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Completeness issue by phenix - revisited
by J. Fleming 04 Feb '10

04 Feb '10

Hi, I'm having a problem using phenix.refine with my x-ray data. My completeness is always 89% when it should be 99%. My data was originally processed with CCP4i. I found an old post (see below) with a potential fix that doesn't work for me. I've tried changing the 'Anomalous flag: True' to 'Anomalous flag: False' but my completeness is still 89%. I've clicked through a variety of other setting in the GUI that I thought would help but no luck. Does anyone have any ideas? Thanks in advance, Jon ----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov <http://www.phenix-online.org/mailman/listinfo/phenixbb>> To: phenixbb at phenix-online.org <http://www.phenix-online.org/mailman/listinfo/phenixbb> Sent: Monday, December 15, 2008 12:59:12 PM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Completeness issue by phenix Hi YoungJin, I suspect phenix.refine decided your mtz file contains anomalous data when you actually have non-anomalous data. Could you look in the phenix.refine output for something like this: ================================== X-ray data ================================= F-obs: 1yjp.mtz:FOBS_X,SIGFOBS_X R-free flags: 1yjp.mtz:R-free-flags Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X Observation type: xray.amplitude Type of data: double, size=495 Type of sigmas: double, size=495 Number of Miller indices: 495 Anomalous flag: False ^^^^^ in particular here If you see "Anomalous flag: True" try adding this to the phenix.refine command line: xray_data.force_anomalous_flag_to_be_equal_to=False Let me know if this doesn't help. If it does help, I'd be interested to know how the .mtz file was generated. Ralf

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BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY
by Cyndi Salbego 02 Feb '10

02 Feb '10

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. Beamline 24ID-C: Equipped with MD2 microdiffractometer, tunable between 6-21KeV, ADSC Q315 Detector, MAD Capable. Outfitted with ALS-style robot that can use ALS pucks or Unipucks. Beamline 24ID-E: Equipped with MD2 microdiffractometer, delivering beam as small as 5 microns. Single energy (12662eV) optimized for Se-SAD experiments, ADSC Q315 Detector. Outfitted with ALS-style robot that can use ALS pucks or Unipucks. For more information on our beamlines (beamline and robot manuals) along with updated schedule availability please see: http://necat.chem.cornell.edu or contact Cyndi Salbego (csalbego(a)anl.gov) for further information. To apply for General User Time (Rapid Access for current run cycle) please follow this link: https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page Cyndi Salbego Administrator, NECAT 630.252.0689

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AUTOSOL for MAD data with error message-'Need a symfile for solve'
by m.b.rajasekaran＠reading.ac.uk 02 Feb '10

02 Feb '10

Dear all, I have a query regarding the Autosol option in the PHENIX-1.6-289 version. We are trying to process a MAD data for a zinc bound protein crystal with AuTOSOL. We uploaded the scaled files, sequence and all other details and started running AUTOSOL. But the program stopped with the following error message pasted below mentioning some missing of symfile. We were not able to locate any parameters file on the installation directory. It would be helpful if we get some useful suggestions on this. Thanks in advance, Mohan *********************************************************** PHENIX AutoSol Tue Feb 2 12:37:41 2010 ************************************************************ Working directory: /home/sar06mbr/30JanDiamondI02/107/107_php22121 PHENIX VERSION: 1.6 of 29-01-2010 PHENIX RELEASE_TAG : 289 PHENIX MTYPE : intel-linux-2.6 PHENIX MVERSION : suse AutoSol_start AutoSol Run 2 Tue Feb 2 12:37:41 2010 INPUT FILE LIST: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] Copied /home/sar06mbr/30JanDiamondI02/107/107_php22121/result.seq to /home/sar06mbr/30JanDiamondI02/107/107_php22121/AutoSol_run_2_/sequence_autosol.dat Setting chain_type to PROTEIN Setting defaults for data_quality moderate Setting thorough_denmod to Yes Settin fix_xyz_after_denmod to False Setting max_ha_iterations to 2 Setting fixscattfactors to No Settin defaults for thoroughness quick Setting best_of_n_hyss_always to 1 Setting max_extra_unique_solutions to 0 Settin ha_iteration to No Setting max_choices to 1 Setting number_of_models to 1 Setting number_of_builds to 1 Setting test_mask_type to No Setting n_cycle_build to 0 Setting thorough_loop_fit to Setting create_scoring_table to No Not truncating ha sites at start of resolve as this is not PHASER SAD phasing Trying to guess refinement file for later use from ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] Choosing guess of refinement file for later use from all files: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_2re', 'SIGF_107_2re', 'F_107_2re(+)', 'SIGF_107_2re(+)', 'F_107_2re(-)', 'SIGF_107_2re(-)', 'DANO_107_2re', 'SIGDANO_107_2re', 'IMEAN_107_2re', 'SIGIMEAN_107_2re', 'I_107_2re(+)', 'SIGI_107_2re(+)', 'I_107_2re(-)', 'SIGI_107_2re(-)'] GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space group: P 2 21 21 (No. 18) CONTENTS: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', 'mtz', 'premerged', 'P 2 21 21', [34.790000915527344, 108.92009735107422, 134.8800048828125, 90.0, 90.0, 90.0], 2.4890566908055836, ['F1', 'SIGF1', 'DANO1', 'SIGDANO1']] File /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz RES: 2.5 FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_3re', 'SIGF_107_3re', 'F_107_3re(+)', 'SIGF_107_3re(+)', 'F_107_3re(-)', 'SIGF_107_3re(-)', 'DANO_107_3re', 'SIGDANO_107_3re', 'IMEAN_107_3re', 'SIGIMEAN_107_3re', 'I_107_3re(+)', 'SIGI_107_3re(+)', 'I_107_3re(-)', 'SIGI_107_3re(-)'] GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit cell: (34.85, 109.18, 135.27, 90, 90, 90) Space group: P 2 21 21 (No. 18) CONTENTS: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', 'mtz', 'premerged', 'P 2 21 21', [34.849998474121094, 109.18000030517578, 135.26980590820312, 90.0, 90.0, 90.0], 2.4889952912293629, ['F1', 'SIGF1', 'DANO1', 'SIGDANO1']] File /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz RES: 2.5 FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_4re', 'SIGF_107_4re', 'F_107_4re(+)', 'SIGF_107_4re(+)', 'F_107_4re(-)', 'SIGF_107_4re(-)', 'DANO_107_4re', 'SIGDANO_107_4re', 'IMEAN_107_4re', 'SIGIMEAN_107_4re', 'I_107_4re(+)', 'SIGI_107_4re(+)', 'I_107_4re(-)', 'SIGI_107_4re(-)'] GUESS FIL TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit cell: (34.87, 109.2, 135.33, 90, 90, 90) Space group: P 2 21 21 (No. 18) CONTENTS: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz', 'mtz', 'premerged', 'P 2 21 21', [34.869998931884766, 109.19999694824219, 135.32989501953125, 90.0, 90.0, 90.0], 2.4890134311310943, ['F1', 'SIGF1', 'DANO1', 'SIGDANO1']] File /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz RES: 2.5 Guess of datafile for refinement: /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz Using /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz for refinement Specify input_refinement_file=/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz to change this HKLIN ENTRY: /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_2re', 'SIGF_107_2re', 'F_107_2re(+)', 'SIGF_107_2re(+)', 'F_107_2re(-)', 'SIGF_107_2re(-)', 'DANO_107_2re', 'SIGDANO_107_2re', 'IMEAN_107_2re', 'SIGIMEAN_107_2re', 'I_107_2re(+)', 'SIGI_107_2re(+)', 'I_107_2re(-)', 'SIGI_107_2re(-)'] GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space group: P 2 21 21 (No. 18) CONTENTS: ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', 'mtz', 'premerged', 'P 2 21 21', [34.790000915527344, 108.92009735107422, 134.8800048828125, 90.0, 90.0, 90.0], 2.4890566908055836, ['F1', 'SIGF1', 'DANO1', 'SIGDANO1']] Inverse hand of space group: P 2 21 21 Creating sg entry from /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space group: P 2 21 21 (No. 18) Space group name is: P 2 21 21 symbol is: p22121 **************************************** AutoSol Input failed Need a symfile for solve ****************************************

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automatically changed refinement parameters
by Sara Züger 02 Feb '10

02 Feb '10

Dear phenixbb, I have some questions regarding refinement parameters: When I run phenix v1.6 via the GUI, starting a fresh refinement session from the main window (I do TLS+isotropic ADP refinement and 5 macrocycles, otherwise everything default), I saw these non-default refinement settings in the run, which I did not specify myself, but the program: adp_restraints { iso { use_u_local_only = True sphere_radius = 1.55 distance_power = 0 average_power = 0 }} In the documentation I found that when doing TLS+isotropic ADP refinement, only Ulocal is restrained, so the first command makes sense. But how is it with the sphere_radius, distance_power and average_power? The default parameters are sphere_radius= 5.0 distance_power= 1.69 average_power= 1.03 What do these parameters mean? What does it mean when these parameters have changed (and why did they change)? And is it ok at all that they changed? And would they have an influence if I modify the start model by setting b_iso to a certain value and then refine "normally" with TLS+isotropic? Another parameter that changed and I did not specify is: Target_weights { wxu_scale = 2.72 } Why did this happen, is it because few cycles before I included optimize_weights? And why would this change the weights permanently? Does it make sense? Thank you for explaining me these things! Sara

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Re: [phenixbb] AUTOSOL for MAD data with error message-'Need a symfile for solve'
by Thomas C. Terwilliger 02 Feb '10

02 Feb '10

Dear Mohan, I'm sorry for the trouble! I have not seen this one, but it must be a bug that I need to fix. Can you possibly send me the data file and exact command used (you can just send data to low-res such as 6 A if you like) and I will fix it? In the meantime...if you split your dataset up into individual files I would expect that to work, particularly if you convert to .sca. All the best, Tom T > >> >> Dear all, >> I have a query regarding the Autosol option in the >> PHENIX-1.6-289 version. We are trying to process a MAD data for a zinc >> bound protein crystal with AuTOSOL. We uploaded the scaled files, sequence >> and all other details and started running AUTOSOL. But the program stopped >> with the following error message pasted below mentioning some missing of >> symfile. We were not able to locate any parameters file on the >> installation >> directory. It would be helpful if we get some useful suggestions on this. >> >> Thanks in advance, >> Mohan >> *********************************************************** >> >> PHENIX AutoSol Tue Feb 2 12:37:41 2010 >> >> ************************************************************ >> >> Working directory: /home/sar06mbr/30JanDiamondI02/107/107_php22121 >> >> PHENIX VERSION: 1.6 of 29-01-2010 PHENIX RELEASE_TAG : 289 PHENIX MTYPE : >> intel-linux-2.6 PHENIX MVERSION : suse AutoSol_start AutoSol Run 2 Tue Feb >> 2 12:37:41 2010 INPUT FILE LIST: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] >> >> Copied /home/sar06mbr/30JanDiamondI02/107/107_php22121/result.seq to >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/AutoSol_run_2_/sequence_autosol.dat >> >> Setting chain_type to PROTEIN Setting defaults for data_quality moderate >> Setting thorough_denmod to Yes Settin fix_xyz_after_denmod to False >> Setting >> max_ha_iterations to 2 Setting fixscattfactors to No Settin defaults for >> thoroughness quick Setting best_of_n_hyss_always to 1 Setting >> max_extra_unique_solutions to 0 Settin ha_iteration to No Setting >> max_choices to 1 Setting number_of_models to 1 Setting number_of_builds to >> 1 Setting test_mask_type to No Setting n_cycle_build to 0 Setting >> thorough_loop_fit to Setting create_scoring_table to No Not truncating ha >> sites at start of resolve as this is not PHASER SAD phasing >> >> Trying to guess refinement file for later use from >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] >> >> Choosing guess of refinement file for later use from all files: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', >> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] >> >> FILE TYPE ccp4_mtz >> >> COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_2re', 'SIGF_107_2re', >> 'F_107_2re(+)', 'SIGF_107_2re(+)', 'F_107_2re(-)', 'SIGF_107_2re(-)', >> 'DANO_107_2re', 'SIGDANO_107_2re', 'IMEAN_107_2re', 'SIGIMEAN_107_2re', >> 'I_107_2re(+)', 'SIGI_107_2re(+)', 'I_107_2re(-)', 'SIGI_107_2re(-)'] >> >> GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1'] Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space >> group: P 2 21 21 (No. 18) CONTENTS: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >> 'mtz', 'premerged', 'P 2 21 21', [34.790000915527344, 108.92009735107422, >> 134.8800048828125, 90.0, 90.0, 90.0], 2.4890566908055836, ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1']] >> >> File >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz >> RES: 2.5 >> >> FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', >> 'F_107_3re', 'SIGF_107_3re', 'F_107_3re(+)', 'SIGF_107_3re(+)', >> 'F_107_3re(-)', 'SIGF_107_3re(-)', 'DANO_107_3re', 'SIGDANO_107_3re', >> 'IMEAN_107_3re', 'SIGIMEAN_107_3re', 'I_107_3re(+)', 'SIGI_107_3re(+)', >> 'I_107_3re(-)', 'SIGI_107_3re(-)'] >> >> GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1'] Unit cell: (34.85, 109.18, 135.27, 90, 90, 90) Space >> group: P 2 21 21 (No. 18) CONTENTS: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', >> 'mtz', 'premerged', 'P 2 21 21', [34.849998474121094, 109.18000030517578, >> 135.26980590820312, 90.0, 90.0, 90.0], 2.4889952912293629, ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1']] >> >> File >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz >> RES: 2.5 >> >> FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', >> 'F_107_4re', 'SIGF_107_4re', 'F_107_4re(+)', 'SIGF_107_4re(+)', >> 'F_107_4re(-)', 'SIGF_107_4re(-)', 'DANO_107_4re', 'SIGDANO_107_4re', >> 'IMEAN_107_4re', 'SIGIMEAN_107_4re', 'I_107_4re(+)', 'SIGI_107_4re(+)', >> 'I_107_4re(-)', 'SIGI_107_4re(-)'] >> >> GUESS FIL TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit cell: >> (34.87, 109.2, 135.33, 90, 90, 90) Space group: P 2 21 21 (No. 18) >> CONTENTS: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz', >> 'mtz', 'premerged', 'P 2 21 21', [34.869998931884766, 109.19999694824219, >> 135.32989501953125, 90.0, 90.0, 90.0], 2.4890134311310943, ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1']] >> >> File >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz >> RES: 2.5 >> >> Guess of datafile for refinement: >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz >> >> Using >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz >> for refinement >> >> Specify >> input_refinement_file=/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz >> to change this >> >> HKLIN ENTRY: >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz >> >> FILE TYPE ccp4_mtz >> >> COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_2re', 'SIGF_107_2re', >> 'F_107_2re(+)', 'SIGF_107_2re(+)', 'F_107_2re(-)', 'SIGF_107_2re(-)', >> 'DANO_107_2re', 'SIGDANO_107_2re', 'IMEAN_107_2re', 'SIGIMEAN_107_2re', >> 'I_107_2re(+)', 'SIGI_107_2re(+)', 'I_107_2re(-)', 'SIGI_107_2re(-)'] >> >> GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1'] Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space >> group: P 2 21 21 (No. 18) CONTENTS: >> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >> 'mtz', 'premerged', 'P 2 21 21', [34.790000915527344, 108.92009735107422, >> 134.8800048828125, 90.0, 90.0, 90.0], 2.4890566908055836, ['F1', 'SIGF1', >> 'DANO1', 'SIGDANO1']] >> >> Inverse hand of space group: P 2 21 21 Creating sg entry from >> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz >> Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space group: P 2 21 21 (No. >> 18) Space group name is: P 2 21 21 symbol is: p22121 >> >> **************************************** >> >> AutoSol Input failed >> >> Need a symfile for solve >> >> **************************************** >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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Phenix version 1.6 released
by Paul Adams 01 Feb '10

01 Feb '10

The Phenix developers are pleased to announce that version 1.6 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Just some of the new features in this version (1.6) are: - New Graphical User Interfaces for AutoMR, and Phaser (in MR and SAD modes) - Improved reflection file editor GUI and command line tool - Updated map calculation GUI - C++ version of Resolve - Refinement of residues spanning symmetry axes in phenix.refine - New RNA sugar pucker geometry restraints in phenix.refine - Torsion angle dynamics refinement updates - Optional real space refinement of ligands in LigandFit wizard For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that there is a new publication that should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Acting Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Patty Jimenez [ PAJimenez(a)lbl.gov ] [ 1-510-486-7963 ] --

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data used in refinement
by Karolina Michalska 01 Feb '10

01 Feb '10

Hi all, I have a question concerning number of reflections used in refinement. In the phenix.refine log I can find a table saying that there are 34314 reflections in a work set and 1104 in a free set. This is in agreement with what Refmac prints out to pdb file under REMARK 3 (DATA USED IN REFINEMENT). However, the same remark in the pdb file produced by phenix.refine says there are 35404, which is neither a work set nor a sum of work and test sets. It is almost the latter option but still 14 reflections are missing and I cannot find in the log file what happened with them. Can anyone help me here? Karolina

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auto-open MTZ scheme
by Paul Emsley 29 Jan '10

29 Jan '10

Dear Phenixers, Prompted by Randy Read, Kevin and I have agreed that Coot should be able to auto-open MTZ files with columns labelled groupname.F_phi.F and groupname.F_phi.phi and groupname.DF_phi.DF, groupname.DF_phi.phi for difference maps for any value of groupname, of course. (Any weights should be applied to Fs before writing the file). We were wondering what the Phenix community/developers thought about that idea (there's not much point in adding this feature if you don't agree). Thanks, Paul.

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For your consideration: Table 1
by SIPPEL,KATHERINE H 29 Jan '10

29 Jan '10

Dear PHENIX programmers, I would like to preface this comment by saying that I love your suite of programs. I have converted to a 100% PHENIX fan girl and am dragging the rest of my lab down with me. I realize that you have a lot on your plates right now, what with all the bug fixes, updates, and bulletin board troubleshooting that you do. I am also primarily a biologist and have no comprehension of the effort required to keep everything running, but I do have a suggestion/request. I was putting the finishing touched on the first draft of a manuscript today and thought to myself, wouldn't it me wonderful if PHENIX could generate that all important crystallographic Table 1. You know the one that I am talking about with the data and refinement statistics. I am thinking a combination of PDB_EXTRACT and MOLEMAN where you input the log files from scaling and refinement and it outputs a handy-dandy test file with "parameter<tab>number that could easily be imported into your favorite spreadsheet (Open Office or Excel). I envision an interface with check boxes for the parameters you want to include and a place were you could input the resid of ligands for atom and b-factor counts. Like I said it is just a suggestion, in case you find yourselves bored and with time on your hands. Thanks for your time, Katherine -- SIPPEL,KATHERINE H Ph. D. candidate McKenna Lab Department of Biochemistry and Molecular Biology College of Medicine University of Florida

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phenix.pdbtools and anomalous?
by Kay Diederichs 28 Jan '10

28 Jan '10

Hi, I like the way I can obtain Fcalc with phenix.pdbtools --f-model. However I need to have the anomalous signal as well, for certain atoms, and a given wavelength. This does not seem to be possible with phenix.pdbtools. Is there a way to do this with phenix.refine ? thanks, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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