[ccp4bb] Input reflection file for refmac runs
Dear CCP4bb users and Refinement experts, As input for (n+1)st run of refmac, should I use as input reflection file the output produced by refmac in the nth run? Currently I have been giving the master mtz file as input for all runs. I would appreciate the clarification from the community. Thanking you Dilip Badgujar Graduate Student ACTREC
Re: [ccp4bb] Input reflection file for refmac runs
Hi Dilip, You've been doing the right thing. Just keep at it. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Dilip Badjugar [dilip@gmail.com] Sent: Tuesday, July 01, 2014 3:35 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Input reflection file for refmac runs Dear CCP4bb users and Refinement experts, As input for (n1)st run of refmac, should I use as input reflection file the output produced by refmac in the nth run? Currently I have been giving the master mtz file as input for all runs. I would appreciate the clarification from the community. Thanking you Dilip Badgujar Graduate Student ACTREC
Re: [ccp4bb] Input reflection file for refmac runs
Using the master mtz file (as you call it) is the safe thing to do. If you use the previous refmac output file, you have to careful the right structure factor columns are selected. They should be non-modified by the previous refmac run, otherwise you are refining both the data and the model. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 1 Jul 2014, at 14:35, Dilip Badjugar wrote: Dear CCP4bb users and Refinement experts, As input for (n+1)st run of refmac, should I use as input reflection file the output produced by refmac in the nth run? Currently I have been giving the master mtz file as input for all runs. I would appreciate the clarification from the community. Thanking you Dilip Badgujar Graduate Student ACTREC
Re: [ccp4bb] Input reflection file for refmac runs
Keep on using the master file. Refmac corrects the observations in a few ways The overall anisotropic B correction is always applied In the worst case scenario where you are refining considering twinning the 2FP2 output is no longer the observed FP but one after a detwinning correction.. So always stick with the master file..Eleanor On 1 July 2014 13:40, Mark J van Raaij mjvanra...@cnb.csic.es wrote: Using the master mtz file (as you call it) is the safe thing to do. If you use the previous refmac output file, you have to careful the right structure factor columns are selected. They should be non-modified by the previous refmac run, otherwise you are refining both the data and the model. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 1 Jul 2014, at 14:35, Dilip Badjugar wrote: Dear CCP4bb users and Refinement experts, As input for (n+1)st run of refmac, should I use as input reflection file the output produced by refmac in the nth run? Currently I have been giving the master mtz file as input for all runs. I would appreciate the clarification from the community. Thanking you Dilip Badgujar Graduate Student ACTREC
