[buster-discuss] Grade2 atom naming

Oliver Smart oliver.s.smart at gmail.com
Wed Jul 28 16:04:39 CEST 2021


Hi Wei-Chun,
Thanks for the positive feedback about Grade2. Currently, the recommended best way to produce a Grade2 restraint dictionary that is consistent with a previously produced Grade restraint dictionary is to:

  *   Start from the PDB file produced by Grade (for instance grade-XXX.pdb)
  *   Load this into CSD Mercury.
     *   select the Mercury option "Edit" -> "Auto Edit"
     *   accept the default options in the popup window:
[Screenshot_2021-07-26_at_15.58.42]<https://gitlab.com/gphl/grade2/uploads/e7c05313e70bdb24b6b25faa02455773/Screenshot_2021-07-26_at_15.58.42.png>

     *   Mercury will show you the bonds in its main window. Check that the bonding applied corresponds to the molecule wanted. If not use Mercury to manually edit the bond definitions.
     *   select the Mercury option "File" -> "Save As" and the option "Mol2 files". Save to a .mol2 file.
  *   Use the .mol2 file as the input to grade2 --in.
Apologies this is rather laborious! In a future release, it is intended to produce an easier process where the Grade output CIF restraint dictionary can be directly used as input to Grade2. (It is already possible to use Acedrg and Grade2 restraint dictionaries as an input to Grade2).
Hope this answer is useful. Please let us know if anything is unclear.
Best regards,
Oliver (for BUSTER developers)

From: buster-discuss <buster-discuss-bounces at globalphasing.com> on behalf of Wei-Chun Kao <wei-chun.kao at biochemie.uni-freiburg.de>
Date: Monday, 26 July 2021 at 12:55
To: buster-discuss at globalphasing.com <buster-discuss at globalphasing.com>
Subject: [buster-discuss] Grade2 atom naming
Hello,

I just started using Grade2 with the latest BUSTER release. For a phospholipid input from SMILES Grade 2 took only 13 second as compared 266 seconds required by the original Grade on the same computer*. The performance of Grade2 is astonishing!

However the atom naming of the output coordinates from Grade2 are different than what produced from Grade, which means that I cannot just re-refine the structure directly using BUSTER for which I would just need to change the restraint paths in my existing refinement /job submission script. Instead the ligand molecules have to be re-modelled from scratch using the new restraints in Coot.

Is there any way to get the same atom naming “conventions” as in the original Grade?

*My system is CentOS7. CCP4-7.1 and CCDC 2021 were installed with the latest updates.

Best regards,

Wei-Chun Kao

—

Dr. rer. nat. Wei-Chun Kao
wei-chun.kao at biochemie.uni-freiburg.de<mailto:wei-chun.kao at biochemie.uni-freiburg.de>
TEL: +49-761-203-5277<tel:%2B49-761-203-5277>
orcid.org/0000-0001-8687-6334<http://orcid.org/0000-0001-8687-6334>

Institute for Biochemistry and Molecular Biology
AG Carola Hunte
Albert-Ludwigs-Universitaet Freiburg
Stefan-Meier-Str. 17
D-79104 Freiburg im Breisgau
Germany

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