Re: [ccp4bb] phaser 2.5.2 in ccp4 6.3.0 does not output Hendrickson Lattman coefficients
Dear Petr, Presumably you're just talking about Phaser for molecular replacement, because Phaser still produces HL coefficients for SAD phasing. There were two major reasons we made this change. First, the presence of HL coefficients can fool some programs into thinking that you have experimental phase information that is independent of your model, which is not true for phases from molecular replacement. Second, for unimodal sources of phase information like model phases, the HL coefficients are redundant and can be generated from the phase and FOM, e.g. by using the HLCONV command in sftools. We could easily put this option back in, controlled for instance by setting the VERBOSE flag, if there were a compelling reason. No-one else has complained since we made this change a year ago, but maybe they have been suffering in silence! Could you let us know why you find this feature extremely useful? Best wishes, Randy Read On 2 Jul 2013, at 18:41, Petr Leiman petr.lei...@epfl.ch wrote: I have just found out that phaser v. 2.5.2 in ccp4 6.3.0-021 does not output columns with HL coefficients. I cannot find a combination of buttons in CCP4i GUI to enable this extremely useful feature. This is the first time I tried phaser in the latest CCP4 release and I am shocked this problem has not been discovered and fixed already. If there is a reason to this new output column behavior, it would be very useful to hear this reason. Sincerely, Petr -- Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerand Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422 -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] phaser 2.5.2 in ccp4 6.3.0 does not output Hendrickson Lattman coefficients
Dear Randy, Thank you for your quick response. Obviously, you have given this a lot of thought. I would like to have the HL coefficients in the phaser output file for downstream compatibility with density modification programs such as resolve. Thank you, Petr On 07/03/2013 10:46 AM, Randy Read wrote: Dear Petr, Presumably you're just talking about Phaser for molecular replacement, because Phaser still produces HL coefficients for SAD phasing. There were two major reasons we made this change. First, the presence of HL coefficients can fool some programs into thinking that you have experimental phase information that is independent of your model, which is not true for phases from molecular replacement. Second, for unimodal sources of phase information like model phases, the HL coefficients are redundant and can be generated from the phase and FOM, e.g. by using the HLCONV command in sftools. We could easily put this option back in, controlled for instance by setting the VERBOSE flag, if there were a compelling reason. No-one else has complained since we made this change a year ago, but maybe they have been suffering in silence! Could you let us know why you find this feature extremely useful? Best wishes, Randy Read On 2 Jul 2013, at 18:41, Petr Leiman petr.lei...@epfl.ch wrote: I have just found out that phaser v. 2.5.2 in ccp4 6.3.0-021 does not output columns with HL coefficients. I cannot find a combination of buttons in CCP4i GUI to enable this extremely useful feature. This is the first time I tried phaser in the latest CCP4 release and I am shocked this problem has not been discovered and fixed already. If there is a reason to this new output column behavior, it would be very useful to hear this reason. Sincerely, Petr -- Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerand Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422 -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
[ccp4bb] phaser 2.5.2 in ccp4 6.3.0 does not output Hendrickson Lattman coefficients
I have just found out that phaser v. 2.5.2 in ccp4 6.3.0-021 does not output columns with HL coefficients. I cannot find a combination of buttons in CCP4i GUI to enable this extremely useful feature. This is the first time I tried phaser in the latest CCP4 release and I am shocked this problem has not been discovered and fixed already. If there is a reason to this new output column behavior, it would be very useful to hear this reason. Sincerely, Petr -- Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerand Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422
