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[ccp4bb] PHENIX & BSS refinement |
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- Protein crystallographyMain steps:- Protein purification- Crystallisation Special:- Programs for crystallography- X-ray detectors Basic tutorials:- Chemistry- Protein - Peptide - Amino Acids Xtal community:- CCP4BB |
CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: PHENIX & BSS refinement From: Jose Casasnovas jcasasnovas {- at -} CNB {- dot -} CSIC {- dot -} ES Date: 2009-02-03 We have seen that the recent versions of phenix (1.3) the structure refinement ends with a bulk solvent correction step, something I found quite unusual (absent in other refinement programs and in older versions of phenix, 1.24.1). We have also seen that the B factor jumps up in this last step (see bellow). Is anybody aware of this? Do you know how to get rid of this final bss step? This step is redundant, as bss is also done at the beginning of each ref cycle. Header of a pdb file after refinement with phenix version 1.3: REMARK R-factors, x-ray target values and norm of gradient of x-ray target REMARK stage r-work r-free xray_target_w xray_target_t REMARK 0 : 0.3729 0.3776 5.594260e+00 5.604698e+00 REMARK 1_bss: 0.3135 0.3236 5.460255e+00 5.490057e+00 BSS refinement step REMARK 1_xyz: 0.3096 0.3226 5.451384e+00 5.487128e+00 refinement of coordinates REMARK 1_adp: 0.2608 0.2858 5.300551e+00 5.386607e+00 refinement of ADPs REMARK 2_bss: 0.2601 0.2843 5.299065e+00 5.384776e+00 REMARK 2_xyz: 0.2545 0.2847 5.285488e+00 5.386100e+00 REMARK 2_adp: 0.2460 0.2821 5.261319e+00 5.375879e+00 REMARK 3_bss: 0.2456 0.2788 5.257944e+00 5.366116e+00 REMARK 3_xyz: 0.2457 0.2809 5.261113e+00 5.371113e+00 REMARK 3_adp: 0.2427 0.2804 5.252685e+00 5.370838e+00 REMARK 3_bss: 0.2427 0.2804 5.252685e+00 5.370838e+00 ??????????? Bfactors REMARK stage b_max b_min b_ave REMARK 0 : 30.00 30.00 30.00 REMARK 1_bss: 30.00 30.00 30.00 REMARK 1_xyz: 30.00 30.00 30.00 REMARK 1_adp: 118.26 1.18 35.04 REMARK 2_bss: 118.26 1.18 35.04 REMARK 2_xyz: 118.26 1.18 35.04 REMARK 2_adp: 157.72 0.00 37.99 REMARK 3_bss: 157.72 0.00 37.99 REMARK 3_xyz: 157.72 0.00 37.99 REMARK 3_adp: 166.60 0.00 38.73 REMARK 3_bss: 203.00 36.40 75.12 ?????? Thanks a lot for your help. Jose M Casasnovas Centro Nacional de Biotecnología (lab. B16) CSIC, Campus UAM Darwin 3 28049 Madrid Spain Ph. 34 915854917(8) Fax. 34 915854506 email: jcasasnovas@cnb.csic.es !!!!!! NEW E-MAIL CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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