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Run Grade2 on your non-confidential ligand

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to setup a Grade2 run

Introduction

Grade2 is a tool for generating restraint dictionaries for ligands in macromolecular structure determination. Please see Introduction to Grade2 help, Grade Web Server Documentation help, and Videos showing how to use Grade Web Server help for more information.

Latest News

03 July 2024
Grade Web Server has been updated to run the latest version of Grade2. There are many improvements: see the Grade2 ChangeLog 1.6.0 for full details.

We have also updated to CSD-Core version 2024.1 so that restraints are now based on over 1.25 millon CSD structures.

19 Jan 2024
The PDB is now issuing 5-character PDB Chemical Component IDs (such as A1LU6), having run out of 3-character IDs. The Grade Web Server can now produce restraints for these cases and the input forms have been altered to stop calling the component ID the "three-letter code".

Click to expand old news

25 Sep 2023
Support for a new option --eh99_sigma_correction that scales up all non-hydrogen bond and angle sigmas to match the mean sigma values of the EH99 amino restraints used by BUSTER. For details see an analysis comparing Grade2 and EH99 Restraints for amino acid side chains.

05 July 2023
Grade Web Server has been updated to run the latest version of Grade2 1.4.1. This fixes bug where Grade2 produces restraints with bond angle sigma set to zero. Now a minimum value of 0.3º is used for bond angle sigmas and 0.005Å for the bond sigmas. Thanks to Christian Schleberger for reporting this bug. See the Grade2 ChangeLog 1.4.1 for full details.

22 May 2023
Grade Web Server has been updated to run the latest version of Grade2 1.4.0. Changes include many improvements to the 2D schematic diagrams and CSD-based restraints for pentafluorosulfanyl SF5. See the Grade2 ChangeLog 1.4.0 for full details.

14 April 2023
Recent problems for some PDB chemical components are now fixed details. Big thanks to the PDBe team, particularly Ibrahim Roshan for the fix.

29 December 2022
Added YouTube videos to the Grade Web Server Documentation. These aim to show a new user how to use the Grade Web Server. Together they demonstrate producing restraints for a ligand, including using the PubChem Sketcher to obtain a SMILES string starting from a molecular diagram.

22 December 2022
Update to Grade Web Server 2.0.3 <2022-12-22> and Grade2 to 1.3.1rc1 improvements in:

  • Fixed bug where Grade2 terminates with IndexError: string index out of range for large ligands that have more than 26 five-membered or six-membered rings. Thanks to Deepak Deepak for reporting this bug. (#532)

  • Fixed bug where Grade2 produced SHELXL restraint files with REM comment lines longer than 80 characters that SHELX cannot process. Thanks to Tim Gruene for reporting this bug. (#544)

14 December 2022
Major upgrade to Grade Web Server to run Grade2. Also included is support for a wider range of input file formats such as SDF. The user interface has been simplified. Grade2 has many improvements over Grade, such as better treatment of planar groups help. Please let us know what you think of the changes.

Acknowledgements

Grade2 is developed at Global Phasing Ltd. Many thanks to:

Current Grade Web Server Usage Statistics

Total of 37832 successful Grade and Grade2 runs since February 2012

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Monthly breakdown:

Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Σ
2012 7 70 79 105 81 84 43 33 139 73 51 765
2013 91 54 70 53 63 38 69 31 39 61 85 58 712
2014 49 154 48 63 74 83 133 146 91 147 59 92 1139
2015 79 121 73 142 144 122 132 120 95 111 78 83 1300
2016 163 165 106 129 229 118 232 170 139 157 107 134 1849
2017 122 169 168 126 166 201 292 169 159 213 165 128 2078
2018 169 205 248 214 227 323 492 179 185 231 203 208 2884
2019 159 155 349 226 272 150 253 104 162 225 163 182 2400
2020 165 235 215 193 130 148 221 131 195 202 281 200 2316
2021 198 261 219 203 171 210 201 123 151 188 244 283 2452
2022 227 234 225 235 213 189 219 188 195 255 245 370 2795
2023 388 593 650 481 562 549 592 612 556 489 577 507 6556
2024 852 718 640 707 653 560 720 445 2693 1440 672 486 10586

Run Original Grade (Deprecated)

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If you want to run the original Grade program (rather than Grade2) this is currently still possible using the
Run Original Grade (Deprecated) interface.

Please email buster-develop@GlobalPhasing.com with any problems, queries or suggestions.

GWS version: 2.0.11 <2024-07-03>