- phenixbb - phenix-online.org

Computing Robs vs Rcalc for twinned data with xtriage
by Pietro Roversi 10 Oct '11

10 Oct '11

Dear all, I am trying to run phenix.xtriage to compute Robs vs Rcalc for twinned data (from A. A. Lebedev, A. A. Vagin and G. N. Murshudov Intensity statistics in twinned crystals with examples from the PDB, Acta Crystallographica, D62, 83-95, (2006) My input: phenix.xtriage xray_data.file_name=$1.mtz xray_data.obs_labels="IMEAN, SIGIMEAN" xray_data.calc_labels="FCalc, PHICalc" xray_data.high_resolution=3.1 > phenix.xtriage.$$.log The FCalc, PHICalc columns (from CCP4-sfall) are in my mtzfile: 1 ASC -27 27 0 100.00 0.7 10.4 52.72 2.60 H H 2 NONE -90 90 0 100.00 0.7 34.2 52.72 2.60 H K 3 NONE 0 15 0 100.00 5.7 5.7 52.72 2.60 H L 4 NONE 0.0 19.0 0 100.00 9.50 9.50 52.72 2.60 I FreeR_flag 5 NONE -244.3 13664.9 0 100.00 467.59 469.74 52.72 2.60 J IMEAN 6 NONE 1.8 990.9 0 100.00 43.05 43.05 52.72 2.60 Q SIGIMEAN 7 NONE 16.2 1157.9 0 100.00 173.14 173.14 52.72 2.60 F F 8 NONE 1.7 51.3 0 100.00 12.91 12.91 52.72 2.60 Q SIGF 9 NONE 0.7 7827.1 0 100.00 257.63 257.63 52.72 2.60 F FCalc 10 NONE 0.0 360.0 0 100.00 180.24 180.24 52.72 2.60 P PHICalc and yet I get the error message: creamint:~/Projects/FactorI/Tetartohedral/P1/DataFiles> ~/Scripts/phenix_xtriage.csh AUTOMATIC_DEFAULT_free.klh_sfall1 Running phenix.xtriage No matching array: scaling.input.xray_data.calc_labels=FCalc, PHICalc Possible choices: AUTOMATIC_DEFAULT_free.klh_sfall1.mtz:IMEAN,SIGIMEAN AUTOMATIC_DEFAULT_free.klh_sfall1.mtz:F,SIGF Please use scaling.input.xray_data.calc_labels to specify an unambiguous substring of the target label. Sorry: No matching array: scaling.input.xray_data.calc_labels=FCalc, PHICalc

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Automated Mg & K ions picking
by Kristen Eisenberg 10 Oct '11

10 Oct '11

Hi Hasan, yes, we plan to extend water picking procedure so it can identify single-atom ions, but no specific tool is available to use right now. You need to inspect waters (for example, a water with "too small" refined B-factor is likely to be a metal), and density peaks (phenix.refine may not place a water into a density peak if it is too different from what is expected for water). Kristen Eisenberg Billige Flüge Marketing GmbH Emanuelstr. 3, 10317 Berlin Deutschland Telefon: +49 (33) 5310967 Email: utebachmeier at gmail.com Site: http://flug.airego.de - Billige Flüge vergleichen

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Re: [phenixbb] PHENIX atom selection language
by Kay Diederichs 09 Oct '11

09 Oct '11

Am 09.10.2011 04:20, schrieb phenixbb-request(a)phenix-online.org: > Date: Thu, 6 Oct 2011 18:19:34 -0400 > From: Jianghai Zhu<jzhu(a)idi.harvard.edu> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] PHENIX atom selection language > Message-ID:<E21B0319-CC1D-47A6-9F23-4493700B319C(a)idi.harvard.edu> > Content-Type: text/plain; charset=us-ascii > > Cool. Thanks, Pavel. It would be nice to have a list of all selection keywords and corresponding definitions somewhere. > > -- Jianghai Hi Jianghai, anybody can contribute to the CCP4 wiki, where a Phenix article already exists - check out <http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Phenix#Atom_sel…> Unfortunately the wiki is hit by spammers, and we regularly delete whole batches of these pseudo-"users" to keep the userlist clean. The spammers use @gmail.com and @hotmail.com email addresses which we now do not accept any more as new users' email - such addresses are just too easy to obtain. So if you would like to contribute make sure a) to use a email adress of your institution (e.g. university) b) and to contribute to an existing article or start a new one since we won't delete "real" users HTH, Kay

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Re: [phenixbb] Simulated annealing composite omit map conversion
by Yuri 09 Oct '11

09 Oct '11

I agree I like 0.25 (I believe thats what CNS spits out). Anything tighter looks fabricated -- Yuri Pompeu

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Simulated annealing composite omit map conversion
by Yuri 09 Oct '11

09 Oct '11

Hello Everyone, I am calculating an SA. composite omit map to show active site density. It looks like the output format is mtz coefficients. How can I get it to ccp4 or .xplor format for PyMol? Thanks -- Yuri Pompeu

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Educative Tool Idea
by Yuri 07 Oct '11

07 Oct '11

Hello Developers, This may be a silly idea after all, nonetheless: Would it be possible (worhtwhile) to have a tool that lets the user input a molecule of a certain type (probably rather small size, i.e, an amino acid or cofactor), and then input a space group. Phenix could then generate a relection file that would be displayed using either data2d or 3d viewer. Obviously there are many other factors to be considered but just an idea... -- Yuri Pompeu

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Occupancy refinement issue
by AFL 07 Oct '11

07 Oct '11

Dear All, I would like to refine the occupancy of _all_ components together for the following system: - free LYS (chain A and resname LYS) - PLP-LYS complex (chain A and resname LLP) - PLP-GLU complex (chian D and resname PPE) The LYS and LLP are defined as alternative conformations. What I've tried so far is: - just phenix.refine without any additional constraints and the result is occupancy refinement of LYS vs. LLP and separately refined PPE. - constrained_group { selection = chain A and resseq 90 # position of LYS, LLP selection = chain C and resseq 1 # PPE } Result is occupancy refinement of LYS+LLP vs. PPE and total mess in the active site (=ligands moved to new positions far away from where they should be). - constrained_group { selection = chain A and resname LYS # ALYS, BLLP doesn't work selection = chain A and resname LLP selection = chain C and resname PPE } Results in occupancy refinement of LYS vs. PPE and the LLP occupancy is set to 0.00. So, the big question is: - is what I'm trying to do doable at all? - what would be the right way to do it? I will appreciate all and any suggestions on how to proceed. Regards, Andrzej Lyskowski -- alnyds(a)gmail.com e-mail home

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PHENIX atom selection language
by Jianghai Zhu 07 Oct '11

07 Oct '11

Hi, Where can I find a complete description of PHENIX atom selection language? The examples in the PHENIX.REFINE manual are not enough. Thanks. -- Jianghai

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Fwd: Really good stats... Unreal!??
by Yuri 05 Oct '11

05 Oct '11

Hi everyone, So I am done refining a structure with around 760 residues in the model to a resolution of 2.29A. Rwork 0.18 Rfree 0.24 RMSD angle 1.1 Bond 0.008, clashscore 28. As a I last round I ran optmize_weights and got some interesting numbers. Rwork 0.17 Rfree 0.23 RMSD Angle 0.68! Bond 0.003! clashscore 10.2 I dont know how real these are. That would make this a new pdb record for tight geometry!!! Any ideas? Best, -- Yuri Pompeu -- Yuri Pompeu

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local refinement of target weights?
by Yarrow Madrona 04 Oct '11

04 Oct '11

Hello, I am wondering if there is a way to restrain geometry target weights for a ligand seperate from the rest of the molecule. I would like to impose higher restraints for the ligand than that of the protein in the same refinement run. Thanks for your help. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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