Difference: SesameDatabase (11 vs. 12)

Revision 1220 Nov 2013 - Main.NicolasCoudray

META TOPICPARENT	name="TemimpsGroup"

Sesame Database

Link

http://sesame.nysbc.org/sesame/
Link is sheherazade.

Overview

See Laboratory_Information_Management_System-SESAME.pptx.

Register someone

See Register.docx.

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

See sesame_uplaod.pptx. On 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: cem100 (or, if it doesn't work, try athena. 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"

Changed:

<
<

Acquired manually

>
>

Images 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.

Added:

>
>

New protein to enter

CSV. Find the source number:
- Options> Lab Res > Source Org. If no number, ask Zsolt.
- or: System > Source Org.
- drag it in our Sesame Org
- Main Id, Sequence, aacode, gcode, molweight... : check gcode (www.expasy.org/translate -- protein Blast. Remove the Met)
Upload
- Options> Lab Resource > Bulk Load
- Bulk Load> Verify Bulk Load ORFs (.csv)
- > Bulk Load ORF. Will show "G.O.......... cluster seed rebuilt........DONE" then should appear on our ORF list.
Put it in TargetTrack
- Search "workgroup"
  - >open last
  - >save "as new"
- SELECT, CLONE, EXPRESS, PURIFY, CRYSTALLIZATION
- change name
- Set it to its protocol:
  - create protocol:
    - >Las res> Lab protocol
    - click SEARCH: everything appears
    - click the last one.
    - save as New
    - Change Title, body and name
- ORF:
  - delete
  - save workgroup
  - drag protein from ORF to workgroup
  - save workgroup
  - select row, click add/action: "Selection - Eukaryotic"/ "Selection - Membrane protein". 1 workgroup for --- selection.
Submit
- Repeat > ORF > TargetTrack. "Labf...: 614 TEMIMPS.... output file name" (create empty output file name)
- Send file to David M.

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

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META FILEATTACHMENT	attr="" autoattached="1" comment="TRPV1 ORF file" date="1334856950" name="TRPV1.csv" path="TRPV1.csv" size="3919" user="Main.RalphLasala" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="NrpR ORF file" date="1334856905" name="NrpR.csv" path="NrpR.csv" size="2732" user="Main.RalphLasala" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="Sesame Updates (as of October 2011)" date="1319571871" name="updates_Sesame.doc" path="updates_Sesame.doc" size="44544" user="Main.RalphLasala" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1314370559" name="Register.docx" path="Register.docx" size="149347" user="Main.NicolasCoudray" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="CACT ORF file" date="1334856994" name="CACT.csv" path="CACT.csv" size="1769" user="Main.RalphLasala" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="KdpE ORF file" date="1334856830" name="KdpE.csv" path="KdpE.csv" size="1464" user="Main.RalphLasala" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="TRPV3 ORF file" date="1334856973" name="TRPV3.csv" path="TRPV3.csv" size="3727" user="Main.RalphLasala" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="" date="1314370453" name="Laboratory_Information_Management_System-SESAME.pptx" path="Laboratory_Information_Management_System-SESAME.pptx" size="1117401" user="Main.NicolasCoudray" version="1"
META FILEATTACHMENT	attr="" autoattached="1" comment="KdpD ORF file" date="1334856811" name="KdpD.csv" path="KdpD.csv" size="4140" user="Main.RalphLasala" version="1"

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