How is SynchWeb used for MX at DLS? - GitHub Pages

How is SynchWebused for MX at DLS?

Dave Hall

User log book

Logistics

Auto-processing results

Data re-processing

User tools

Staff tools

User Logbook

I03

I04

I04-1

I24

I23

VMXi

VMXm

I19 – small molecule

Event driven

Data collection events –view at visit and proposal level

User filterable Defined filters

Sample changer status

VMXi – fully automated, user free, in

situ data collection

Logistics

Tracking of samples, dewars& sample information essential for users and staff across MX beamlines

Add Add samples

Add Add containers

Add Add dewars

Create Create shipment

Creating a shipment

Tracking sample information

Protein information can include sequence or PDB files or codes

Used by downstream processing pipelines. Presence of

Sequence triggers MrBUMP and is used in BigEP for model building

PDB file or code triggers DIMPLE

Tracking sample information

Sample information added when creating containers

UK/EU academic users book shipping with DHL API

DHL info available to users and staff

Dewar transfer or shipment home requested from here

Dewar store 3 x 3 x 7.75 m, > 100 dewarsCentrally sited between I23, I24 and I03, I04, I04-1

Dewar storage

• Improved tracking of dewars in storage area, interface shows:

• Location of dewars on-site

• Which dewars need to be refilled with LN2 or dispatched

• Which dewars need to be returned to users

• Email to LCs listing dewars needed for next day expts

Puck barcodes are read when (un)loading robot

Omron system to read barcodes

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THISREVISION

I03 BEAMLINEPUCK BAR CODE READER ASSEMBLYPUCK BAR CODE READER ASSEMBLY

DRNDATE

AG06/06/17

DIAMOND LIGHT SOURCE LTD.DIAMOND HOUSE

HARWELL SCIENCE ANDINNOVATION CAMPUS,

DIDCOT, OXFORDSHIRE,OX11 0DE

CHKDATE

AG06/06/17

APPDDATE

GMAD06/06/17 AG 13/04/17 Approved

PDMLink 1127439 1 OF 2 B

N DRG N DESCRIPTION QTY REMARKS

1 1127434 PUCK POSITIONING ASSEMBLY 1

2 1127440 BAR CODE READER MOUNTING PLATE 1

3 1127938 TOUCH FINDER PANEL BRACKET 1

4 1127939 CODE READER MOUNTING BRACKET 1

5 NUT_M04_STST NUT M04 STST A4-70 2

6 SHS_M03_X_16_SP SKT HD CAPSCREW M3 X 16 A4-70 SP 2

7 SHS_M04_X_12_STST SKT HD CAPSCREW M4 X 12 A4-70 4



10 STP124773 FQ-CR2 (BAR CODE READER) 1

11 STP124774 FQ-XPM TOUCH FINDER HOUSING 1

12 STP125403 D30-MONITOR (TOUCH FINDER) 1

13 STP125404 BAR CODE READER BOX 1

14 WAS_M03_STST PLAIN WASHER, NORMAL, M3 STST 2



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ASEE SHEET 2

Barcode reading station with puck sensor/trigger. Success sound.

Laser pointer to indicate location in robot dewar

Scanned pucks are

auto-assigned in ISPyB ready for users in

GDA

Autoprocessing results

Screening for data collection strategies

Data Collections

Difference Maps - DIMPLE

https://uglymol.github.io

Phasing and Model Building – BigEP

Auto-processing summary

https://ispyb.diamond.ac.uk/dc/visit/mx17201-34

Data Re-processing

Define reprocessing requirements

• Select pipeline

• Provide high res cut-off if required

• Provide space group if wish to constrain pipeline

Select images

Can process multiple ranges from data set

• Click + to add more from same data collection

Can add more data sets

• Click reprocess button on relevant data collection

• Clicking Integrate will combine all 3 together with 1 set of constraints

Many collections reprocessing

• Filter using search field for protein interested in (this time “gst”)

• Scroll down page

• Define parameters for integration

• Select images

• Integrate

Reprocessing results

• Can see status of submitted jobs

• Access results from links to Files on right

• Takes you to the standard analysis results where reprocessed jobs will be added

User Tools

Webcams

VisitStats

ProposalStats

Staff Tools

Beamline staff login screen

Beamline status

Dewar overview in SynchWeb

Fault database

Summary

• Users

• From preparing and shipping

• Providing information for unattended collections and downstream pipelines

• Following data collections and outcomes of processing

• Interrogating usage

• Long term log book

• Staff

• Preparing for upcoming expts

• Finding samples/dewars

• Following user expts

• Beamline and user statistics

• Fault logging and solving

• Future

• Improved interfaces for unattended data collection, interface & results

• VMXi improvements for data collection and results presentation

• VMXm including SEM

• SSX interfaces

• Shipping improvements – 31st Dec 2020 deadline

• ….

How is SynchWeb used for MX at DLS? - GitHub Pages

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