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HELP. semelno met refinement not working.
by Kenneth A. Satyshur 24 Apr '14

24 Apr '14

When I refine my seleno met residues in Phenix (1.8.4-1496) ALL my MSE are restrained to ONE conformer, in coot terms ptp #11 with a Chi 1 of 60 deg. This happens at the start of the second cycle when it does 'rsrl'. I can watch it happen in coot. POP! There is goes. Some of the MSE are in this conformation, but not all of them. This refinement is wrong, so how do I correct it? thanks kas -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

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BCA/CCP4 Summer School in Protein Crystallography at Diamond
by Airlie McCoy 24 Apr '14

24 Apr '14

Applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond (UK) from Tuesday 26th August to Sunday 31st August 2014. Applications close 1st May 2014. References are due by 8th May 2014. The BCA/CCP4 Protein Crystallography Summer School is intended for students and researchers new to crystallography. Its dual aims are to provide comprehensive training in crystallography and to promote best practise within the British crystallographic community. The lectures cover the gamut of techniques required for a structure solution, from protein expression through to structure validation. Intensively supervised computer tutorials enable students to relate the theory presented in the lectures to practice. Although CCP4 programs will primarily be used in these tutorials, the aim will be to approach crystallographic questions in a software-agnostic manner. There will also be a crystal manipulation and cooling workshop. Note that the course is scheduled during Diamond synchrotron downtime, so there will not be active data collection at the Diamond beamlines. For more information on eligibility, cost, and applications see: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School.html Application form: http://extranet2.diamond.ac.uk/ISV/EventWidget/BCA/ApplicationsForm.aspx

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inputing tNCS into phenix?
by Yarrow Madrona 23 Apr '14

23 Apr '14

Hello, I recently posted a question about stalled R-factors and and obtained excellent help resulting in the realization that I have tNCS even though it is not picked up by X-triage. I know the transformation matrix of one molecule onto another but I am not sure how to input this into phenix (both the translation and the rotation) to improve refinement. Is there a way to do this? I'm sorry if this has already been covered. -Yarrow

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Trouble Refining Ligand in Phenix
by Chris Fage 22 Apr '14

22 Apr '14

Hi Everyone, I am trying to refine a structure with a phosphorylated amino acid. After refining in Phenix, the Fo-Fc density (green) overlaps the 2Fo-Fc density for all atoms of the derivatized amino acid in Coot, almost as if I had not built in the residue. I am loading a .cif for the derivative when I run phenix.refine. I have also tried ReadySet, but when I click the "Run in phenix.refine" button, I see the message Error interpreting command line argument as parameter definition: "refine_65-coot-2.metal.edits" RuntimeError: Unexpected end of output. Am I just seeing noise, or is Phenix not actually refining this portion of the model? I would appreciate any suggestions. Best, Chris

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Saenger class in nucleic acids
by Chen Zhao 22 Apr '14

22 Apr '14

Dear all, Could anybody point me to a reference for the saenger_class and leontis_westhof_class in nucleic acids? I just failed to find it in the long reference list in the phenix.refine online tutorial. Thanks a lot in advance, Chen

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inputing tNCS into phenix?
by Yarrow Madrona 21 Apr '14

21 Apr '14

Hello, I recently posted a question about stalled R-factors and and obtained excellent help resulting in the realization that I have tNCS even though it is not picked up by X-triage. I know the transformation matrix of one molecule onto another but I am not sure how to input this into phenix (both the translation and the rotation) to improve refinement. Is there a way to do this? I'm sorry if this has already been covered. -Yarrow

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Re: [phenixbb] Phenix composite omit map
by Chen Zhao 21 Apr '14

21 Apr '14

Dear all, Thank you all for your help and the program is running now. However, I met a AttributeError as " 'twin_model_manager' object has no attribute 'f_model_scaled_with_k1' ". Sorry for so many problems. Thank you so much, Chen On Mon, Apr 21, 2014 at 1:13 PM, Chen Zhao <c.zhao(a)yale.edu> wrote: > Dear Engin, > > Thank you so much for your reply! Yes, this is the problem because I am > using phenix-1.8.4-1496. I will download the newest version! > > Best, > Chen > > > On Mon, Apr 21, 2014 at 1:10 PM, Engin Özkan <eozkan(a)uchicago.edu> wrote: > >> Dear Chen, >> >> What version of Phenix are you using? phenix.composite_omit_map was >> recently added (post 1.8.4 release). Are you using a recent nightly >> (presumably dev-1579 as you suggest or even newer, like the release >> candidate for 1.9)? >> >> Engin >> >> >> On 4/21/14, 12:05 PM, Chen Zhao wrote: >> >> Thank you Tom, >> >> I understand what "command not found" mean, but I already sourced >> "phenix_env" in my bashrc. "phenix.list" works, also I have already run >> "phenix.autosol", "phenix.autobuild", "phenix.refine" without any problems. >> >> Thank you so much again! >> >> Sincerely, >> Chen >> >> >> On Mon, Apr 21, 2014 at 1:01 PM, Terwilliger, Thomas C < >> terwilliger(a)lanl.gov> wrote: >> >>> Hi Chen, >>> >>> "command not found" usually means the shell cannot find a particular >>> command. It often can be fixed by sourcing the right setup commands. >>> >>> If you type: >>> >>> phenix.list >>> >>> does it also say "command not found"? If so, you just need to source >>> the phenix version you want. When you install it phenix lists where this >>> directory is...If you are on a mac you will say something like this: >>> >>> >>> source /Applications/PHENIX-1.8.3-1479/Contents/phenix-1.8.3-1479/phenix_env >>> >>> and you can put that in your .cshrc file too (if you are using csh). >>> >>> Let me know if that doesn't do it! >>> All the best, >>> Tom T >>> >>> >>> >>> >>> On Apr 21, 2014, at 10:53 AM, Chen Zhao wrote: >>> >>> Dear all, >>> >>> Hello! I am now running into a simple technical problem but I just >>> cannot figure it out. I am trying to create a composite omit map by phenix, >>> but when I typed in the command phenix.composite_omit_map XXX.eff based >>> on the instructions on >>> http://www.phenix-online.org/version_docs/dev-1579/composite_omit_map.htm, >>> I got the error message "command not found". Could anybody help me out? >>> >>> Thank you so much in advance! >>> >>> Sincerely, >>> Chen >>> >>> >>> >> >> >> _______________________________________________ >> phenixbb mailing [email protected]://phenix-online.org/mailman/listinfo/phenixbb >> >> >> -- >> Assistant Professor >> Dept of Biochemistry and Molecular Biology >> University of Chicago >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> >

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Berkeley Ligands workshop: registration deadline tomorrow
by Peter Zwart 21 Apr '14

21 Apr '14

Dear All, On May 2, 2014 the BCSB will be hosting a full day event dedicated to ligands in the life sciences. Access is free, but is limited to 30 participants. The lectures will be streamed allowing remote participation to this event. For onsite and remote attendance, please register to receive further instructions. The registration for on-site participation will be on a first come, first serve basis and will close tomorrow at noon. The program will cover structural science associated with ligands in the life sciences. Viewpoints from macromolecular crystallography, quantum chemistry, small molecule crystallography and solution scattering will provide the participants with a 360-degree perspective of the role of and technology associated with ligands in structural biology. Please have a look at https://sites.google.com/a/lbl.gov/ligands/home for more information. Regards Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

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Re: [phenixbb] Phenix composite omit map
by Terwilliger, Thomas C 21 Apr '14

21 Apr '14

Hi Chen, "command not found" usually means the shell cannot find a particular command. It often can be fixed by sourcing the right setup commands. If you type: phenix.list does it also say "command not found"? If so, you just need to source the phenix version you want. When you install it phenix lists where this directory is...If you are on a mac you will say something like this: source /Applications/PHENIX-1.8.3-1479/Contents/phenix-1.8.3-1479/phenix_env and you can put that in your .cshrc file too (if you are using csh). Let me know if that doesn't do it! All the best, Tom T On Apr 21, 2014, at 10:53 AM, Chen Zhao wrote: Dear all, Hello! I am now running into a simple technical problem but I just cannot figure it out. I am trying to create a composite omit map by phenix, but when I typed in the command phenix.composite_omit_map XXX.eff based on the instructions on http://www.phenix-online.org/version_docs/dev-1579/composite_omit_map.htm, I got the error message "command not found". Could anybody help me out? Thank you so much in advance! Sincerely, Chen

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Re: [phenixbb] Stalled refinement
by Dale Tronrud 19 Apr '14

19 Apr '14

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, In P21 the equivalent positions are: xyz; -x,y+1/2,-z. In matrix form the operation to transform chain A onto the symmetry image of A is: Transform A -> Symmetry related A /-1 0 0\ /x\ / 0 \ | 0 1 0 | |y| + |1/2| \ 0 0 -1/ \z/ \ 0 / Now let's assume there are two molecules in the ASU related by a perfect two-fold, axis parallel to the crystal screw axis, but with arbitrary translations perpendicular. The equation to transform chain B onto A is: Transform B -> A /-1 0 0\ /x\ /t1\ | 0 1 0 | |y| + |0 | \ 0 0 -1/ \z/ \t3/ Now, the question is "What is the transformation that takes chain B directly onto the symmetry image of A?" We can derive that by transforming B onto A and then transforming that by the crystal screw axis. Transform B -> symmetry related A /-1 0 0\ //-1 0 0\ /x\ /t1\\ / 0 \ | 0 1 0 | || 0 1 0 | |y| + |0 || + |1/2| \ 0 0 -1/ \\ 0 0 -1/ \z/ \t3// \ 0 / Now simplify: / 1 0 0\ /x\ /-t1\ / 0 \ | 0 1 0 | |y| + | 0 | + |1/2| \ 0 0 1/ \z/ \-t3/ \ 0 / / 1 0 0\ /x\ /-t1\ | 0 1 0 | |y| + |1/2| \ 0 0 1/ \z/ \-t3/ What we get is an identity operator with a translation. Note, I didn't make any other assumptions. Whenever you have space group P21 and two-fold ncs with the same symmetry axis direction you will get pseudo-translation. With your crystal the ncs matrix is not aligned with the y axis all that well. I haven't calculated it exactly but it seems to be about 10 deg away. That must be enough to wipe out the Patterson peak and the pseudo-translation check in xtriage. As a side note, you mentioned that you didn't think this was pseudo-translation because the translation was not 0.5. A translation of 0.5 could lead to pseudo-centering which is a special case of pseudo-translation. If you had that your crystal would be nearly space group C2 and half your reflections would be systematically weak and this can cause problems with the free R. Dale Tronrud On 4/18/2014 2:16 PM, Yarrow Madrona wrote: > Hi Dale, > > You know a lot more (and probably have forgotten more) > crystallography theory than I will every know. But I thought that > rotational and translational NCS can be completely separate from > the space group symmetry. They can become confused when the NCS > operator is close to a crystallographic symmetry axis. I have P21 > symmetry between dimers but there is only one dimer in the unit > cell. They appear to have near perfect 2-fold symmetry between them > on the b-axis (according to the transformation matrix). However, > the translation between them is not close to 1/2 of a unit cell as > would be expected for a 2(1) screw axis. This makes sense because I > don't see a peak on the patterson map but I do see a peak on the > self rotation. X-triage also confirms the first part. > > I also get a translation of (0, 0.3, 0.3) but I thought this > wouldn't show up as translational "NCS" because it was not near > 0.5. I thought the difference between the vectors would not > perfectly superimpose to give a strong peak on a patterson map. > > Please correct me if I am wrong (because I probably am). It is > entirely possible I sound like an idiot. If so please let me know. > Otherwise I will never learn more about the fundamentals of > crystallography. If you have a good reference please let me know. > > -Yarrow > > > On Fri, Apr 18, 2014 at 9:34 AM, Dale Tronrud > <detBB(a)daletronrud.com <mailto:[email protected]>> wrote: > > Hi, > > I don't see how you can not have translational ncs. You are in > space group P21 and have an ncs two-fold parallel to y. Doesn't > this combination have to give rise to translational ncs? > > I may have screwed up my paper matrix multiplications but I come > up with a translational ncs of about (0, 0.3, 0.3) in fractional > coordinates. If the translation were 0.3333 you would only see > strong reflections for k+l=3n. This would result in a lot of weak > data and higher than expected free R's. > > Of course, xtriage should be screaming bloody murder and you > should be seeing the peak in the Patterson. I'm confused. > > Dale Tronrud > > On 4/17/2014 6:05 PM, Yarrow Madrona wrote: >> There is no significant peaks for translational NCS. I also >> didn't see anything in the patterson map. > >> However, the Multivariate Z score L-test gives 6.218. Also the >> observed Centric reflections are more intense than they should >> be but I don't suspect twinning in a monoclinic space group. > >> -Yarrow > > >> On Thu, Apr 17, 2014 at 4:37 PM, Paul Adams <pdadams(a)lbl.gov > <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> wrote: > > >> What does triage say about translation NCS? > > >> On Thu, Apr 17, 2014 at 4:25 PM, Yarrow Madrona >> <amadrona(a)uci.edu > <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> wrote: > >> Hello, > >> I using the latest stable build of phenx.refine (1.8.4) I >> recently collected data, processed and obtained an MR solution >> using phaser. I am stuck trying to refine with an Rfree sitting >> at 40% > >> I really want to know if the high Rfree is due to poor data >> quality or if non-crystallographic symmetry involving a near >> perfect two fold rotation between the two molecules in the ASU >> could somehow impede refinement. Stats and other information is >> below. Thank you for any help you can give. > >> -Yarrow > > >> Visually, the quality of the data is marginal at best >> (streaky/ice rings in many frames) despite good processing stats >> from XDS. Processing with mosflm or HKL2000 managed to index but >> failed pretty bad in integration and scaling. > >> Phaser gave high TFZ scores for 2 molecules in the asu (see >> below). > >> Density for a cholesterol like ligand shows up even though not >> present in the search model. > >> MolRep Self rotation shows rotational symmetry. > > https://www.dropbox.com/s/2zsajl5o091k50r/CYP142A2-032814_21_rf%20copy.pdf > > >> The 2 molecules in the ASU are related by almost a 2 fold >> rotation: > >> Rotation matrix for chain A to chain B: > >> new_ncs_group rota_matrix 1.0000 0.0000 0.0000 >> rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 >> 0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 > >> center_orth 15.2016 0.5245 33.7070 > >> rota_matrix -0.9860 -0.1636 -0.0309 rota_matrix -0.1659 >> 0.9511 0.2605 rota_matrix -0.0132 0.2620 -0.9650 >> tran_orth 34.3310 -24.0033 107.0457 > >> center_orth 15.7607 7.2426 77.7512 > >> RMSD, B onto A = 0.0007 after phaser RMSD, B onto A = 0.347 >> after one round of refinement in phenix > > >> Refinement using aniostropically corrected data (ucla web >> server: Services.mbi.ucla.edu/anisoscale > <http://Services.mbi.ucla.edu/anisoscale> >> <http://Services.mbi.ucla.edu/anisoscale>) did not improve the >> Rfree in refinement. > > >> Statistics are listed below: > >> UNIT CELL: 51.487 88.923 89.592 90 97.15 90 P21 > >> RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR >> R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno >> Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed >> expected Corr > >> 5.99 8280 1927 2087 92.3% 3.1% 3.3% >> 8246 35.09 3.5% 99.8* 20* 0.909 1296 4.30 14606 >> 3401 3487 97.5% 3.3% 3.5% 14580 33.37 >> 3.8% 99.9* 11* 0.843 2273 3.53 17961 4244 >> 4445 95.5% 3.8% 3.9% 17944 31.11 4.4% 99.8* >> -2 0.789 2721 3.06 21954 5068 5221 97.1% >> 4.9% 5.1% 21933 24.81 5.6% 99.7* -2 0.780 3455 >> 2.74 25741 5830 5933 98.3% 7.6% 7.6% 25713 >> 18.88 8.6% 99.5* -2 0.782 4165 2.51 27859 >> 6311 6483 97.3% 10.8% 10.8% 27824 14.06 12.3% >> 99.1* -2 0.774 4385 2.32 31336 6979 7084 >> 98.5% 14.9% 15.3% 31296 10.49 16.8% 98.5* -4 >> 0.748 5095 2.17 32396 7347 7567 97.1% >> 22.3% 22.7% 32341 7.46 25.4% 97.3* -7 0.728 >> 5055 2.05 32254 7339 8047 91.2% 33.1% 33.5% >> 32075 5.06 37.5% 94.8* -6 0.724 5155 total >> 212387 48446 50354 96.2% 7.8% 7.9% 211952 >> 16.57 8.8% 99.7* -3 0.768 33600 > >> Processing with mosflm or HKL2000 managed to index but failed >> pretty bad in integration and scaling. > > >> Phaser: > >> SOLU SET RFZ=27.5 TFZ=24.2 PAK=0 LLG=1711 RF++ TFZ=64.6 PAK=0 >> LLG=3610 LLG=4865 > > >> _______________________________________________ phenixbb mailing >> list phenixbb(a)phenix-online.org >> <mailto:[email protected]> >> <mailto:[email protected] > <mailto:[email protected]>> >> http://phenix-online.org/mailman/listinfo/phenixbb > > > > >> -- Paul Adams Deputy Division Director, Physical Biosciences >> Division, Lawrence Berkeley Lab Division Deputy for Biosciences, >> Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, >> Department of Bioengineering, U.C. Berkeley Vice President for >> Technology, the Joint BioEnergy Institute Laboratory Research >> Manager, ENIGMA Science Focus Area > >> Building 64, Room 248 Tel: 1-510-486-4225 <tel:1-510-486-4225>, > Fax: 1-510-486-5909 <tel:1-510-486-5909> >> http://cci.lbl.gov/paul > >> Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 >> Berkeley, CA 94720, USA. > >> Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov > <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> ][ > 1-510-495-2506 <tel:%5B%201-510-495-2506> ] > > > > >> _______________________________________________ phenixbb mailing >> list phenixbb(a)phenix-online.org >> <mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/phenixbb > > _______________________________________________ phenixbb mailing > list phenixbb(a)phenix-online.org > <mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/phenixbb > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlNSKBMACgkQU5C0gGfAG12g4gCgqgM2umswKaUkxKYQFccDXeOc 3GgAoL5FjHVPUKyK+jkwLQ/BaVv15iiW =Phy4 -----END PGP SIGNATURE-----

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