f_prime and f_double_prime in MIRAS/SIRAS
Hi, how can one enter f_prime and f_double_prime values for SIRAS/MIRAS experiments in phenix.autosol? Could not find any examples of that in manual, only for MAD. Just putting them in as f_prime=... and f_double_prime=... does not work, it then assumes MAD experiment. Thanks! -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-dunn.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915
Hi Leo, I'm sorry, in your version of autosol the f' and f" values for MIRAS/ SIRAS are always taken from tables at a wavelength of 1.54A. Our development version has a much more flexible input for MIR data that allows setting wavelength and scattering factors; I hope that this will be available soon. All the best, Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss On Jan 14, 2009, at 6:03 AM, Leo Sazanov wrote:
Hi, how can one enter f_prime and f_double_prime values for SIRAS/ MIRAS experiments in phenix.autosol? Could not find any examples of that in manual, only for MAD. Just putting them in as f_prime=... and f_double_prime=... does not work, it then assumes MAD experiment. Thanks!
-- Dr. Leonid A. Sazanov Research group leader Medical Research Council Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-dunn.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915
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Hi all - I have a good quality native set (to 2.2) and two derivatives going to about 3.5. Ano signal is there but in a good day you would call it 4.5 A, unless you ask xtriage and it tells you it is up to 7-8 A. Since SAD does not appear to work (Hyss seems to think it finds sites in one dataset but I am less than convinced, cc of 20-35% depending on resolution cutoffs), rather low FOMs from phaser (0.5 -0.3), I thought to treat it as MIRAS of some sort. Is the correct way in the phenix.autosol wizard to treat that as two SIRAS datasets ? cell 79.9201 80.1374 142.2119 90.0000 90.0000 90.0000 # cell params resolution 2.2 # Resolution input_seq_file ttk.seq ############## DATASET 1 ################ expt_type sir # MIR dataset is set of SIR datasets input_file_list nat_201208_9_scala1.sca se_cd474a_p212121_scala1.sca # Native and deriv 1 nat_der_list Native Se1 # identify files by ha type inano_list noinano inano # say if ano diffs to be used n_ha_list 0 8 # number of heavy-atoms run_list start # read in datafiles for dataset run_list read_another_dataset # about to start a new dataset here ############## DATASET 2 ################ expt_type sir # our second dataset is SAD input_file_list nat_201208_9_scala1.sca se_ca560a_5_p212121_scala1.sca # Native and deriv 1 nat_der_list Native Se2 # identify files by ha type inano_list noinano inano # say if ano diffs to be used n_ha_list 0 8 # number of heavy-atoms ######################################### A.
Hi Tassos, Yes, that looks correct. As I mentioned to Leo earlier today, the way to set it up will be considerably simplified in the next version. All the best, Tom T On Jan 14, 2009, at 9:07 AM, Anastassis Perrakis wrote:
Hi all -
I have a good quality native set (to 2.2) and two derivatives going to about 3.5. Ano signal is there but in a good day you would call it 4.5 A, unless you ask xtriage and it tells you it is up to 7-8 A.
Since SAD does not appear to work (Hyss seems to think it finds sites in one dataset but I am less than convinced, cc of 20-35% depending on resolution cutoffs), rather low FOMs from phaser (0.5 -0.3), I thought to treat it as MIRAS of some sort.
Is the correct way in the phenix.autosol wizard to treat that as two SIRAS datasets ?
cell 79.9201 80.1374 142.2119 90.0000 90.0000 90.0000 # cell params resolution 2.2 # Resolution input_seq_file ttk.seq ############## DATASET 1 ################ expt_type sir # MIR dataset is set of SIR datasets input_file_list nat_201208_9_scala1.sca se_cd474a_p212121_scala1.sca # Native and deriv 1 nat_der_list Native Se1 # identify files by ha type inano_list noinano inano # say if ano diffs to be used n_ha_list 0 8 # number of heavy-atoms run_list start # read in datafiles for dataset run_list read_another_dataset # about to start a new dataset here ############## DATASET 2 ################ expt_type sir # our second dataset is SAD input_file_list nat_201208_9_scala1.sca se_ca560a_5_p212121_scala1.sca # Native and deriv 1 nat_der_list Native Se2 # identify files by ha type inano_list noinano inano # say if ano diffs to be used n_ha_list 0 8 # number of heavy-atoms #########################################
A.
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participants (3)
-
Anastassis Perrakis -
Leo Sazanov -
Tom Terwilliger