Re: [ccp4bb] the f' and f'' of heavy cluster
Dear Dr. Matthias Zebisch, how to do the specific cluster search in phaser sad pipline? Thank you. Lisa On Thu, Nov 21, 2013 at 3:37 PM, Matthias Zebisch matthias.zebi...@bbz.uni-leipzig.de wrote: Dear Lisa, if you have proper anomalous data I rather recommend using the Phaser SAD pipeline and specify cluster search. Worked instantly for me. Good luck! - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk - On 11/21/2013 6:29 AM, LISA wrote: Dear All, I am running autosharp with a single wavelength data soked with Ta6Br12. This data collected at the wavelength of 1.254A. I told the autosharp the f' -20 and f''10.5. The autosharp result said these values are not correct? How can we get the f' and f'' of this cluster? Thank you. Lisa
Re: [ccp4bb] the f' and f'' of heavy cluster
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Lisa, the wavelength indicates you collected the data at a synchrotron. Do you have a fluorescence scan of your crystal? That should tell you f' and f''. Other than that you can use Ethan Merritt's excellent server at http://skuld.bmsc.washington.edu/scatter/ - this, however, tells you the same values you already mentioned, so unless sharp tells you why it thinks these values were incorrect, I would carry on redardless. Best, Tim On 11/21/2013 07:29 AM, LISA wrote: Dear All, I am running autosharp with a single wavelength data soked with Ta6Br12. This data collected at the wavelength of 1.254A. I told the autosharp the f' -20 and f''10.5. The autosharp result said these values are not correct? How can we get the f' and f'' of this cluster? Thank you. Lisa - -- - -- 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 Icedove - http://www.enigmail.net/ iD8DBQFSjcwpUxlJ7aRr7hoRAn27AKDldnStuPdHKyjYedQq2wdJI61eawCeIYLX zPj1+cptJsiSH8uUnr8SuZo= =YgjB -END PGP SIGNATURE-
Re: [ccp4bb] the f' and f'' of heavy cluster
Dear Lisa, You could try using SHELXD (e.g. via hkl2map) to find the heavy atoms, it doesn't need f' and f. However you should take into account that many soaks have not absorbed the intended heavy atoms or clusters, and that if a tantalum bromide cluster has actually been incorporated it will probably be disordered. Best wishes, George On 11/21/2013 07:29 AM, LISA wrote: Dear All, I am running autosharp with a single wavelength data soked with Ta6Br12. This data collected at the wavelength of 1.254A. I told the autosharp the f' -20 and f''10.5. The autosharp result said these values are not correct? How can we get the f' and f'' of this cluster? Thank you. Lisa -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582
Re: [ccp4bb] the f' and f'' of heavy cluster
Dear Lisa, [there is a SHARP discussion list at http://www.globalphasing.com/mailman/listinfo/sharp-discuss] On Thu, Nov 21, 2013 at 02:29:23PM +0800, LISA wrote: Dear All, I am running autosharp with a single wavelength data soked with Ta6Br12. This data collected at the wavelength of 1.254A. I told the autosharp the f' -20 and f''10.5. The autosharp result said these values are not correct? Are these values from a fluorescence scan? or just theoretical values? How can we get the f' and f'' of this cluster? By far the best: look at the processed fluorescence scan for your crystal. If you didn't do one (unlikely) or you don't have it any more (unlucky) you can use calculated values (e.g. with the CCP4 crossec program). Remember that for clusters there are two steps you have to be concerned about: (1) HA detection and (2) HA refinement. SHARP itself implements a 'spherical cluster' approach for the second tasks (ie. once you have some sites), which can be very powerful if your clusters are truly disordered. See http://www.globalphasing.com/sharp/manual/appendix3.html#generalSPHCLUSTER http://www.globalphasing.com/sharp/manual/chapter4.html#CLISTspecify Often you will need to use a more manual/traditional approach here: * finding the HA positions by running e.g. SHELXD by hand instead of as part of an automatic pipeline * running the HA parameter refinement and phasing program with the correct parametrisation for your cluster (see above), followed by manual inspection of LLG residual maps to find minor sites and decide if your cluster is ordered/disordered. * deciding on the correct hand/enantiomorph * doing density modification, averaging, model building etc. Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] the f' and f'' of heavy cluster
If you set the atom type to TX, phaser will use the built-in scattering factors for the tantalum bromide cluster. This will be represented as a point scatterer rather than the actual cluster - if you have very good data you may be able to actually position the tantalum atoms in the cluster and get better phase information that way. Jason. -- Jason Busby PhD Student Laboratory of Structural Biology School of Biological Sciences University of Auckland Thomas Building 110 3a Symonds St Private Bag 92019 Auckland 1142 New Zealand ph: +64 9 3737599 ext 84155 fx: +64 9 3737414 On 21/11/2013, at 9:32 PM, LISA wrote: Dear Dr. Matthias Zebisch, how to do the specific cluster search in phaser sad pipline? Thank you. Lisa On Thu, Nov 21, 2013 at 3:37 PM, Matthias Zebisch matthias.zebi...@bbz.uni-leipzig.demailto:matthias.zebi...@bbz.uni-leipzig.de wrote: Dear Lisa, if you have proper anomalous data I rather recommend using the Phaser SAD pipeline and specify cluster search. Worked instantly for me. Good luck! - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.ukmailto:matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.ukhttp://www.strubi.ox.ac.uk/ - On 11/21/2013 6:29 AM, LISA wrote: Dear All, I am running autosharp with a single wavelength data soked with Ta6Br12. This data collected at the wavelength of 1.254A. I told the autosharp the f' -20 and f''10.5. The autosharp result said these values are not correct? How can we get the f' and f'' of this cluster? Thank you. Lisa
Re: [ccp4bb] the f' and f'' of heavy cluster
Hi, one could indeed get much better phases with the correct positions of the HA cluster. If there is sufficient anomalous signal one could use the cluster as search model for Molecular replacement using the anomalous data as described in Dahms et al. to get the exact position of the cluster in the crystal. Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement. Acta Crystallogr D Biol Crystallogr. 2013 Feb;69(Pt 2):284-9 Cheers Christian Am 21.11.2013 19:36, schrieb Jason Busby: If you set the atom type to TX, phaser will use the built-in scattering factors for the tantalum bromide cluster. This will be represented as a point scatterer rather than the actual cluster - if you have very good data you may be able to actually position the tantalum atoms in the cluster and get better phase information that way. Jason. -- Jason Busby PhD Student Laboratory of Structural Biology School of Biological Sciences University of Auckland Thomas Building 110 3a Symonds St Private Bag 92019 Auckland 1142 New Zealand ph: +64 9 3737599 ext 84155 fx: +64 9 3737414 On 21/11/2013, at 9:32 PM, LISA wrote: Dear Dr. Matthias Zebisch, how to do the specific cluster search in phaser sad pipline? Thank you. Lisa On Thu, Nov 21, 2013 at 3:37 PM, Matthias Zebisch matthias.zebi...@bbz.uni-leipzig.de mailto:matthias.zebi...@bbz.uni-leipzig.de wrote: Dear Lisa, if you have proper anomalous data I rather recommend using the Phaser SAD pipeline and specify cluster search. Worked instantly for me. Good luck! --__--- Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk mailto:matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk http://www.strubi.ox.ac.uk/ --__--- On 11/21/2013 6:29 AM, LISA wrote: Dear All, I am running autosharp with a single wavelength data soked with Ta6Br12. This data collected at the wavelength of 1.254A. I told the autosharp the f' -20 and f''10.5. The autosharp result said these values are not correct? How can we get the f' and f'' of this cluster? Thank you. Lisa
[ccp4bb] the f' and f'' of heavy cluster
Dear All, I am running autosharp with a single wavelength data soked with Ta6Br12. This data collected at the wavelength of 1.254A. I told the autosharp the f' -20 and f''10.5. The autosharp result said these values are not correct? How can we get the f' and f'' of this cluster? Thank you. Lisa
Re: [ccp4bb] the f' and f'' of heavy cluster
Dear Lisa, if you have proper anomalous data I rather recommend using the Phaser SAD pipeline and specify cluster search. Worked instantly for me. Good luck! - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk - On 11/21/2013 6:29 AM, LISA wrote: Dear All, I am running autosharp with a single wavelength data soked with Ta6Br12. This data collected at the wavelength of 1.254A. I told the autosharp the f' -20 and f''10.5. The autosharp result said these values are not correct? How can we get the f' and f'' of this cluster? Thank you. Lisa
