[ccp4bb] Refinement with pseudo-translation
Dear CCP4bb members I have a 3.0 Å dataset which has an off-origin peak of height 36% in patterson map. The peak is at fractional co-ordinates 0, 0.5, 0.5. Data has been indexed in P2(1)22(1) SG using HKL2000. I have located all the molecules in asu (as far as I know) using Molrep with the 'locked rotation' and 'Use' PST feature. After 1 round (20 cycles) of rigid body and 1 round (10 cycles) of restrained refinement (Refmac), the R and Rfree are 49 and 53 %. Although the R factors are very high, I feel the solution might be correct because the electron density follows c-alpha trace in almost all places. To be sure, I deleted a beta strand from the structure's core and repeated the refinement and found that the electron density for the strand was still present (I have no experimental phases). I have the following questions: 1) Are the final R factors never expected to reduce to acceptable values given the 36% off-origin peak? 2) What is the best way to settle the SG? I was considering P2(1)2(1)2(1), P2(1)22, P2(1)2(1)2 and P2(1)22(1), considering the off-origin peak is at 0,0.5,0.5. I found all the molecules in asu only using the P2(1)22(1) data in Molrep. Is this the best way to settle my SG? 3) Some CCP4bb archives advise either refining against weak and strong reflections alternatively (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1010L=ccp4bbD=01=ccp4bb9=AJ=ond=No+Match%3BMatch%3BMatchesz=4P=204490) or refining against medium intensity reflections. Should I also be doing these things? If yes, then what is the best way of doing it? Your suggestions and corrections to my interpretation of our data would be appreciated. Regards Shiva
[ccp4bb] TLSANL total B factor question
Dear Crystallographers I am trying to print out my total B factors using TLSANL (version: 6.1) in CCP4- 6.1.1. My TLSANL’s input file.pdb is coming from refmac (version: 5.5.0072) using the TLS restraint refinement option and isotropic B factors. The TLSANL’s output file.pdb contains the following ATOM and ANISOU records as an example. REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS :2 REMARK 3 ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS REMARK 3 ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS ATOM 88 C ASN A 14 0.748 -5.841 -6.258 1.00 35.84 C ANISOU 88 C ASN A 14 5335 4549 3734 0 0 0 C ATOM 89 O ASN A 14 0.807 -6.941 -6.845 1.00 35.04 O ANISOU 89 O ASN A 14 5229 4375 3709 0 0 0 O I am not able to understand why my ANISOU record contains ‘0 0 0’ for the anisotropic component. Something is not correct and I'm not sure why I am not able to print out my total B factors. I would appreciate it if someone could tell me what is going wrong and how can I print my total B factors. Thanks Regards Shiva Kumar
Re: [ccp4bb] TLSANL total B factor question
The simplest explanation would be that those particular atoms are not in any TLS group, and therefore they have only an isotropic ADP component. Unfortunately, the '0 0 0' for the anisotropic component in ANISOU record is for all of my protein atoms. If that is not the case, please show the contents of the header records that describe these 2 TLS groups. The header records are: REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS :2 REMARK 3 ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS REMARK 3 ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3NUMBER OF COMPONENTS GROUP :1 REMARK 3COMPONENTSC SSSEQI TO C SSSEQI REMARK 3RESIDUE RANGE : A4A 372 REMARK 3ORIGIN FOR THE GROUP (A): 5.8065 -0.6242 -14.8498 REMARK 3T TENSOR REMARK 3 T11: 0.0568 T22: 0.0595 REMARK 3 T33: 0.0153 T12: -0.0103 REMARK 3 T13: 0.0065 T23: 0.0022 REMARK 3L TENSOR REMARK 3 L11: 1.1685 L22: 1.8292 REMARK 3 L33: 0.8417 L12: 0.0945 REMARK 3 L13: 0.2145 L23: 0.5509 REMARK 3S TENSOR REMARK 3 S11: 0.0110 S12: -0.1328 S13: -0.1118 REMARK 3 S21: 0.2334 S22: 0.0025 S23: -0.0249 REMARK 3 S31: 0.1311 S32: 0.0150 S33: -0.0134 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3NUMBER OF COMPONENTS GROUP :1 REMARK 3COMPONENTSC SSSEQI TO C SSSEQI REMARK 3RESIDUE RANGE : A 373A 469 REMARK 3ORIGIN FOR THE GROUP (A): 1.9633 16.6927 8.0263 REMARK 3T TENSOR REMARK 3 T11: 0.0322 T22: 0.0531 REMARK 3 T33: 0.0250 T12: -0.0032 REMARK 3 T13: 0.0021 T23: -0.0070 REMARK 3L TENSOR REMARK 3 L11: 1.7358 L22: 0.5530 REMARK 3 L33: 2.3849 L12: 0.2397 REMARK 3 L13: -0.5610 L23: -0.8025 REMARK 3S TENSOR REMARK 3 S11: 0.0490 S12: -0.0959 S13: -0.0548 REMARK 3 S21: 0.0573 S22: -0.0352 S23: -0.0473 REMARK 3 S31: -0.0729 S32: 0.1153 S33: -0.0139 REMARK 3 Thanks Regards Shiva
