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Refinement: Difference between revisions
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* [[CNS]] | * [[CNS]] | ||
* [[PHENIX|phenix.refine]] | * [[PHENIX|phenix.refine]] | ||
== restraints for ligands == | |||
All refinement programs come with a set of ligands known to them, i.e. the files describing the topology and parameters of these ligands are part of the distribution. Both Refmac and phenix.refine use one large file called mon_lib_list.cif . CNS uses files in the $CNS_TOPPAR directory. | |||
If you have a ligand that is unknown to the refinement program, you could either | |||
* identify a similar ligand among the known ones and modify it | |||
* use the [http://davapc1.bioch.dundee.ac.uk/prodrg/index.html PRODRG server] to obtain the ligand description | |||
* use [http://xray.bmc.uu.se/hicup G. Kleywegt's HIC-Up] to obtain the ligand description | |||
* try to identify the ligand in the list of chemical compounds occurring in [http://www.rcsb.org PDB] files, at http://www.wwpdb.org/ccd.html - maybe it is known under a different name than you thought, and you just have to adjust your PDB file | |||
== what can go wrong in refinement? == | == what can go wrong in refinement? == | ||
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=== R_free much higher than R === | === R_free much higher than R === | ||
=== how large should the difference between R_free and R be? === | ==== how large should the difference between R_free and R be? ==== | ||
For now, see [http://www.ncbi.nlm.nih.gov/pubmed/11937051 Kleywegt GJ, Jones TA."Homo crystallographicus--quo vadis?" Structure. 2002 Apr;10(4):465-72.] | For now, see [http://www.ncbi.nlm.nih.gov/pubmed/11937051 Kleywegt GJ, Jones TA."Homo crystallographicus--quo vadis?" Structure. 2002 Apr;10(4):465-72.] | ||