- phenixbb - phenix-online.org

EG4 not in phenix dictionary?
by Yarrow Madrona 03 Jun '13

03 Jun '13

Hello, I have previously refined EG4 and EG2 (tetra and diethylene glycol) as ligands and these were in the standard phenix library. I was under the impression that phenix shares the library from the CCP4 monomer library which I know should have EG4. Can anyone help me with this. I guess the alternative is to generate a restraints file. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

2 1

MAX IV Life Science Director position
by Derek Logan 03 Jun '13

03 Jun '13

Hi, If anyone fancies becoming Life Science Director at the world's brightest light source, look no further than here: http://www.lunduniversity.lu.se/o.o.i.s?id=24914&Dnr=547454&Type=E /Derek ________________________________________________________________________ Derek Logan tel: +46 46 222 1443 Associate Professor mob: +46 76 8585 707 Dept. of Biochemistry and Structural Biology www.cmps.lu.se<http://www.cmps.lu.se> Centre for Molecular Protein Science www.maxlab.lu.se/node/307<http://www.maxlab.lu.se/node/307> Lund University, Box 124, 221 00 Lund, Sweden

1 0

Re: [phenixbb] Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1"
by Michael Thompson 01 Jun '13

01 Jun '13

As another follow up to this point, I have had a recent example where Xtriage reported that my intensity statistics indicated twinning (<|L|>=0.399 and <L^2>=0.227, alpha=0.4). After having refined the structure with the suggested twin law, and making composite omit maps along the way (using autobuild with no twin law), I ran model vs. data at the end of refinement and noticed that it reported R/Rfree that were about 10% higher than the R/Rfree from refinement, similar to what the original post described. I checked the model vs. data logfile and found that the L-test routine used by model vs. data was failing, so the subsequent analysis was carried out as if there was no twinning. So in my case, the crystal was twinned, but model vs. data was not able to perform the L-test so it was outputting incorrect R-factors. The error message at the top of the model vs. data log file is: Twin analysis failed: Python argument types in l_test.__init__(l_test, miller_index, double, space_group, bool, float, float, float, int) did not match C++ signature: __init__(_object*, scitbx::af::const_ref<cctbx::miller::index<int>, scitbx::af::trivial_accessor> miller_indices, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> intensity, cctbx::sgtbx::space_group space_group, bool anomalous_flag, long parity_h, long parity_k, long parity_l, unsigned long max_delta_h) Twin analysis failed: Python argument types in l_test.__init__(l_test, miller_index, double, space_group, bool, float, float, float, int) did not match C++ signature: __init__(_object*, scitbx::af::const_ref<cctbx::miller::index<int>, scitbx::af::trivial_accessor> miller_indices, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> intensity, cctbx::sgtbx::space_group space_group, bool anomalous_flag, long parity_h, long parity_k, long parity_l, unsigned long max_delta_h) Perhaps there are some other users who are seeing this behavior because the L-test fails within model vs. data. Mike ----- Original Message ----- From: "Nathaniel Echols" <nechols(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Wednesday, May 29, 2013 5:18:57 PM GMT -08:00 US/Canada Pacific Subject: Re: [phenixbb] Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1" On Wed, May 29, 2013 at 4:13 PM, Sam Stampfer <Samuel.Stampfer(a)tufts.edu> wrote: > When I refined my model in phenix, I used the twin law h,-h-k,-l. I read in > the documentation that twinning can account for some of this discrepancy, > but that the program is supposed to take twinning into account if it will > lower the calculated R-work by more than 2%, which it doesn't seem to have > done (or there is some other problem with my data). Okay, the problem is that your data don't actually appear to be twinned. The automatic method used by phenix.model_vs_data (which is used internally for Table 1 and the validation GUI) only tries possible twin laws if the results of the "L test" show a suspicious distribution of intensities. Your data look fine, so it doesn't bother trying the twin laws. That the R-factors are lower when you refine with a twin law isn't necessarily indicative of the data actually being twinned - Garib Murshudov has looked into this in detail but I confess to being ignorant of the math (but I can probably dig up his paper on the subject if anyone is interested). However, I'm pretty sure the data are actually in a higher-symmetry space group. Will send details and new files off-list (probably tomorrow at this rate). I should probably change some of the programs and/or documentation to make it more clear what is being done internally, since it took me a bit of digging to realize what was going on. In general, though, always be very careful before running twinned refinement! I have seen several users do this by mistake when they really had higher symmetry. The maps will also be more model-biased when using twinned refinement, so it's good to avoid doing this unless absolutely necessary. -Nat _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

4 4

Re: [phenixbb] refinement of partly occupied water molecules?
by krimmer＠staff.uni-marburg.de 31 May '13

31 May '13

Dear Nathaniel, dear Pavel, thank you for your fast answers! > currently phenix.refine can add automatically only fully occupied > waters (I am not sure it will ever use atomic model for partially > occupied waters). If necessary, add partially occupied waters > yourself manually. Make sure they have properly set altlocs > (alternative location identifiers): non blank (say A and B). Is it current praxis to let phenix.refine freely refine the occupancy of water molecules (adding partially occupied water molecules in coot and don’t fix the occupancy in phenix)? If I do so, these water molecules are refined by phenix.refine with occupancies between 0.4-0.8. My resolution range was 1.1 – 1.4 Å. > The nightly builds have an option in phenix.refine to place ions > automatically based on a variety of criteria (still being tuned). > However, what you describe doesn't sound like any ion coordination > motif that I've read about. Could you please send us a picture that > shows the density in context? Some of the other readers with more > experience in "blobology" may recognize it. [if our list server > complains about the size of the message, just ignore it, I'll approve > it for posting] Attached you will find the image of the blob. I think it’s easily visible that the density blob is in the middle of the five-ring and that there is also a (smaller) blob in the middle of the six-ring. The water which occupies the blob was not yet refined with phenix, I just put it there to measure the distances to the carbon atoms. Best regards, Stefan

2 1

gap between Wilson B and average B
by fn1＠rice.edu 30 May '13

30 May '13

Dear all, I have a structure at about 3.5 A, which has a wilson B of about 109 and has an average B factor from model is only 49 (I did not use TLS). I read from the previous posts that wilson B is sometimes smaller than average B, but in my case it is reversed. I look at the distribution of model B factors, they are in the range of 8 to 132. Is there any problem with the refinement of this structure? Thanks in advance for all advice! Regards, Fengyun

2 3

refinement of partly occupied water molecules?
by krimmer＠staff.uni-marburg.de 30 May '13

30 May '13

Dear all, I have a question concerning the refinement of partly occupied water molecules: in some of my macromolecular crystal structures with resolutions between 1.1 - 1.4 Å, mainly in the second solvation shell round positive Fo-Fc electron density blobs are detectable which show after assignment of a water molecule to these blob and subsequent refinement with Phenix refine a good-looking calculated 2Fo-Fc electron density (round shape, the 2Fo-Fc map appears at a contour level of σ = 1.0 - 1.4), but there also occurs a small negative Fo-Fc electron density detectable inside the 2Fo-Fc density blob. The negative Fo-Fc electron density disappears if the occupancy of the water molecule is refined by Phenix or manually set lower than 100% occupancy. Therefore, I think these positions are partly occupied by water molecules, but I am not sure how I should handle it/how it is generally handled. I would be thankful for any advice and/or literature about this topic. My second question is concerning a density blob in perfect coordination distance to an indolyl group (perfectly located in the middle of the five-ring, with 3.4 Å distance to every of the five carbon atoms of the five-ring). What‘s the best way to find out which ion possibly occupies this position? I tried Na+ and Ca2+, but after refinement big negative Fo-Fc blobs appear in both cases (maybe the ion at this position is only partly occupied?). There is no anomalous signal detectable at this position (data collection wavelength was 0.91841 nm). After the refinement of a water molecule at this position, a positive Fo-Fc election density is still there. Thank you for your help! Stefan

3 2

R-merge
by Mengbin Chen 30 May '13

30 May '13

Dear Phenix Users, I have R-merge values equal 0.000 from highest resolution shell (which corresponds to values larger than 1.000) in a data set processed by HKL2000, with redundancies higher than 10 (I know this may help in increasing R-merge). I am not sure if this is going to be a problem of Table 1 for the reviewers. Could you kindly drop me your suggestions? Thank you in advance, Mengbin Chen -- Mengbin Chen Department of Chemistry University of Pennsylvania

5 9

phenix.refine using anomalous concepts for neutron data?
by Derek Logan 29 May '13

29 May '13

Hi, I'm doing a joint X-ray neutron refinement in Phenix and have run into some behaviour that puzzles me. I had not been paying any attention to the use or non-use of anomalous signal in the neutron dataset, as This is what I get if I let phenix.refine itself decide whether or not to use anomalous data: ================================= Neutron data ================================ F-obs: neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM Miller array info: neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM Observation type: xray.reconstructed_amplitude Type of data: double, size=16672 Type of sigmas: double, size=16672 Number of Miller indices: 16672 Anomalous flag: True Unit cell: (removed) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 1258 Resolution range: 29.22 1.89826 Completeness in resolution range: 0.785008 Completeness with d_max=infinity: 0.78486 Bijvoet pairs: 6832 Lone Bijvoet mates: 1750 Anomalous signal: 0.0876 Number of F-obs in resolution range: 16672 Number of F-obs<0 (these reflections will be rejected): 0 Number of F-obs=0 (these reflections will be used in refinement): 0 Refinement resolution range: d_max = 29.2200 d_min = 1.8983 and this is what I get if I forcibly switch off use of anomalous data in the phenix.refine GUI: ================================= Neutron data ================================ F-obs: neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM Miller array info: neutron.mtz:FO,SIGFO,DANO,SIGDANO,ISYM Observation type: xray.reconstructed_amplitude Type of data: double, size=16672 Type of sigmas: double, size=16672 Number of Miller indices: 16672 Anomalous flag: True Unit cell: (removed) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 1258 Resolution range: 29.22 1.89826 Completeness in resolution range: 0.785008 Completeness with d_max=infinity: 0.78486 Bijvoet pairs: 6832 Lone Bijvoet mates: 1750 Anomalous signal: 0.0876 force_anomalous_flag_to_be_equal_to=False Reducing data to non-anomalous array. R-linear = sum(abs(data - mean(data))) / sum(abs(data)) R-square = sum((data - mean(data))**2) / sum(data**2) In these sums single measurements are excluded. Redundancy Mean Mean Min Max Mean R-linear R-square unused: - 29.2234 bin 1: 29.2234 - 4.0863 1 2 1.699 0.0240 0.0011 bin 2: 4.0863 - 3.2448 1 2 1.793 0.0302 0.0022 bin 3: 3.2448 - 2.8350 1 2 1.800 0.0417 0.0041 bin 4: 2.8350 - 2.5760 1 2 1.764 0.0486 0.0054 bin 5: 2.5760 - 2.3914 1 2 1.745 0.0505 0.0051 bin 6: 2.3914 - 2.2505 1 2 1.717 0.0513 0.0051 bin 7: 2.2505 - 2.1378 1 2 1.658 0.0533 0.0056 bin 8: 2.1378 - 2.0448 1 2 1.614 0.0611 0.0074 bin 9: 2.0448 - 1.9661 1 2 1.575 0.0634 0.0075 bin 10: 1.9661 - 1.8983 1 2 1.485 0.0736 0.0097 unused: 1.8983 - Fobs statistics after all cutoffs applied: Miller array info: None Observation type: xray.amplitude Type of data: double, size=9840 Type of sigmas: double, size=9840 Number of Miller indices: 9840 Anomalous flag: False Unit cell: (removed) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 1258 Resolution range: 29.22 1.89826 Completeness in resolution range: 0.855801 Completeness with d_max=infinity: 0.855503 What's going on here? If I let phenix.refine decide automatically, it looks like it's reading in F+ and F- separately and regarding them as independent in the refinement. If I force "no anomalous" it merges them. However I can't work out whether in either case it has actually read FOBS instead of the Friedel mates. According to the SCALA manual the I+ and I- columns will always be written out even if the keyword ANOMALOUS OFF is used, so this is a potential pitfall for many. In addition, phenix.refine seems to identify the neutron data first as xray.reconstructed_amplitude then as xray.amplitude even though the data are explicitly defined as neutron data in the GUI. I can send more information if required! Thanks Derek ________________________________________________________________________ Derek Logan tel: +46 46 222 1443 Associate Professor mob: +46 76 8585 707 Dept. of Biochemistry and Structural Biology www.cmps.lu.se<http://www.cmps.lu.se> Centre for Molecular Protein Science www.maxlab.lu.se/node/307<http://www.maxlab.lu.se/node/307> Lund University, Box 124, 221 00 Lund, Sweden www.saromics.com<http://www.saromics.com>

3 5

Structure Comparison questions
by Heather Condurso 29 May '13

29 May '13

Dear all, I have a few related structures that I would like to compare to make figures for publication but I have a few issues. The biggest issue is that my structures are large (12- 422aa chains) and any attempt at simple alignment in pymol results in a crash. I would like to first compare entire structures, but also compare the differences between related chains in the same structure. I want to look at the small differences in the active site density. What is the best way to do this? Is there a simple way to do this or do I need to make separate pdb files for each chain? Can I use the same mtz or should I rename copies? I will try a few things but any advice would be greatly appreciated. Heather condurso(a)bc.edu

6 8

R: problem refining RNA structure at 4Å resolution
by fulvio.saccoccia＠uniroma1.it 29 May '13

29 May '13

Any signs of twinning? Check also the correctness of your space group: probably you could index In a lower symmetry Laue group with a slight increased distorsion index. Fulvio ----Messaggio Originale---- Da: Benoît Masquida Inviato: 29/05/2013, 14:53 A: PHENIX user mailing list Oggetto: [phenixbb] problem refining RNA structure at 4Å resolution Dear phenix users, I solved using MR a low resolution RNA structure taking data up to 4.3Å and a model of a structure with slight differences. However, when I try to refine, Rwork decreases quickly (start 47, final 32 but Rfree remains high (start 48, final 44). The data are pretty good up to 4.0 with I/sigma above 1. The map doesn't point clearly to wrong regions of the model. What can I try to improve the maps and build the correct model? Thanks in advance. Benoit _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

1 0