Re: [ccp4bb] TLSANL total B factor question
That was a bug in TLSANL, introduced in 6.1.0 and fixed in 6.1.2. So you need to update your CCP4, or at least extract a newer tlsanl binary. Apologies for that. Martyn On Fri, 2010-05-21 at 04:46 +0100, Shiva Kumar wrote: 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 -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603634Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
Re: [ccp4bb] TLSANL total B factor question
Hi Shiva, Not directly related to the problem you reported, but I wanted to warn you that in refmac 5.5.0072 the default is for the keyword TLSD WATERS ADD to be applied. This keyword tells refmac to assign all of your water molecules to existing TLS groups. (It does this quietly without any notice as to which waters are assigned to which groups in the TLS header of the pdb, TLSOUT or to the log file and no listing of the default setting of this keyword in the logfile.) So unless you included the non-default keyword TLSD WATERS EXCLUDE then your waters have residual B's as well in your pdb file and TLSANL cannot convert them to full B's since it has no record of which waters belong to which TLS groups. Thus the output from TLSANL will be a file with mixed full (on protein atoms) and residual (on water atoms) B-factors. If you did not give the keyword TLSD WATERS EXCLUDE, then the only method I know to ensure that the B-factors on the waters are properly converted to full-B is to re-run your last refmac job and add the keyword TLSO ADDU which will give you full B's on your output. (Note that you should not use this file for input into another round of refmac refinement -- unless you do a B-factor reset first). Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Shiva Kumar Sent: Thursday, May 20, 2010 8:46 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [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
[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
On Thursday 20 May 2010, Shiva Kumar wrote: 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. The simplest explanation would be that those particular atoms are not in any TLS group, and therefore they have only an isotropic ADP component. If that is not the case, please show the contents of the header records that describe these 2 TLS groups. Ethan 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
