- phenixbb - phenix-online.org

Re: [phenixbb] clash guarde failure phenix coot
by Pavel Afonine 20 Jan '10

20 Jan '10

Hi Georg, I think the refinement .log file should contain the lines like these below: Warning: very small nonbonded interaction distances. Nonbonded interactions: 12604 Sorted by model distance: nonbonded pdb=" CG ARG A 3 " pdb=" CG ARG A 4 " model vdw 0.000 3.840 nonbonded pdb=" NE ARG A 3 " pdb=" NE ARG A 4 " model vdw 0.000 3.200 which pinpoints you the offending atoms. Does this answer your question? Pavel. On 1/19/10 9:57 AM, Georg Mlynek wrote: > > Dear All, > > I´m refining a 2.1A with phenix 1.5-2 and get when I click on > automatically add hydrogens to model following error message: > refinement.pdb_interpretation.clash_guard.failure: Number of nonbonded > interaction distances < 0.5:391 > > I suppose that this comes, because coot mixes up the hydrogens. >

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rigid body refinement problem
by Jianghai Zhu 19 Jan '10

19 Jan '10

Hi, I am using phenix.refine_dev_282 for a rigid body refinement. The output pdb file is exactly the same as the input model even though there are obviously some large movements. Here are some information from the log file. Information about total rigid body shift of selected groups: rotation (deg) translation (A) xyz total xyz total group 1: 0.051 -5.493 -1.073 5.60 0.55 -3.15 -1.35 3.47 group 2: 0.254 0.562 0.252 0.67 0.36 -3.99 0.87 4.10 group 3: 3.807 4.001 -2.262 5.92 -0.81 -3.17 1.06 3.44 group 4: 2.275 -4.215 1.909 5.12 -0.18 -2.95 -1.43 3.28 group 5: -1.902 -5.750 -3.206 6.81 -1.99 -4.44 0.27 4.88 group 6: -4.932 -3.939 -5.340 8.16 -0.18 -2.08 -0.25 2.11 group 7: -1.140 -0.769 -7.715 7.83 0.73 -2.91 0.04 3.00 group 8: 2.008 -1.858 -1.236 3.02 -1.10 -5.44 -0.82 5.61 But then the model didn't change at all. stage Deviation of refined model from start model max min mean 0 : 0.000 0.000 0.000 1_bss: 0.000 0.000 0.000 1_rbr: 0.000 0.000 0.000 1_bss: 0.000 0.000 0.000 1_adp: 0.000 0.000 0.000 1_bss: 0.000 0.000 0.000 Is this a bug? -- Jianghai

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difference density map
by 丁玮 19 Jan '10

19 Jan '10

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Where is phenix.refine finding starting r values?
by Bart, Aaron G 19 Jan '10

19 Jan '10

Greetings, I am fairly new to crystallography, and have just started to use Phenix for structural refinement. I am currently working on a 2.8A structure that was run through multiple rounds of rigid body refinement via Refmac and manual revision using Coot. I eventually got stuck where large portions of my molecule had very poor density and the rwork and rfree stayed around 0.3. I then performed a TLS refinement which resulted in better density, and tried running it through phenix.refine with default ADP settings, as well as simulated annealing. It worked beautifully, however when I looked at the log file for the refinement, phenix was reporting a starting rwork and rfree that represented my first stage of refinement in refmac, 0.38/0.44. My question is, is phenix somehow neglecting the refinement that was done in refmac? Regards -Aaron

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Re: [phenixbb] merohedral twinned refinement
by JXQI 19 Jan '10

19 Jan '10

Zwart, Cherney and all, Thanks for the suggestions.The problem is fixed when I tried P31. Best regards J.X. Qi > > 3. If I try P3,the Matthews coeffs tell 2 or 3 molecules in the ASU,the > molecules will crash.Besides,the overall FOM ( lower than 0.4) and the > R/Rfree values (about 0.45/0.56) suggest that the P3 is the wrong sg. try P31 or otherwise P1. You should get a solution in those groups. It could of course mean that there are OD type issues, but I would not jump there yet. Can you send the intensity statistics from xtriage?

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right symmetry?
by Gabriela Guédez 19 Jan '10

19 Jan '10

Hi Phenixbb, I have a data that indexes in P6122, also P61 and P31. Data analysis in phenix.xtriage says no twinning is suspected according to the L-test. However, after MR and twin RB refinement, the model improves from P6122 or P61 to P31 5% Rfacs and 0.5 the FOM. I thought the data might have RPS and twinning not detected with the L-test. So, i ran xtriage to compute the RvsR statistics using the obs_and_calc.mtz file and the results were: in P61 R_abs_twin observed data : 0.112 R_abs_twin calculated data : 0.047 in P31 R_abs_twin observed data : 0.117 R_abs_twin calculated data : 0.139 "misespecified crystal symmetry", according to Lebedev, Vagin, Murshudov et al 2006, Acta Cryst. D62,83-95. I would like to know a test that tells me the right symmetry. I appreciate your help. Thanks, Gabriela

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Re: [phenixbb] merohedral twinned refinement
by JXQI 19 Jan '10

19 Jan '10

Dr.Zwart, Thanks for the reply. 2. The systematic absences and the Rsym support the P3121.I already mentioned the model fit very with the map if I use the P3121. 3. If I try P3,the Matthews coeffs tell 2 or 3 molecules in the ASU,the molecules will crash.Besides,the overall FOM ( lower than 0.4) and the R/Rfree values (about 0.45/0.56) suggest that the P3 is the wrong sg. 4. TLS refinement also did not imrove the results. 5. There are totally 88 aa in my protein, I could build 86 aa clearly. The intensity ststistics is attached in the message. J.X. QI ************************************************************************ Shell I/Sigma in resolution shells: Lower Upper % of of reflections with I / Sigma less than limit limit 0 1 2 3 5 10 20 >20 total 50.00 4.95 0.9 1.5 1.9 2.4 2.8 4.0 9.5 90.5 100.0 4.95 3.93 0.0 0.2 0.3 0.5 0.8 2.0 6.6 93.4 100.0 3.93 3.44 0.2 0.3 0.6 1.0 2.5 5.4 15.4 84.6 100.0 3.44 3.12 0.0 0.2 0.5 0.7 2.5 7.6 22.7 77.3 100.0 3.12 2.90 0.3 1.0 2.1 3.2 7.2 17.6 41.4 58.6 100.0 2.90 2.73 0.0 0.7 2.0 3.2 9.9 20.8 52.9 47.1 100.0 2.73 2.59 0.0 1.4 2.9 5.7 12.4 30.0 60.8 39.2 100.0 2.59 2.48 0.7 1.6 4.7 7.7 16.3 36.0 71.5 28.5 100.0 2.48 2.38 0.6 2.1 5.0 10.2 21.9 42.0 76.2 23.8 100.0 2.38 2.30 0.8 2.3 7.4 12.7 25.3 49.4 83.4 16.6 100.0 All hkl 0.4 1.1 2.7 4.7 10.0 21.1 43.4 56.6 100.0 Summary of reflections intensities and R-factors by shells R linear = SUM ( ABS(I - <I>)) / SUM (I) R square = SUM ( (I - <I>) ** 2) / SUM (I ** 2) Chi**2 = SUM ( (I - <I>) ** 2) / (Error ** 2 * N / (N-1) ) ) In all sums single measurements are excluded Shell Lower Upper Average Average Norm. Linear Square limit Angstrom I error stat. Chi**2 R-fac R-fac 50.00 4.95 619.8 13.8 3.5 1.039 0.046 0.050 4.95 3.93 834.6 17.5 5.0 1.156 0.048 0.052 3.93 3.44 521.9 14.6 4.5 1.026 0.059 0.062 3.44 3.12 333.7 11.1 4.1 1.073 0.071 0.068 3.12 2.90 172.5 7.1 3.6 1.153 0.098 0.096 2.90 2.73 131.4 6.0 3.4 1.256 0.116 0.108 2.73 2.59 102.8 5.2 3.4 1.306 0.140 0.130 2.59 2.48 77.7 4.6 3.4 1.381 0.173 0.158 2.48 2.38 64.1 4.3 3.3 1.355 0.195 0.177 2.38 2.30 54.7 4.1 3.3 1.345 0.221 0.197 All reflections 297.8 8.9 3.7 1.209 0.071 0.059 Intensities of systematic absences h k l Intensity Sigma I/Sigma 0 0 2 -0.2 0.4 -0.5 0 0 4 0.1 1.0 0.1 0 0 5 0.4 1.4 0.3 0 0 7 1.1 2.5 0.4 0 0 8 0.4 2.1 0.2 0 0 10 7.3 3.4 2.2 0 0 11 6.0 3.5 1.7 0 0 13 -2.3 4.9 -0.5 0 0 14 6.1 4.3 1.4 0 0 16 8.1 5.1 1.6 0 0 17 3.9 4.9 0.8 0 0 19 0.8 4.5 0.2 0 0 20 4.0 4.6 0.9 ********************************************************************* 1. How do the intensity statistic look like? 2. How did you choose P3121? 3. Did you try solving and refining in P3? 4. TLS? 5. How complete is your model 2010/1/17 JXQI <jxqi at mail.im.ac.cn>: > Dear all, > > I have a 2.3A data set processed with HKL2000. The space group is P3121 with > 63% of solvent content and 1 molecule in the ASU. I used a 40% homology > model to do molecular replacement. Both the Phaser and Molrep gave similar > solution with good packing. After further refinement with phenix, the built > model fit well with the 2mFo-DFc map. However the R/Rfree were stuck to > 0.34/0.38. > > I rechedked the data set with xtriage and found the data set is merohedral > twinned (with twin law"-h,-k,l", the estimated twin fraction is about 0.05). > When I used the twin law in further refinement, the R/Rfree were only > decreased to 0.32/0.36. Any suggestions are appreciated, thanks! > > > J.X. QI > _______________________________________________ > phenixbb mailing list > phenixbb at phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

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merohedral twinned refinement
by JXQI 18 Jan '10

18 Jan '10

Dear all, I have a 2.3A data set processed with HKL2000. The space group is P3121 with 63% of solvent content and 1 molecule in the ASU. I used a 40% homology model to do molecular replacement. Both the Phaser and Molrep gave similar solution with good packing. After further refinement with phenix, the built model fit well with the 2mFo-DFc map. However the R/Rfree were stuck to 0.34/0.38. I rechedked the data set with xtriage and found the data set is merohedral twinned (with twin law"-h,-k,l", the estimated twin fraction is about 0.05). When I used the twin law in further refinement, the R/Rfree were only decreased to 0.32/0.36. Any suggestions are appreciated, thanks! J.X. QI

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Twin fraction in phenix refine
by Pietro Roversi 18 Jan '10

18 Jan '10

Dear all, phenix.xtriage estimates a twin fraction of between 24 and 30% but then when I start the refinement I get 47-49%. In CNS if I fix the twin fraction in a series of refinements the Rfactors jump from 44% (twin fraction 0) to 37% (from 25% to 49%, only marginal improvement upon going from alpha=25% to 49%). Questions: 1. Is the refinement of alpha dependent on the model? 2. I am tempted to work with the 30% that xtriage estimates but do not know how: is there a way to fix alpha? Thanks Pietro -- Sent from my Desktop Pietro Roversi EP Abraham Fellow in Biochemistry - Lincoln College - Oxford Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385

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Re: [phenixbb] [ccp4bb] Adding H in refinement
by Schubert, Carsten [PRDUS] 14 Jan '10

14 Jan '10

Hi Pavel, sorry I hijacked the thread a bit... A question about the riding Hydrogens and their B-factors. I noticed that at least with earlier versions of PHENIX the B-factor of the Hydrogens was not fixed to the B-factor of the bonded atoms. If I would generate the Hydrogens in reduce they would inherit the appropriate B-factors, but during the course of the refinement and rebuilding they would start to diverge, sometimes drastically. Are you saying the current implementation restrains the B-factors to the bonded atoms and forces them to be equal or are they just inherited and are allowed to float afterwards? Cheers, Carsten > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > Pavel Afonine > Sent: Tuesday, January 12, 2010 12:24 PM > To: CCP4BB(a)JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Adding H in refinement > > Hi Sara, > > - what you observe should not happen since phenix.refine uses riding > model for H atoms. The hydrogen's B-factors are automatically inherited > from the atoms these hydrogens are bonded to. For example, in X-H bond > the B-factor of X should be equal to B-factor of H. > > - make sure you are using the latest version of PHENIX: > http://www.phenix-online.org/download/ > > - if this does not help, please contact me directly, and send the data > and model so I can tell you what exactly is not right (all the files > will be handled confidentially). > > - there is PHENIX bulletin board: > http://www.phenix-online.org/mailman/listinfo/phenixbb > > Pavel. > > > I did refinement with phenix of my 1.9-2.0 Angstroem structures and > included the hydrogens (riding). However, when I checked on the > statistics (refinement close to the end), the average B-factor was > extremely high (in phenix.polygon it was higher than with any other > structure in similar resolution range). It makes sense though that this > happens, if you have a residue which has a high B-factor and carries a > lot of hydrogens the average B-factor will raise quite a lot (since the > B-factor of hydrogens is calculated 1-1.5x of B-factor from the atom > it sits on), right? > > (When I removed the hydrogens again, the average B-factor was > fine...) > > > > My question is now did I do something wrong in my refinement (-> do I > have to change something that this does not happen), or is this > something everybody sees? > > > > If this is common, what would happen (during evaluation) if you want > to publish a structure and the statistics show such a high average B- > factor? Is it better to have hydrogens on, but a bad average B, or no > hydrogens on and a good average B... Obviously, I never published a > structure ;) > >

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