From 4105e872badb97ca1b848708c36e1f0f1e5dc4cf Mon Sep 17 00:00:00 2001 From: Cezary Czaplewski Date: Fri, 28 Feb 2020 12:57:06 +0100 Subject: [PATCH] dock tutorial txt corrections --- django_simple/todo/templates/tutorial_dock.html | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/django_simple/todo/templates/tutorial_dock.html b/django_simple/todo/templates/tutorial_dock.html index 652cfa9..9b4eb3e 100644 --- a/django_simple/todo/templates/tutorial_dock.html +++ b/django_simple/todo/templates/tutorial_dock.html @@ -18,7 +18,7 @@ utilizes multiplexed replica exchange MD simulation (MREMD) with The monomers are placed to interact weakly with each other, the smallest periodic-box size prohibiting interactions between a molecule with its image is estimated. A set of log-Gaussian restraints are imposed on both -monomers for protein-protein docking, and only on the first monomer for +monomers for protein-protein docking, and only on the first chain for protein-peptide docking.

Use the "Save & submit" button to start calculations. @@ -39,7 +39,7 @@ change to "running", "postprocessing", and "done". While the job has the 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 and whose progress is not monitored. The page is -autorefreshed every 30 sec.

Any single job can by accessed later (for +autorefreshed every 30 sec.

Any single job can be 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/ @@ -64,7 +64,7 @@ Docking simulation for two chains of Drosophila Insulin-Like Peptide 5

After a UNRES-Dock MREMD run is accomplished, the same data -as for regules MREMD run is shown: +as for reguler MREMD run is shown: a table showing replica-exchange statistics (a), plots of histograms of UNRES energy for each temperature (b), a plot of energy vs. temperature (c), a temperature-colored scatter plot of energy vs. RMSD @@ -83,7 +83,7 @@ while different replicas are colored from black to yellow in panel (f). The weighted histogram analysis method (WHAM) is applied to compute the probabilities of the obtained complexes to occur at particular temperatures and, consequently, the plots of heat capacity -(g) and ensemble-averaged RMSD (h) as a functions +(g) and ensemble-averaged RMSD (h) as functions of temperature; these are shown in the respective graphs.

(g) @@ -92,8 +92,8 @@ of temperature; these are shown in the respective graphs. Note! Panels are labeled in this tutorial only and labels are not displayed in the outputs from real server jobs.

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

@@ -151,7 +151,7 @@ Note! Panels are labeled in this tutorial only and labels are not displayed in the outputs from real server jobs.

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

-- 1.7.9.5