for 5 final models are plotted.

      +

      + + +

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

      6. +
      +
      + Show + + +
      diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py index f91e57c..33276ac 100644 --- a/django_simple/todo/views.py +++ b/django_simple/todo/views.py @@ -518,7 +518,7 @@ def add_remd_a(request,task_id): data= {'name':task.name,'pdbid':'2KMS','md_pdbref':True,'md_start':'pdbstart', 'md_2d':'----EEEEEE-EEEEE-------EEEEEEEEE--EEEEEE-EEEE---EEEEEEEEE-----EEEEEEE-EEE-HHHHH-EEEE-EEEEEEEEE----EEEEEE---EEE-----', 'md_nstep':200000,'md_lang':'langevin','unres_ff':'FF2','md_seed':-39912345, - 'remd_cluter_temp':280, + 'remd_cluter_temp':280, 'min_maxfun':50, 'scal_rad':5.0,'wsaxs':1000.0,'saxs_data': """0.7100E-00 0.2036E-03 0.1420E+01 0.4221E-03 diff --git a/static/md1.png b/static/md1.png index 47fb994..be339f6 100644 Binary files a/static/md1.png and b/static/md1.png differ diff --git a/static/md2.png b/static/md2.png index 25db984..dce4faf 100644 Binary files a/static/md2.png and b/static/md2.png differ diff --git a/static/md3.png b/static/md3.png index 09d7127..8770007 100644 Binary files a/static/md3.png and b/static/md3.png differ diff --git a/static/md4.png b/static/md4.png index e856a3e..e0ed9ac 100644 Binary files a/static/md4.png and b/static/md4.png differ diff --git a/static/md5.png b/static/md5.png index 4f5c0c9..bd5c130 100644 Binary files a/static/md5.png and b/static/md5.png differ diff --git a/static/md6.png b/static/md6.png index 1935ea7..1bb8f41 100644 Binary files a/static/md6.png and b/static/md6.png differ diff --git a/static/md7.png b/static/md7.png index 779c5f5..36196f0 100644 Binary files a/static/md7.png and b/static/md7.png differ diff --git a/static/md8.png b/static/md8.png index 44081d7..ac878b5 100644 Binary files a/static/md8.png and b/static/md8.png differ diff --git a/static/md_adv.png b/static/md_adv.png new file mode 100644 index 0000000..852007a Binary files /dev/null and b/static/md_adv.png differ diff --git a/static/md_adv0.png b/static/md_adv0.png new file mode 100644 index 0000000..d3efea5 Binary files /dev/null and b/static/md_adv0.png differ diff --git a/static/md_adv1.png b/static/md_adv1.png new file mode 100644 index 0000000..c05083a Binary files /dev/null and b/static/md_adv1.png differ diff --git a/static/md_adv2.png b/static/md_adv2.png new file mode 100644 index 0000000..64e17d8 Binary files /dev/null and b/static/md_adv2.png differ diff --git a/static/md_adv3.png b/static/md_adv3.png new file mode 100644 index 0000000..db21aab Binary files /dev/null and b/static/md_adv3.png differ diff --git a/static/md_adv4.png b/static/md_adv4.png new file mode 100644 index 0000000..13b2620 Binary files /dev/null and b/static/md_adv4.png differ diff --git a/static/md_adv5.png b/static/md_adv5.png new file mode 100644 index 0000000..b51d340 Binary files /dev/null and b/static/md_adv5.png differ diff --git a/static/md_adv6.png b/static/md_adv6.png new file mode 100644 index 0000000..c016a49 Binary files /dev/null and b/static/md_adv6.png differ diff --git a/static/md_adv7.png b/static/md_adv7.png new file mode 100644 index 0000000..f5b94e7 Binary files /dev/null and b/static/md_adv7.png differ diff --git a/static/min2.png b/static/min2.png index 83277f1..0e2f980 100644 Binary files a/static/min2.png and b/static/min2.png differ diff --git a/static/min_adv.png b/static/min_adv.png new file mode 100644 index 0000000..40c2726 Binary files /dev/null and b/static/min_adv.png differ diff --git a/static/min_adv1.png b/static/min_adv1.png new file mode 100644 index 0000000..6ca6264 Binary files /dev/null and b/static/min_adv1.png differ diff --git a/static/min_adv2.png b/static/min_adv2.png new file mode 100644 index 0000000..00c70aa Binary files /dev/null and b/static/min_adv2.png differ diff --git a/static/min_adv3.png b/static/min_adv3.png new file mode 100644 index 0000000..f51171e Binary files /dev/null and b/static/min_adv3.png differ diff --git a/static/remd1.png b/static/remd1.png index 57c815a..fde0758 100644 Binary files a/static/remd1.png and b/static/remd1.png differ diff --git a/static/remd2.png b/static/remd2.png index d6e177a..ca87e98 100644 Binary files a/static/remd2.png and b/static/remd2.png differ diff --git a/static/remd3.png b/static/remd3.png index 0f1bdcd..de252bd 100644 Binary files a/static/remd3.png and b/static/remd3.png differ diff --git a/static/remd4.png b/static/remd4.png index 23cdf1a..c4dba6a 100644 Binary files a/static/remd4.png and b/static/remd4.png differ diff --git a/static/remd5.png b/static/remd5.png index b303828..9a7c5a8 100644 Binary files a/static/remd5.png and b/static/remd5.png differ diff --git a/static/remd6.png b/static/remd6.png index a1b568f..360bf94 100644 Binary files a/static/remd6.png and b/static/remd6.png differ diff --git a/static/remd7.png b/static/remd7.png index 6143e49..8aca2dd 100644 Binary files a/static/remd7.png and b/static/remd7.png differ diff --git a/static/remd8.png b/static/remd8.png index 9a48b06..feba521 100644 Binary files a/static/remd8.png and b/static/remd8.png differ diff --git a/static/remd9.png b/static/remd9.png index 4498b7f..66a0ab1 100644 Binary files a/static/remd9.png and b/static/remd9.png differ diff --git a/static/remd_adv.png b/static/remd_adv.png new file mode 100644 index 0000000..c425206 Binary files /dev/null and b/static/remd_adv.png differ diff --git a/static/remd_adv01.png b/static/remd_adv01.png new file mode 100644 index 0000000..bbc6231 Binary files /dev/null and b/static/remd_adv01.png differ diff --git a/static/remd_adv02.png b/static/remd_adv02.png new file mode 100644 index 0000000..bfd0a54 Binary files /dev/null and b/static/remd_adv02.png differ diff --git a/static/remd_adv03.png b/static/remd_adv03.png new file mode 100644 index 0000000..ba595f9 Binary files /dev/null and b/static/remd_adv03.png differ diff --git a/static/remd_adv1.png b/static/remd_adv1.png new file mode 100644 index 0000000..fc8b632 Binary files /dev/null and b/static/remd_adv1.png differ diff --git a/static/remd_adv2.png b/static/remd_adv2.png new file mode 100644 index 0000000..93a68e9 Binary files /dev/null and b/static/remd_adv2.png differ diff --git a/static/remd_adv3.png b/static/remd_adv3.png new file mode 100644 index 0000000..b04b565 Binary files /dev/null and b/static/remd_adv3.png differ diff --git a/static/remd_adv4.png b/static/remd_adv4.png new file mode 100644 index 0000000..92c4a2f Binary files /dev/null and b/static/remd_adv4.png differ diff --git a/static/remd_adv5.png b/static/remd_adv5.png new file mode 100644 index 0000000..e6d4995 Binary files /dev/null and b/static/remd_adv5.png differ diff --git a/static/remd_adv6.png b/static/remd_adv6.png new file mode 100644 index 0000000..6eef0a1 Binary files /dev/null and b/static/remd_adv6.png differ diff --git a/static/remd_adv7.png b/static/remd_adv7.png new file mode 100644 index 0000000..ac03ef1 Binary files /dev/null and b/static/remd_adv7.png differ diff --git a/static/remd_adv8.png b/static/remd_adv8.png new file mode 100644 index 0000000..85640a2 Binary files /dev/null and b/static/remd_adv8.png differ diff --git a/static/remd_adv9.png b/static/remd_adv9.png new file mode 100644 index 0000000..7e53a2d Binary files /dev/null and b/static/remd_adv9.png differ diff --git a/static/saxs10.png b/static/saxs10.png index 02c19a9..fff926e 100644 Binary files a/static/saxs10.png and b/static/saxs10.png differ diff --git a/static/saxs11.png b/static/saxs11.png index 765bf97..60c7e2e 100644 Binary files a/static/saxs11.png and b/static/saxs11.png differ diff --git a/static/saxs12.png b/static/saxs12.png index 1a37850..e72d1c1 100644 Binary files a/static/saxs12.png and b/static/saxs12.png differ diff --git a/static/saxs2.png b/static/saxs2.png index b5da815..5a3a01c 100644 Binary files a/static/saxs2.png and b/static/saxs2.png differ diff --git a/static/saxs2_1.png b/static/saxs2_1.png new file mode 100644 index 0000000..305ea88 Binary files /dev/null and b/static/saxs2_1.png differ diff --git a/static/saxs2_10.png b/static/saxs2_10.png new file mode 100644 index 0000000..9007633 Binary files /dev/null and b/static/saxs2_10.png differ diff --git a/static/saxs2_11.png b/static/saxs2_11.png new file mode 100644 index 0000000..6ce3bea Binary files /dev/null and b/static/saxs2_11.png differ diff --git a/static/saxs2_12.png b/static/saxs2_12.png new file mode 100644 index 0000000..c10c2af Binary files /dev/null and b/static/saxs2_12.png differ diff --git a/static/saxs2_13.png b/static/saxs2_13.png new file mode 100644 index 0000000..5071e2b Binary files /dev/null and b/static/saxs2_13.png differ diff --git a/static/saxs2_2.png b/static/saxs2_2.png new file mode 100644 index 0000000..c1d4f9c Binary files /dev/null and b/static/saxs2_2.png differ diff --git a/static/saxs2_3.png b/static/saxs2_3.png new file mode 100644 index 0000000..cf5845b Binary files /dev/null and b/static/saxs2_3.png differ diff --git a/static/saxs2_4.png b/static/saxs2_4.png new file mode 100644 index 0000000..303b0db Binary files /dev/null and b/static/saxs2_4.png differ diff --git a/static/saxs2_5.png b/static/saxs2_5.png new file mode 100644 index 0000000..4b0d14b Binary files /dev/null and b/static/saxs2_5.png differ diff --git a/static/saxs2_6.png b/static/saxs2_6.png new file mode 100644 index 0000000..0fc659f Binary files /dev/null and b/static/saxs2_6.png differ diff --git a/static/saxs2_7.png b/static/saxs2_7.png new file mode 100644 index 0000000..4a4f42c Binary files /dev/null and b/static/saxs2_7.png differ diff --git a/static/saxs2_8.png b/static/saxs2_8.png new file mode 100644 index 0000000..2dc372b Binary files /dev/null and b/static/saxs2_8.png differ diff --git a/static/saxs2_9.png b/static/saxs2_9.png new file mode 100644 index 0000000..ddc40f6 Binary files /dev/null and b/static/saxs2_9.png differ diff --git a/static/saxs3.png b/static/saxs3.png index f01c227..41603c3 100644 Binary files a/static/saxs3.png and b/static/saxs3.png differ diff --git a/static/saxs4.png b/static/saxs4.png index 0174768..2952c90 100644 Binary files a/static/saxs4.png and b/static/saxs4.png differ diff --git a/static/saxs5.png b/static/saxs5.png index 8039452..b88f084 100644 Binary files a/static/saxs5.png and b/static/saxs5.png differ diff --git a/static/saxs6.png b/static/saxs6.png index 648fede..c325a0e 100644 Binary files a/static/saxs6.png and b/static/saxs6.png differ diff --git a/static/saxs7.png b/static/saxs7.png index 70db5b1..ae96ac9 100644 Binary files a/static/saxs7.png and b/static/saxs7.png differ diff --git a/static/saxs8.png b/static/saxs8.png index b362a16..6396ec6 100644 Binary files a/static/saxs8.png and b/static/saxs8.png differ diff --git a/static/saxs9.png b/static/saxs9.png index ddf93b8..10a5274 100644 Binary files a/static/saxs9.png and b/static/saxs9.png differ