Re: [ccp4bb] Rpim and how its related to anomalous signal
In my opinion Rpim is not related directly to anomalous signal, so perhaps that is why there is some confusion. Also I think some folks confused Rpim with Rrim. The latter is also called Rmeas. But once again, these are not related directly to anomalous signal. I do not find Rpim very useful for anything since when the data has high multiplicity Rpim gets very low, but as Michael Blum told me, "Precision does not trump accuracy." I would personally rather have accurate data than highly redundant but inaccurate data. I like to look at the deltaF / sigma(deltaF) value reported by SHELXC and other programs, where deltaF is ||F+| - |F-||. This might also be called . There are other things to look at as well. Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vijayakumar.B [vijaybioscie...@gmail.com] Sent: Tuesday, September 18, 2012 4:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Rpim and how its related to anomalous signal Dear CCP4BB users, I am very much interested to work in Anomalous scattering technique for macromolecular structure determination. I have already gone through some literature in which they have explained about a parameter called “Rpim”. I am little bit confused about Rpim values. Can anyone tell me about the use of this parameter in structure determination by anomalous techniques and how Rpim is related to anomalous signal? Thanks in advance With kind regards B. Vijayakumar
Re: [ccp4bb] Unusually low B factors with phenix
Joao, I am using the latest version of phenix 1.8.1-1168 1.8.1-1168 should not have that "problem". If you suspect there is still a problem, you can send me the data and model files off list, explain what exactly the problem is, and I will have a look right away. FYI: there is Phenix mailing list for Phenix-specific questions, where I can also explain in great details the behavior with the B-factors you observe. All the best, Pavel
Re: [ccp4bb] Unusually low B factors with phenix
Hi, I am using the latest version of phenix 1.8.1-1168 for the MacOSX and I see a similar behaviour with the B-factors. Which version do you suggest to update to? There might be a problem with over-refinement and one workaround might be to limit the Rfree-R=0.05, but your Rfree will likely to increase. Your B-factors will make more sense though. Cheers, Joao On 02/11/2012 10:54, "Jeffrey, Philip D." wrote: >That sounds like the bug in Phenix.refine v1.8 that a few of us >encountered - updating to the latest release will help. > >Actually wasn't so much a bug but a "feature", albeit not the best one >imaginable. Anyone using older v1.8 versions should update. > >--- >Phil Jeffrey >Princeton > >On Nov 2, 2012, at 6:41 AM, "Demetres D. Leonidas" > wrote: > >> Dear Tim, >> >> this affects all atoms and yes I did reset the B-factors to 20.00 prior >>to refinement. I have not tried REFMAC but now I will give it a try >>since phenix does not seem to do the job. >> >> best >> >> Demetres >> >> >> On 2/11/2012 1:34 μμ, Tim Gruene wrote: >>> -BEGIN PGP SIGNED MESSAGE- >>> Hash: SHA1 >>> >>> Dear Demetres, >>> >>> does this affect all atoms, or only a few selected ones? >>> >>> Did you compare with refmac5 (for e.g. input script errors), or did >>> you reset the B-factors to a reasonable value (e.g. 20-30) prior to >>> refinement? pdbset can do this conveniently. >>> >>> Best, >>> Tim >>> >>> On 11/02/2012 11:06 AM, Demetres D. Leonidas wrote: Hello, I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine (1.8.1.-1168) and a structure at 1.9 A resolution. The ADP values after the refinement are very very low, less than 2 and sometimes 0. I am getting the same result with and without optimization of the X-ray/ADP weight. Has anyone else noticed that and is there a workaround ? Demetres >>> - -- Dr Tim Gruene >>> Institut fuer anorganische Chemie >>> Tammannstr. 4 >>> D-37077 Goettingen >>> >>> GPG Key ID = A46BEE1A >>> -BEGIN PGP SIGNATURE- >>> Version: GnuPG v1.4.12 (GNU/Linux) >>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ >>> >>> iD8DBQFQk6+vUxlJ7aRr7hoRAvCZAKDxzmLYV74HKanTuoNiqLEu6AmlRwCgkVQs >>> Q+SZVN6ISb0X38ZekG119/s= >>> =xKhB >>> -END PGP SIGNATURE- >> >> -- >> --- >> Dr. Demetres D. Leonidas >> Associate Professor of Biochemistry >> Department of Biochemistry & Biotechnology >> University of Thessaly >> 26 Ploutonos Str. >> 41221 Larissa, Greece >> - >> Tel. +302410 565278 >> Tel. +302410 565297 (Lab) >> Fax. +302410 565290 >> E-mail: ddleoni...@bio.uth.gr >> http://www.bio.uth.gr >> --- > Contact and registered office address: Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX. The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please make no use of its contents and contact the sender.
Re: [ccp4bb] Unusually low B factors with phenix
That sounds like the bug in Phenix.refine v1.8 that a few of us encountered - updating to the latest release will help. Actually wasn't so much a bug but a "feature", albeit not the best one imaginable. Anyone using older v1.8 versions should update. --- Phil Jeffrey Princeton On Nov 2, 2012, at 6:41 AM, "Demetres D. Leonidas" wrote: > Dear Tim, > > this affects all atoms and yes I did reset the B-factors to 20.00 prior to > refinement. I have not tried REFMAC but now I will give it a try since phenix > does not seem to do the job. > > best > > Demetres > > > On 2/11/2012 1:34 μμ, Tim Gruene wrote: >> -BEGIN PGP SIGNED MESSAGE- >> Hash: SHA1 >> >> Dear Demetres, >> >> does this affect all atoms, or only a few selected ones? >> >> Did you compare with refmac5 (for e.g. input script errors), or did >> you reset the B-factors to a reasonable value (e.g. 20-30) prior to >> refinement? pdbset can do this conveniently. >> >> Best, >> Tim >> >> On 11/02/2012 11:06 AM, Demetres D. Leonidas wrote: >>> Hello, >>> >>> I am experiencing a weird problem with B factor refinement >>> (individual, isotropic) in phenix.refine (1.8.1.-1168) and a >>> structure at 1.9 A resolution. The ADP values after the refinement >>> are very very low, less than 2 and sometimes 0. I am getting the >>> same result with and without optimization of the X-ray/ADP weight. >>> Has anyone else noticed that and is there a workaround ? >>> >>> Demetres >>> >> - -- Dr Tim Gruene >> Institut fuer anorganische Chemie >> Tammannstr. 4 >> D-37077 Goettingen >> >> GPG Key ID = A46BEE1A >> -BEGIN PGP SIGNATURE- >> Version: GnuPG v1.4.12 (GNU/Linux) >> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ >> >> iD8DBQFQk6+vUxlJ7aRr7hoRAvCZAKDxzmLYV74HKanTuoNiqLEu6AmlRwCgkVQs >> Q+SZVN6ISb0X38ZekG119/s= >> =xKhB >> -END PGP SIGNATURE- > > -- > --- > Dr. Demetres D. Leonidas > Associate Professor of Biochemistry > Department of Biochemistry & Biotechnology > University of Thessaly > 26 Ploutonos Str. > 41221 Larissa, Greece > - > Tel. +302410 565278 > Tel. +302410 565297 (Lab) > Fax. +302410 565290 > E-mail: ddleoni...@bio.uth.gr > http://www.bio.uth.gr > ---
Re: [ccp4bb] Unusually low B factors with phenix
It could be a problem with your data, e.g. many overloaded reflections not being removed or F and F^2 mixed up. What is your Wilson B-value? George -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] Unusually low B factors with phenix
Dear Tim, this affects all atoms and yes I did reset the B-factors to 20.00 prior to refinement. I have not tried REFMAC but now I will give it a try since phenix does not seem to do the job. best Demetres On 2/11/2012 1:34 μμ, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Demetres, does this affect all atoms, or only a few selected ones? Did you compare with refmac5 (for e.g. input script errors), or did you reset the B-factors to a reasonable value (e.g. 20-30) prior to refinement? pdbset can do this conveniently. Best, Tim On 11/02/2012 11:06 AM, Demetres D. Leonidas wrote: Hello, I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine (1.8.1.-1168) and a structure at 1.9 A resolution. The ADP values after the refinement are very very low, less than 2 and sometimes 0. I am getting the same result with and without optimization of the X-ray/ADP weight. Has anyone else noticed that and is there a workaround ? Demetres - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQk6+vUxlJ7aRr7hoRAvCZAKDxzmLYV74HKanTuoNiqLEu6AmlRwCgkVQs Q+SZVN6ISb0X38ZekG119/s= =xKhB -END PGP SIGNATURE- -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry & Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr http://www.bio.uth.gr ---
Re: [ccp4bb] Unusually low B factors with phenix
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Demetres, does this affect all atoms, or only a few selected ones? Did you compare with refmac5 (for e.g. input script errors), or did you reset the B-factors to a reasonable value (e.g. 20-30) prior to refinement? pdbset can do this conveniently. Best, Tim On 11/02/2012 11:06 AM, Demetres D. Leonidas wrote: > Hello, > > I am experiencing a weird problem with B factor refinement > (individual, isotropic) in phenix.refine (1.8.1.-1168) and a > structure at 1.9 A resolution. The ADP values after the refinement > are very very low, less than 2 and sometimes 0. I am getting the > same result with and without optimization of the X-ray/ADP weight. > Has anyone else noticed that and is there a workaround ? > > Demetres > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQk6+vUxlJ7aRr7hoRAvCZAKDxzmLYV74HKanTuoNiqLEu6AmlRwCgkVQs Q+SZVN6ISb0X38ZekG119/s= =xKhB -END PGP SIGNATURE-
[ccp4bb] Unusually low B factors with phenix
Hello, I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine (1.8.1.-1168) and a structure at 1.9 A resolution. The ADP values after the refinement are very very low, less than 2 and sometimes 0. I am getting the same result with and without optimization of the X-ray/ADP weight. Has anyone else noticed that and is there a workaround ? Demetres -- --- Dr. Demetres D. Leonidas Associate Professor of Biochemistry Department of Biochemistry & Biotechnology University of Thessaly 26 Ploutonos Str. 41221 Larissa, Greece - Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleoni...@bio.uth.gr http://www.bio.uth.gr ---
