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View Code? Open in Web Editor NEWConformational diversity of Native State database Quaternary
Home Page: https://codnasq.herokuapp.com/
License: GNU General Public License v3.0
Conformational diversity of Native State database Quaternary
Home Page: https://codnasq.herokuapp.com/
License: GNU General Public License v3.0
When searching from the home page with a PDB code (e.g. 2ff2) the results are different according to the search field selected:
If searching for "All fields", the table of search results is returned:
http://codnasq.ddns.net/cluster/search?query=2ff2&criteria=all
If searching for "PDB", the cluster view is returned.
http://codnasq.ddns.net/cluster/search?query=2ff2&criteria=pdb
This should be consistent and it should always direct to search results (i.e. as if searching in "All fields").
Only if the user enters a cluster ID (e.g. CQ2ff2) it may lead to the cluster view directly.
As part of #55.
The question is, how to tell which row should be highlighted?
Nota bene: There is .is-selected
css class which changes the background-color
In the footer, the section Rooms 31-33, Department of Science & Technology, UNQ links to:
http://ufq.unq.edu.ar/sbg/files/map_sbg-unq.png
This is incorrect. It should read images instead of files. as follows:
http://ufq.unq.edu.ar/sbg/images/map_sbg-unq.png
For demo purposes and as an easy way to see how the navigation is, we want 3 examples below main search bar.
Blocked by #9 issue
Split protein class, into conformer, protein pair, cluster and each repository.
add>
-'Ligands'
-'pH'
-'Temperature'
-'Description' (title)
-'Type of Movement' (a,b,c)
modify>
-rename 'siblings' por 'other conformers'
-rename 'Longitude' as 'length'
-diferent colour, font for the opened conformer in the list
delete>
-'cluster' column (because all here are inside the same cluster)
-switch 'conformer type' to 'name'
-switch 'conformer source' to 'species' if the string is a part of the species text, should show all that in results
-switch 'cluster ID' to 'PDB' *when a pdb code is written here, the page shows the cluster belonging to the code pdb *
-switch examples>
Example entries: 2vcq | hydrolase | mus musculus
-add 'All fields' by default
-if no text is ingresed, the search shows all results for that field
##Outcome
Create a route where you pass the protein id and you get the protein details page.
Conformer information page
rename 'Longitude' -> 'Length'
rename 'Siblings' -> 'Other conformers'
mark somehow the row of opened conformer of the list
Cluster information
remove 'Average RMSD Tertiary' (we dont have that data)
add 'Representative conformer type:' (with the title of the conformer. People wanna know what kind of cluster are they seeing)
add space between number and Å in Max RMSD Quaternary
Maximum RMSD Pair information
add chains of query and target for 'RMSD Tertiary' row (included in the csv file)
Conformers in cluster
delete 'Cluster' column
rename 'Longitude' -> 'Length'
Statistics page
resize images
http://localhost:8080/cluster/search?query=HOMO+SAPIENS&criteria=source&page=4
actual>
Page 4
Total pages: 290
new>
Total 2900
Page 4
Total pages: 290
shown when specie from 'conformer lists' is clicked
same thing with 'name' is clicked
To have a basic form with a file selector to insert a csv with a protein list.
e.g. http://localhost:8080/cluster/show/CQ2vcq
add:
max RMSD Q the same mentionated below on 'Maximum RMSD Pair information'
average RMSD Q
max RMSD T
average RMSD T
Group
Subsection "Representative conformer":
'Description' of main conformer (in this case title of 2vcq "Complex structure of prostaglandin D2 synthase at 1.95A.")
'length'
'Species'
if it's posible Standar deviation of RMSD Q and RMSD T, https://www.mathsisfun.com/data/standard-deviation-formulas.html
link in 'Conformer numbers' (in this case 18 ) that scroll down to 'Conformers' list
Add>
'Oligomeric state' filter
Switch>
Names of filters (make iqual to home page filters)
description of what we can find on this website
E. g.:
'Longitude' to 'Length'
'Species' to 'Organism'
'Cluster' to 'Cluster ID'
etc.
the changes will be done using the new names file
When resizing the browser to less than 1024 px wide, the sections on the header dissapear.
get the '|' separator and show it as ','
Precondición:
aceptación:
Estuve haciendo algunas pruebas locales y logré dockerizar la aplicación:
Preparamos un directorio hacemos:
mkdir cuis-docker
cd cuis-docker
wget -O cogspur.tgz https://github.com/OpenSmalltalk/opensmalltalk-vm/releases/download/201807260206/squeak.cog.spur_linux64x64_201807260206.tar.gz
git clone --depth 1 https://github.com/Cuis-Smalltalk/Cuis-Smalltalk-Dev.git
tar -zxvf cogspur.tgz
rm cogspur.tgz
mv ./sqcogspur64linuxht ./cogspur
Probablemente se pueden borrar varios archivos de Cuis-Smalltalk-Dev
.
Sobre el mismo directorio crear un Dockerfile con:
FROM debian:9-slim
WORKDIR /opt/cuis
COPY . .
CMD cogspur/squeak -vm-display-null -vm-sound-null Cuis-Smalltalk-Dev/Cuis5.0-3665.image
Después buildeamos la imagen con:
docker build -t "cuis_web:testing" ./
docker run -p 8080:8080 cuis_web:testing
Y con eso ya tenemos el servidor levantado, si la imagen estaba en condiciones (con el webserver levantado).
switch Average number of conformers per protein
old > 15.09
new > 5.15
Display conformer pair with max rmsd on cluster with each conformer details and properties of comparison
how to use the site
Given that Cluster and conformers uses the same ID, we want to distinguish between Cluster id and Conformer id, so we'll add CQ
before cluster id.
en la vista de detalle de un conformero tengo que ver la cantidad de integrantes del mismo cluster
add>
-max RMSD Tertiary pair information (next to the Quaternary)
-'pH' (row)
-'Temperature' (row)
modify>
-rename title, to 'max RMSD Quaternary pair information'
-rename 'Source' row to 'Organism'
-rename 'Sequence identity' to 'Sequence identity (%)'
-rename 'Structural similarity' to 'Structural similarity (%)'
-rename 'RMSD' to ''RMSD (Å)' (angstrom symbol= Unicode Character 'ANGSTROM SIGN' (U+212B))
-new value 'Structural similarity (%)' defined as: Structural similarity * 100 / Structurally equivalent residue pairs
-move 'Sequence identity (%)' below 'Organism'
-move 'Structurally equivalent residue pairs' below 'Sequence identity (%)'
delete>
-Permutations
-Type of alignment
-rank of alignment
The following could be added to the home page:
CoDNaS-Q is a high-quality collection of homo-oligomeric conformers obtained from the Protein Data Bank (PDB). It allows the exploration of conformational diversity and its determinants at the quaternary level, for a large number of proteins determined under different experimental conditions and from a wide variety of families and species. Find out more about CoDNaS-Q in the About and Help pages.
(include links to About and Help pages)
As part of #55.
The big question is, how to get the chains?
make more narrow?
add>
-scroll bar on list box (or something like that)
modify>
-rename title 'Conformers' to 'Conformers in cluster'
delete>
-cluster column (is allways the same cluster here)
To have a handy way to find proteins by code 1 / code 2.
replacing 'XXXX' with the PDB code
https://www.rcsb.org/structure/XXXX
add>
-last page button
-conformer quantity column
-maxRMSD-Q of clusters column
-show only 1 result per cluster
-fix empty last page
delete>
-Biological Assembly column
-Resolution
fixes #26
Ligand code (1-3 characters) followed by ligand's name inside parenthesis
e.g>
PDB ID:
1wuq
old ligands:
ZN zinc ion, 8GT 8-oxo-guanosine-5'-triphosphate
new ligands:
ZN (zinc ion), 8GT (8-oxo-guanosine-5'-triphosphate)
on this page, we will be able to search the clusters ordened by certain criteria (e. g. organism, family, etc.)
Setup project
Groups:
a >> 'Tertiary deformations'
b >> 'Mixed motions'
c >> 'Rigid-body displacements'
'not found' legend when the search is not successful
Relacionado con #4 esto nos permitiría acceder a la aplicación desde una url provista por el equipo de redes de la UNQ.
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