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Refining sucrose
by Priit Eek 23 May '11

23 May '11

Hi, I couldn't find this (probably basic knowledge) in the manual or here, so... I have a problem with refining a sucrose ligand. It is not covalently bound to the protein – just electrostatic interaction. The density isn't the best, but it's still obvious it must be there. LigandFit can find the blob and fits the sucrose in there quite well, but when I run phenix.refine it distorts the geometry of the molecule and complains about it later in MolProbity - Basic Geometry validation in almost every possible way. How can I apply more stringent restraints to the ligand so its geometry wouldn't get so twisted? This might not be the most appropriate list for my second question, but the problem is the same and somebody probably knows: how to manually modify that sucrose in Coot (eg rotate only one ring or a -CH2OH group) or perform real space refinement? Right now I can only rotate/translate the whole sucrose and trying to perform a real space refinement results in an error ("Failed to match (to the dictionary) the following model atom names: SUC C1 C2 C3 C4 C5 C6 O1 O2 O3 O4 O6. That would cause exploding atoms, so the refinement didn't start.") I haven't specified any custom cif libraries as SUC should be present in the built-in library of both Phenix and Coot. I'm using Phenix v1.7.1-743 and Coot v0.6.2-pre-1-rev3450 on OS X 10.6.7. Thank you in advance! Regards, Priit Eek

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Call for articles and short communications for Computational Crystallography Newsletter
by Nigel Moriarty 23 May '11

23 May '11

Dear Colleagues I'm accepting short communications and articles of general interest to crystallographers working on macromolecular systems for the next issue of the Computational Crystallography Newsletter. You can see recent issues at http://www.phenix-online.org/newsletter/ as well as the word template for article submission. The deadline is June 17th but early submission is appreciated. Nigel -- Nigel W. Moriarty, PhD Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Weird R-free discrepancy.
by Yuri 22 May '11

22 May '11

I was working on a model for at 1.9 A using the previous phenix release (650). I was almost finished r-free was 0.197. I installed the newest release and refined again and my r-free went up to 0.228!!. The values for bsol and ksol look significantly different. I do not understand where the biggest difference is coming from... Below I pasted part of the .log files. Old and new, respectively. =============================== refinement start ============================== ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.90 - 28.74 A; n_refl. = 32203)------------------------------| | | | r_work= 0.1747 r_free= 0.1967 ksol= 0.40 Bsol= 39.70 scale= 0.064 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (-1.65,-1.65,3.31,-0.00,0.00,0.00); trace/3= -0.00 | | | | maximum likelihood estimate for coordinate error: 0.21 A | | x-ray target function (ml) for work reflections: 2.567485 | =============================== refinement start ============================== ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.90 - 28.74 A; n_refl. = 34277)------------------------------| | | | r_work= 0.1911 r_free= 0.2279 ksol= 0.40 Bsol= 59.62 scale= 0.063 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (-1.73,-1.73,3.47,0.00,0.00,-0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.55 A | | x-ray target function (ml) for work reflections: 2.591014 | |-----------------------------------------------------------------------------| -- Yuri Pompeu

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BRU error
by Krystle Williams McLaughlin 20 May '11

20 May '11

Hi, I'm using phenix for refinement and I keep getting an error. My DNA strand has a bromo-uridine in it and phenix.refine keeps crashing on this nucleotide. Here is the error: Number of atoms with unknown nonbonded energy type symbols: 40 "ATOM 2770 P BRU P 5 .*. P " "ATOM 2771 O1P BRU P 5 .*. O " "ATOM 2772 O2P BRU P 5 .*. O " "ATOM 2773 O5* BRU P 5 .*. O " "ATOM 2774 C5* BRU P 5 .*. C " "ATOM 2775 C4* BRU P 5 .*. C " "ATOM 2776 O4* BRU P 5 .*. O " "ATOM 2777 C1* BRU P 5 .*. C " "ATOM 2778 N1 BRU P 5 .*. N " "ATOM 2779 C6 BRU P 5 .*. C " ... (remaining 30 not shown) Here is what I have in my pdb: ATOM 2901 P BRU E 5 33.977 -16.324 24.303 1.00 27.21 P ATOM 2902 O1P BRU E 5 34.027 -15.724 22.919 1.00 28.22 O ATOM 2903 O2P BRU E 5 33.857 -15.340 25.393 1.00 25.06 O ATOM 2904 O5* BRU E 5 32.721 -17.236 24.418 1.00 28.02 O ATOM 2905 C5* BRU E 5 32.487 -18.228 23.495 1.00 28.50 C ATOM 2906 C4* BRU E 5 31.047 -18.347 23.082 1.00 32.59 C ATOM 2907 O4* BRU E 5 30.337 -18.858 24.152 1.00 28.61 O ATOM 2908 C1* BRU E 5 29.369 -17.891 24.535 1.00 29.63 C ATOM 2909 N1 BRU E 5 29.279 -17.855 25.962 1.00 29.72 N ATOM 2910 C6 BRU E 5 30.426 -17.755 26.799 1.00 30.57 C ATOM 2911 C5 BRU E 5 30.251 -17.738 28.232 1.00 30.89 C ATOM 2912 BR BRU E 5 31.869 -17.591 29.321 1.00 57.08 Br ATOM 2913 C4 BRU E 5 28.917 -17.845 28.826 1.00 30.70 C ATOM 2914 O4 BRU E 5 28.768 -17.825 30.033 1.00 29.36 O ATOM 2915 N3 BRU E 5 27.785 -17.945 27.981 1.00 29.36 N ATOM 2916 C2 BRU E 5 27.961 -17.966 26.552 1.00 29.05 C ATOM 2917 O2 BRU E 5 26.994 -18.064 25.848 1.00 35.29 O ATOM 2918 C3* BRU E 5 30.464 -17.006 22.751 1.00 34.58 C ATOM 2919 C2* BRU E 5 29.845 -16.605 23.968 1.00 33.10 C ATOM 2920 O3* BRU E 5 29.526 -17.213 21.768 1.00 37.93 O I have already run a BRU molecule through ReadySet and when I use the cif file generated from this phenix.refine will run through but when the Bromine atom is in the structure has a large negative density peak in the Fo-Fc map. I think it may just be a naming thing. BRU is already in the monomer library so I don't understand why I get an error at first also without the readyset cif file. Any suggestions? Thanks, Krystle

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Phenix 1.7 with Rosetta and PBS/Torque
by Jeremy Mann 20 May '11

20 May '11

Reading the documentation is is unclear with queue system will work with Phenix 1.7. qsub is mentioned but not referred as the qsub from Torque/PBS or qsub from Grid Engine. Which qsub are the developers referring to? -- Jeremy Mann jeremy(a)biochem.uthscsa.edu University of Texas Health Science Center Bioinformatics Core Facility http://www.bioinformatics.uthscsa.edu Phone: (210) 767-3419 ^^^^^^^^ ** NEW OFFICE NUMBER **

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map error?
by Christian Roth 19 May '11

19 May '11

Dear all, I got a error message in the last round of phenix.refine which seesm to be related to map or mtz file creation (error.txt attached). I used the GUI and I unchecked the map creation option in ccp4 or Xplor before I started the run. I am not sure whats going wrong here. Please could you point me to the problem. Best regards Christian

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AutoSol
by Nora Cronin 19 May '11

19 May '11

Whilst I can input SAD SAD data ie two different SAD datasets using Group =1 and Group =2 with the "Wavelength" keyword, how do I input 2 different crystals using the "crystal_info" keyword which does not recognize Group = Inputting .sca unmerged anomalous data how do I input data for 2 different crystal_info keywords with different heavy atoms and different unit cells? thanks Nora Dr N B Cronin X-Ray Laboratory Manager Tel. (+44) 020 7153 5445 Section of Structural Biology Fax. (+44) 020 7153 5457 Chester Beatty Laboratories mobile: (+44) 07787554059 The Institute of Cancer Research 237 Fulham Road London SW3 6JB The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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mr_rosetta on a supercomputer
by Patricia Amara 18 May '11

18 May '11

Hello, I have been trying to run phenix.mr_rosetta on a supercomputer where we are limited to 24h for parallel jobs and we have different queues for job mono. Thus to run we have two files. We do not really understand how the code proceeds with nproc so we just put 6 for now. When we sent it, it created 1000 jobs on MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1 it sent 10 jobs mono, but ran only 5 first than the other five. Then the job running the script hangs. when we looked at the log files in the MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1 directories it filled up only 4 if we re-run only 3 and never the same. do you have any idea what we're doing wrong? thanks in advance for your input Patricia Amara ps; Thus to run we have two files. One to send the script #!/bin/bash #MSUB -e ros1_%I.e #MSUB -o ros1_%I.o #MSUB -n 6 #MSUB -T 86400 cd /scratch/cont003/amara/Rosetta-NadA ./rosetta.run and the script itself: phenix.mr_rosetta \ seq_file=/scratch/cont003/amara/Rosetta-NadA/NADA.seq \ data=/scratch/cont003/amara/Rosetta-NadA/NadA-7-BM16-remote-no_ano-P21212-Rfree_shell.mtz \ search_models=/scratch/cont003/amara/Rosetta-NadA/model_2.pdb \ run_prerefine=True \ number_of_prerefine_models=1000 \ fragment_files = /scratch/cont003/amara/Rosetta-NadA/aat000_03_05.200_v1_3.gz \ fragment_files = /scratch/cont003/amara/Rosetta-NadA/aat000_09_05.200_v1_3.gz \ rescore_mr.relax=False \ rosetta_models=20 \ ncs_copies=3 \ space_group=p21212 \ use_all_plausible_sg=False \ max_wait_time=100 \ nproc=6 \ group_run_command= "/usr/share/lsf/7.0/linux2.6-glibc2.3-x86_64/bin/bsub -n 1 -q mono -W 03:00"

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phenix.model_vs_data enhancement request
by Schubert, Carsten [PRDUS] 18 May '11

18 May '11

Hi Pavel, do you think it would be possible to extend the statistics printed out by phenix.model_vs_data, so it also does a break-down by chains? Right now the stats are listed by residue type, i.e. protein/ligand/solvent/etc. For instance if I am interested in the B-factors of a glycosylated protein with ligands, the sugars and ligands all get muddled together. Breaking this down by chains as well would allow for finer control. Cheers, Carsten

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Polygon graphs
by Tanner, John J. 17 May '11

17 May '11

Does anyone know whether the polygon graphs from the following paper were ever incorporated into phenix? Crystallographic model quality at a glance Acta Crystallogr D Biol Crystallogr. 2009 March 1; 65(Pt 3): 297300. -- John J. Tanner Professor of Chemistry and Biochemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-2754 Email: tannerjj(a)missouri.edu http://www.chem.missouri.edu/TannerGroup/tanner.html

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