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Question regarding phenix.fmodel
by zhangh1＠umbc.edu 25 Apr '11

25 Apr '11

Hi, According to the instruction, phenix.fmodel was supposed to calculate Fc only; however, when I try the following 2 scripts, they ended up with different Fc values (at the same hkl point): 1. phenix.fmodel ${PDB} high_resolution=XX 2. phenix.fmodel ${PDB} ${MTZ} The instruction says (2) will output Fcalc that will match the set of Miller indices of the data in reflection_data.mtz file, so I thought 1 and 2 should have the same values at the same hkl points... One more question about fmodel. I have 2 models with different sizes, and want to compare their Fc in the same scale. If I use (1), there will be no scaling by default I think, so the Fc results can be directly compared, right? (A most direct way would be checking the Fc at h0k0l0 point and see whether they are proportional to the molecular size, but it seems phenix.fmodel will ignore this point even I expicitly add it to the MTZ file.) Thanks! Hailiang

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Residue number error after autoMR or PhaserMR
by Zhang yu 23 Apr '11

23 Apr '11

Hi, When I run MR in Phenix, I found that there is a numbering error in the solution PDB file The error is that Phenix numbers residues from 0 again when the residue numbers are over 999, though they belong to the same chain. For example "ATOM 11504 N HIS C 999 -37.389 50.436 57.144 1.00 56.62 N ATOM 11505 CA HIS C 999 -36.908 51.569 57.924 1.00 60.55 C ATOM 11506 C HIS C 999 -37.438 51.479 59.337 1.00 61.73 C ATOM 11507 O HIS C 999 -38.648 51.484 59.549 1.00 60.99 O ATOM 11508 CB HIS C 999 -37.382 52.895 57.326 1.00 63.09 C ATOM 11509 CG HIS C 999 -36.353 53.577 56.478 1.00 66.67 C ATOM 11510 ND1 HIS C 999 -35.280 52.912 55.925 1.00 68.12 N ATOM 11511 CD2 HIS C 999 -36.247 54.865 56.070 1.00 68.95 C ATOM 11512 CE1 HIS C 999 -34.559 53.762 55.214 1.00 69.21 C ATOM 11513 NE2 HIS C 999 -35.122 54.953 55.285 1.00 69.80 N ATOM 11514 N MET C 0 -36.544 51.378 60.309 1.00 64.17 N ATOM 11515 CA MET C 0 -36.992 51.355 61.688 1.00 66.45 C ATOM 11516 C MET C 0 -37.290 52.797 62.083 1.00 68.10 C ATOM 11517 O MET C 0 -37.018 53.716 61.302 1.00 68.58 O ATOM 11518 CB MET C 0 -35.903 50.763 62.605 1.00 67.35 C ATOM 11519 CG MET C 0 -36.051 49.272 62.997 1.00 67.14 C ATOM 11520 SD MET C 0 -36.534 48.947 64.735 1.00 65.84 S ATOM 11521 CE MET C 0 -35.169 49.744 65.675 1.00 66.20 C ATOM 11522 N VAL C 1 -37.840 53.015 63.272 1.00 69.46 N ATOM 11523 CA VAL C 1 -38.160 54.373 63.711 1.00 69.99 C ATOM 11524 C VAL C 1 -36.911 55.251 63.875 1.00 70.28 C ATOM 11525 O VAL C 1 -37.029 56.452 64.122 1.00 70.20 O ATOM 11526 CB VAL C 1 -38.908 54.379 65.057 1.00 70.57 C ATOM 11527 CG1 VAL C 1 -40.322 53.847 64.873 1.00 71.16 C ATOM 11528 CG2 VAL C 1 -38.148 53.537 66.061 1.00 70.54 C" Does anyone has idea about it? Thanks Yu Zhang

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fwd: Workshop on "Soft X-ray Crystallography" at the APS, May 4, 2011
by Nathaniel Echols 22 Apr '11

22 Apr '11

---------- Forwarded message ---------- From: Bi-Cheng Wang <wang(a)bcl1.bmb.uga.edu> To: phenixbb(a)phenix-online.org Date: Fri, 22 Apr 2011 12:13:02 -0400 Subject: Workshop on "Soft X-ray Crystallography" at the APS, May 4, 2011 We would like to call your attention to a workshop associated with the upcoming 2011 APS Users Meeting, which will be held on May 4, 2011 at the APS, Argonne National Laboratory, USA. The title of the workshop is “Soft X-ray Crystallography”. You may find the workshop program at http://2011usersmeeting.conference.anl.gov/APSWK1Agenda.htm The web links for meeting registration and the application for a permit to enter the Argonne National Laboratory are: https://2011usersmeeting.conference.anl.gov/register http://www.aps.anl.gov/Users/Site_Access We hope you will be able to attend the APS Users Meeting and our workshop. All the best, B.C. Wang, John Rose, Gerd Rosenbaum and John Chrzas

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b factors reporting
by Maia Cherney 21 Apr '11

21 Apr '11

To: PHENIX user mailing list<phenixbb(a)phenix-online.org> Date: Thu, 21 Apr 2011 15:09:19 -0600 Subject: Re: [phenixbb] B factor for DNA and Protein Pavel Afonine wrote: > > Yes, this trivial combination of two commands will do it: > > phenix.pdbtools model.pdb keep=protein output.file_name=protein_only.pdb > phenix.pdbtools model.pdb keep=rna output.file_name=rna_only.pdb > phenix.pdbtools model.pdb keep=water output.file_name=water_only.pdb > Dear Pavel, These commands did not work for me (version 1.7-650). I need to report average b factors separately for the protein, water, several ligands and ions, all of them in one chain A. Traceback (most recent call last): File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/command_line/pdbtools.py", line 3, in<module> from mmtbx import pdbtools File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/__init__.py", line 3, in<module> import cctbx.array_family.flex File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/cctbx/cctbx/array_family/flex.py", line 1, in<module> import scitbx.array_family.flex File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/scitbx/scitbx/array_family/flex.py", line 2, in<module> import boost.optional File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/optional.py", line 1, in<module> import boost.python File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/python.py", line 45, in<module> ext = import_ext("boost_python_meta_ext") File "/raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx/boost/python.py", line 24, in import_ext + [" "+p for p in sys.path])) ImportError: __import__("boost_python_meta_ext"): /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/phaser-2.1.4/build/intel-linux/lib/libboost_python.so: undefined symbol: PyUnicodeUCS2_AsWideChar sys.path: /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx/mmtbx/command_line /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/mmtbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/iotbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/PyCifRW /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/source/phaser /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/cctbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/scitbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/boost_adaptbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/lib/cctbx/cctbx_sources/libtbx /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/src/phaser/phaser-2.1.4/build/intel-linux/lib /raid/programs/linux/ccp4-6.1.0/ccp4-6.1.3/share/python /usr/lib/python2.6 /usr/lib/python2.6/plat-linux2 /usr/lib/python2.6/lib-tk /usr/lib/python2.6/lib-old /usr/lib/python2.6/lib-dynload /usr/lib/python2.6/dist-packages /usr/lib/python2.6/dist-packages/Numeric /usr/lib/python2.6/dist-packages/PIL /usr/lib/python2.6/dist-packages/gst-0.10 /var/lib/python-support/python2.6 /usr/lib/python2.6/dist-packages/gtk-2.0 /var/lib/python-support/python2.6/gtk-2.0 /usr/local/lib/python2.6/dist-packages

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Creating cif file of ligands by Elbow/ReadySet
by Ngan Nguyen Bich 21 Apr '11

21 Apr '11

Dear Phenix developers, I'm quite new in crystallography and use PhenixGUI for refinement my protein. I got a problem when I had to create cif file of the new ligand to feed in phenix_refine by Elbow/ReadySet I saw that program creates some bonds shorter or longer compared to the statistic value from the CSD for example. Here are some examples when I play with Elbow (same problem with ReadySet) 1. when I feed program the chemical string, (template PDB file is the mylidand_idea.pdb) CR2 C3 CA3 single 1.569 0.038 and if I choose AM1 optimization CR2 C3 CA3 single 1.602 0.040 2. when I feed program the .pdb file, choose Use geometry for Initial geometry. GYC N CA1 single 1.409 0.020 * GYC N HN1 single 0.902 0.020 GYC N HN2 single 0.901 0.020 GYC SG1 CB1 single 1.797 0.020 GYC SG1 HG1 single 1.204 0.020 GYC CB1 CA1 single 1.500 0.020 GYC CB1 HB11 single 1.006 0.020 GYC CB1 HB12 single 0.972 0.020 GYC CA1 C1 single 1.528 0.020 GYC CA1 HA1 single 1.010 0.020 GYC C1 N2 aromatic 1.412 0.020 GYC C1 N3 aromatic 1.304 0.020 GYC N2 CA2 aromatic 1.505 0.020 ** GYC N3 C2 aromatic 1.349 0.020 GYC N3 CA3 single 1.423 0.020 GYC C2 O2 double 1.370 0.020 GYC C2 CA2 aromatic 1.509 0.020 GYC CA2 CB2 single 1.532 0.020 GYC CA3 C single 1.496 0.020 It's strange to me when comparing * and ** and if I run AM1 GYC CB1 CA1 single 1.533 0.035 GYC CA3 C single 1.564 0.035 as I know, the C-C single bond should be about 1.51. Does anyone get a problem like me? I wonder if I didn't do properly or some thing else, or any suggestion for my case. One more questions is that afterward I found cif file (seemly mmcif file) of my ligand in phenix-1.7-650/chem_data/chemical_components And I'm wondering that How the program use these cif file, or I can use them in which way? Thank you in advance. Best regards, Ngan Nguyen Bich KULeuven Belgium

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unit cell discrepancies
by Michael Hothorn 21 Apr '11

21 Apr '11

Dear all, I am sure there is a simple explanation for this, but I cannot find a solution. I am reading in an .mtz file in phenix.refine. mtzdump reports the following unit cell constants on the file test.mtz itself: 175.0930 67.2510 119.0500 90.0000 121.5500 90.0000 The refined .pdb file and .maps report however a slightly different unit cell, as does the logfile >snip Miller array info: test.mtz:FP,SIGFP Observation type: xray.amplitude Type of data: double, size=39702 Type of sigmas: double, size=39702 Number of Miller indices: 39702 Anomalous flag: False Unit cell: (175.17, 67.236, 119.246, 90, 121.416, 90) What am I missing? Thanks! Michael

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Installation issue
by Simon Kolstoe 21 Apr '11

21 Apr '11

Hi, I've just installed the latest stable version of phenix on a new macbook pro using phenix-installer-1.7-650-mac-intel-osx.tar However, as I like running phenix.refine on the command line, I normally source the script phenix_env.sh which on my other computer is in the directory /Applications/PHENIX-1.7-650/Contents/phenix-1.7-650/ However the latest install doesn't seem to have the final phenix-1.7-650 directory! Has phenix_env.sh moved somewhere else and if so where? Thanks, Simon

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Out of Memory Errors
by Heather Condurso 21 Apr '11

21 Apr '11

Hello all, I am currently running the Phenix GUI version 1.7-650 on an iMac with an 3.2Ghz Intel Core i3 processor, 8GB of memory operating under OS 10.6. During many of my runs (mostly AutoMR runs but sometimes refine) I get out of memory errors. I have my system booted in 64 bit mode and I watch the activity monitor and find that phenix doesn't use much more than 2GB of memory. My search model is very large. My unit cell contains 4 trimers (each monomer is 48kDa). I hadn't encountered this issue until I began to increase my search model from one trimer to four. Do you have any suggestions as to how I could avoid this error without minimizing my search model? Often my AutoMR runs get the out of memory error at the start of refinement, but just now the memory was exhausted during the fast rotation function. During this run I used all default parameters with a max res of 4.0 and RMSD of 1.0. Any advice you can give would be greatly appreciated! Heather

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R free test set size
by Yuri 20 Apr '11

20 Apr '11

hello everyone, I just noticed that the latest model I am working on has only 2% of reflections marked as free R after refinement! I usually give the GUI the .sca files out of HKL2000 that do not have an Rfree array pre-defined. The GUI lets you know about the lack of it and asks me if I want generate a test set of 10%. I say yes. However the pdb header shows the only 2.14% are chosen for free R. I see that some of my other models (lower resolution) have test arrays of around 7-10% as I would expect. How can I explicitly define the size I want? Thanks -- Yuri Pompeu

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optimizing weights
by Alexandra Deaconescu 20 Apr '11

20 Apr '11

Dear all: I would like to optimize my weights during Phenix refinement. I am running Phenix 1.6.4-486 using the gui, and I have checked the "optimize weights", but I cannot see the results of the optimization in the output, so I do not know the relationship between Rfree/geometry and wc and wxc_scale (I might not want to pick the automatically selected wxc_scale for the lowest Rfree, but would like to find a reasonable values to give me good geometry). Some earlier posts indicated that this is not output in the log file, but I am running a more recent version... Also, in case I wanted to adjust the weights manually, do I have set wxc_scale AND check the fix wc at the same time in the gui? Or just one of them? What would be typical values to start with at 2.8A (even if the answer depends on the particular data)? Same question for the ADP refinement.... I am working at 2.8A and my B factors are high (higher I think than what one would expect at this resolution). Thanks for your help, Alex -- Alexandra M. Deaconescu, Ph.D. Research Associate, HHMI c/o Grigorieff Laboratory Rosenstiel Center MS029 Brandeis University 415 South St. Waltham, MA 02454 phone: 781-736-2498 For FEDEX Brandeis University Kalman Receiving Dock 415 South St. Waltham, MA 02454

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