Re: [ccp4bb] Phaser 2.8.3: Hendrickson-Lattman coefficients generated from dataset lacking anomalous signal
If I remember for coefficients with FOM and a precise PHI calculated, A = FOM*cos(phi) B = FOM*sin(phi) C=D=0 If you have a probability curve for PHI. 0 to 360 such as you get from experimental phasing, A B C D mirror this bimodal curve better .. On Fri, 9 Feb 2024 at 09:58, Nitin Kulhar < 9dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear sir > > Thank you for clearing that. I checked back to see that HLC/D are > invariably 0 for all reflections, with the non-zero HLA/B supposedly having > been originated from the probability distribution of phases *calculated* > by phaser. Hopefully, I have not misunderstood it. > > Thanks and regards > Nitin Kulhar > > On Thu, Feb 8, 2024 at 9:07 PM Randy John Read wrote: > >> Hi, >> >> Hendrickson-Lattman coefficients are just a way of storing phase >> probability information, and they can come from different sources including >> atomic models. Phaser puts in HL coefficients because they could be handy >> under some circumstances for combining the phase information from >> experimental phasing. You might notice that only A and B are non-zero for >> the molecular replacement HL coefficients. That’s because the phase >> probability distribution is unimodal for calculated phases, whereas it’s >> generally bimodal for experimental phases (thus requiring more >> coefficients). >> >> Best wishes, >> >> Randy Read >> >> > On 8 Feb 2024, at 14:32, Nitin Kulhar < >> 9dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote: >> > >> > Dear all >> > >> > Is anomalous diffraction necessary for determining experimental phases >> and the Hendrickson-Lattman coefficients (HLA, HLB, HLC, and HLD)? >> > >> > MR solution from Phaser 2.8.3 (interfaced in ccp4 8.0.000 suite) seems >> to be generating HLA/B/C/D coefficients from an x-ray diffraction dataset. >> > >> > Wavelength: >> > 1.54179 Angstrom. >> > >> > Sample: >> > • >> > Protein-small molecule ligand complex crystal. >> > • No anomalous scatterer in the protein, the ligand, or the >> crystallization condition. >> > >> > Data reduction: >> > Xtriage and aimless analyses did not indicate significant anomalous >> signal. >> > >> > I would appreciate any help in understanding the reasons for these >> observations. >> > >> > Thanks and regards >> > Nitin Kulhar >> > PhD student >> > c/o Dr Rajakumara Eerappa >> > Macromolecular Structural Biology Lab >> > Department of Biotechnology >> > Indian Institute of Technology Hyderabad >> > Kandi, Sangareddy >> > Telangana, India - 502284 >> > >> > Disclaimer:- This footer text is to convey that this email is sent by >> one of the users of IITH. So, do not mark it as SPAM. >> > To unsubscribe from the CCP4BB list, click the following link: >> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> >> - >> Randy J. Read >> Department of Haematology, University of Cambridge >> Cambridge Institute for Medical Research Tel: +44 1223 336500 >> The Keith Peters Building >> Hills Road E-mail: >> rj...@cam.ac.uk >> Cambridge CB2 0XY, U.K. >> www-structmed.cimr.cam.ac.uk >> >> > Disclaimer:- This footer text is to convey that this email is sent by one > of the users of IITH. So, do not mark it as SPAM. > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Phaser 2.8.3: Hendrickson-Lattman coefficients generated from dataset lacking anomalous signal
Dear sir Thank you for clearing that. I checked back to see that HLC/D are invariably 0 for all reflections, with the non-zero HLA/B supposedly having been originated from the probability distribution of phases *calculated* by phaser. Hopefully, I have not misunderstood it. Thanks and regards Nitin Kulhar On Thu, Feb 8, 2024 at 9:07 PM Randy John Read wrote: > Hi, > > Hendrickson-Lattman coefficients are just a way of storing phase > probability information, and they can come from different sources including > atomic models. Phaser puts in HL coefficients because they could be handy > under some circumstances for combining the phase information from > experimental phasing. You might notice that only A and B are non-zero for > the molecular replacement HL coefficients. That’s because the phase > probability distribution is unimodal for calculated phases, whereas it’s > generally bimodal for experimental phases (thus requiring more > coefficients). > > Best wishes, > > Randy Read > > > On 8 Feb 2024, at 14:32, Nitin Kulhar < > 9dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote: > > > > Dear all > > > > Is anomalous diffraction necessary for determining experimental phases > and the Hendrickson-Lattman coefficients (HLA, HLB, HLC, and HLD)? > > > > MR solution from Phaser 2.8.3 (interfaced in ccp4 8.0.000 suite) seems > to be generating HLA/B/C/D coefficients from an x-ray diffraction dataset. > > > > Wavelength: > > 1.54179 Angstrom. > > > > Sample: > > • > > Protein-small molecule ligand complex crystal. > > • No anomalous scatterer in the protein, the ligand, or the > crystallization condition. > > > > Data reduction: > > Xtriage and aimless analyses did not indicate significant anomalous > signal. > > > > I would appreciate any help in understanding the reasons for these > observations. > > > > Thanks and regards > > Nitin Kulhar > > PhD student > > c/o Dr Rajakumara Eerappa > > Macromolecular Structural Biology Lab > > Department of Biotechnology > > Indian Institute of Technology Hyderabad > > Kandi, Sangareddy > > Telangana, India - 502284 > > > > Disclaimer:- This footer text is to convey that this email is sent by > one of the users of IITH. So, do not mark it as SPAM. > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > - > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > The Keith Peters Building > Hills Road E-mail: > rj...@cam.ac.uk > Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk > > -- Disclaimer:- This footer text is to convey that this email is sent by one of the users of IITH. So, do not mark it as SPAM. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Phaser 2.8.3: Hendrickson-Lattman coefficients generated from dataset lacking anomalous signal
Hi, Hendrickson-Lattman coefficients are just a way of storing phase probability information, and they can come from different sources including atomic models. Phaser puts in HL coefficients because they could be handy under some circumstances for combining the phase information from experimental phasing. You might notice that only A and B are non-zero for the molecular replacement HL coefficients. That’s because the phase probability distribution is unimodal for calculated phases, whereas it’s generally bimodal for experimental phases (thus requiring more coefficients). Best wishes, Randy Read > On 8 Feb 2024, at 14:32, Nitin Kulhar > <9dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote: > > Dear all > > Is anomalous diffraction necessary for determining experimental phases and > the Hendrickson-Lattman coefficients (HLA, HLB, HLC, and HLD)? > > MR solution from Phaser 2.8.3 (interfaced in ccp4 8.0.000 suite) seems to be > generating HLA/B/C/D coefficients from an x-ray diffraction dataset. > > Wavelength: > 1.54179 Angstrom. > > Sample: > • > Protein-small molecule ligand complex crystal. > • No anomalous scatterer in the protein, the ligand, or the > crystallization condition. > > Data reduction: > Xtriage and aimless analyses did not indicate significant anomalous signal. > > I would appreciate any help in understanding the reasons for these > observations. > > Thanks and regards > Nitin Kulhar > PhD student > c/o Dr Rajakumara Eerappa > Macromolecular Structural Biology Lab > Department of Biotechnology > Indian Institute of Technology Hyderabad > Kandi, Sangareddy > Telangana, India - 502284 > > Disclaimer:- This footer text is to convey that this email is sent by one of > the users of IITH. So, do not mark it as SPAM. > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Phaser 2.8.3: Hendrickson-Lattman coefficients generated from dataset lacking anomalous signal
Dear all Is anomalous diffraction necessary for determining experimental phases and the Hendrickson-Lattman coefficients (HLA, HLB, HLC, and HLD)? MR solution from Phaser 2.8.3 (interfaced in ccp4 8.0.000 suite) seems to be generating HLA/B/C/D coefficients from an x-ray diffraction dataset. Wavelength: 1.54179 Angstrom. Sample: 1. Protein-small molecule ligand complex crystal. 2. No anomalous scatterer in the protein, the ligand, or the crystallization condition. Data reduction: Xtriage and aimless analyses did not indicate significant anomalous signal. I would appreciate any help in understanding the reasons for these observations. Thanks and regards Nitin Kulhar PhD student c/o Dr Rajakumara Eerappa Macromolecular Structural Biology Lab Department of Biotechnology Indian Institute of Technology Hyderabad Kandi, Sangareddy Telangana, India - 502284 -- Disclaimer:- This footer text is to convey that this email is sent by one of the users of IITH. So, do not mark it as SPAM. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
