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Elmir edited this page Oct 11, 2022 · 10 revisions

Project Crystals CSV file

Defines all crystals that are part of the project. Include necessary and optional meta-data about the crystals. This file must be uploaded when a new project is created within the FragMAXapp.

The meta-data is used for:

  • processing of collected diffraction data
  • for placing potentional ligands
  • for keeping track of experimental conditions during crystals preparation in the lab
  • for submitting results to PDB

For each crystal it's possible to include data on:

  • fragment used
  • crystalization conditions and method
  • solvent information

Terms

Apo crystal - crystal without any fragment

Example

Below is an example of a valid CSV file.

sampleID,fragmentLibrary,fragmentCode,crystallizationMethod,crystallizationPH,crystallizationTemperature,crystallizationCondition,compoundConcentration,solvent,solventConcentration,soakTime,soakCondition
X0001,,,"VAPOR DIFFUSION, SITTING DROP",7.4,86.3,cloudy,0.42,DMS,5.4,,
X0002,,,"VAPOR DIFFUSION, SITTING DROP",7.4,86.3,cloudy,0.42,EDO,5.4,,
X0003,AcmeFrags,AF014,"VAPOR DIFFUSION, HANGING DROP",7.4,86.3,cloudy,0.42,DMS,5.4,12h,salty
X0004,MordorLib,MDL023,"VAPOR DIFFUSION, HANGING DROP",7.4,86.3,cloudy,0.42,EDO,5.4,30s,salty

The above CSV defines a project with 4 crystals. The X0001 and X0002 crystals will be treated as apo crystals. The X0003 crystal have AF014 fragment from AcmeFrags fragment library. The X0003 crystal have MDL023 fragment from MordorLib fragment library.

CSV format

  • must include header row
  • columns may be listed in any order
  • must use , as cell delimiter
  • must use . as decimal number separator

Time Duration

Time duration is specified using seconds, minutes or hours.

The format is <N><unit>. Where <N> is as an integer and <unit> is the time unit used.

Valid <unit> strings are:

  • h (hours)
  • m (minutes)
  • s (seconds)

Below are examples of valid time duration expressions:

  • 24s (24 seconds)
  • 45m (45 minutes)
  • 12h (12 hours)

Note that decimal expression are not allowed for time duration. If you need to specify for example half an hour, use 30m expression.

All Supported Columns

  • sampleID
  • fragmentLibrary
  • fragmentCode
  • crystallizationMethod
  • crystallizationTemperature
  • crystallizationCondition
  • compoundConcentration
  • solvent
  • solventConcentration
  • soakTime
  • soakCondition

boldColumn is a required column

Required and Optional columns

sampleID, fragmentLibrary and fragmentCode columns are required, and must be present in the CSV file. If any of required columns are omitted, the FragMAXapp will not accept the CSV file.

All other columns are optional. If omitted, the FragMAXapp will treat the value as unknown.

Columns Specification

sampleID

A unique ID for a crystal. The ID can be any combination of letters and numbers. The ID will be used to construct file paths to crystal's dataset files. The ID used must match the naming scheme used for dataset files paths.

fragmentLibrary

Name of the fragment library for the fragment used. The name of the library must be known a priori by the FragMAXapp, otherwise the CSV file will be rejected. This value must be empty for apo crystals.

fragmentCode

The fragment's code within the specified library. The code must match some known fragment in the specified library, otherwise the CSV file will be rejected. This value must be empty for apo crystals.

crystallizationMethod

The crystallization method used. Must be one of the following strings:

  • VAPOR DIFFUSION, SITTING DROP
  • VAPOR DIFFUSION, HANGING DROP
  • BATCH MODE
  • LIPIDIC CUBIC PHASE
  • MICROBATCH
  • MICROFLUIDIC

crystallizationTemperature

The crystalizaion temperature in kelvin degrees. This must be a valid decimal number.

crystallizationCondition

Crystallization conditions. This can be any string.

compoundConcentration

Compound concentration during crystallization in millimolar. Must be a valid decimal number.

solvent

Solvent used during crystallization. This can be any string. For cases where no solvent was used, this must be an empty string.

solventConcentration

Solvent concentration during crystallization in percent. This must be a valid decimal number. For cases where no solvent was used, this must be an empty string.

soakTime

The time crystal have been soaked in the fragment solution. This must be a valid time duration expression.

soakCondition

The conditions while crystal have been soaked in the fragment solution. This can be any string.

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