Sesame Database

Overview

Register someone

How to add a target ORF

• Create the .csv file (fill in source organism, protein name/ID, aa sequence, molecular weight, DNA sequence)
• Go to Options >> Lab Resources >> Bulk Load >> Verify ORF from CSV (add TargetTrack Rationale) >> Load ORF from CSV

Create a new experiment

• Select the default experiment
• Then "save as" >> "New EM screen"
• a new Number XXX is associated. Use this XXX number for the Leginon experiments
• In the screen tab:
  • add "new raw to screen"
  • (if you did a mistake "Remove rows from Screen")
  • Complete the table
  • In the main window, under ORF:
    • Search ORF Ids
    • let the "default Lab only" parameter
    • find the ORF corresponding to your protein
    • drag and drop it to your EM sheet
    • Click OK to link. It should appear on the "linked items", under the "general" tab
• Only when the table is finished, under the "scores" tab, "Add a Scoring" column

Transfer images

From Leginon to Sesame

• In the menu, select "> Search > EM Screen (EM)" and open (double click) the desired experiment. "Board Sheherazade" window should open.
• Select the "Scores" Tab
• In the menu, select "> Edit > Leginon Image Bulk Load"
• Fill the fields as follow:
  • Database Host: athena (or, if it doesn't work, try cem100. You'll have to connect your computer to it first)
  • Database Port: 3306
  • Database Username: usr_object
  • Database Password (leave field empty)
  • Base Path: select the path "/cem100/data/leginon_converted"

Selection of images from Leginon to Sesame

• select images:
  • go to cem100>data> leginon_converted >data>leginon>j1230
  • select the folder of the current experiment (E...). Copy it.
  • Paste it under cem100>data> leginon_forsesame >data>leginon>j1230.
  • Delete the images you're not interested in keeping
• Import into sesame:
  • In the menu, select "> Edit > Leginon Image Bulk Load"
  • Fill the fields as follow:
    • Database Host: cem100
    • Database Port: 3306
    • Database Username: usr_object
    • Database Password (leave field empty)
    • Base Path: select the path "/cem100/data/leginon_forsesame"

Acquired manually

• Put each image in a folder name according to the well position (A1, A2, A3...)
• In the menu, select "> Edit > Leginon Image Bulk Load", select the main folder where the A1, A2... wells subfolders are.

• Set ALLOWTOPICVIEW =

-- NicolasCoudray - 04 Aug 2011

* updates_Sesame.doc: Sesame Updates (as of October 2011)

* KdpD.csv: KdpD^? ORF file

* KdpE.csv: KdpE^? ORF file

* NrpR.csv: NrpR^? ORF file

* TRPV1.csv: TRPV1 ORF file

* TRPV3.csv: TRPV3 ORF file

* CACT.csv: CACT ORF file