- phenixbb - phenix-online.org

estimated coordinate error
by Jianghai Zhu 01 Aug '07

01 Aug '07

Hi, I am refining a 2.6 A structure using both phenix.refine and refmac5. Both programs give me similar R and Rfree values. But the estimated coordinate errors are quite different. From phenix.refine: maximum likelihood estimate for coordinate error: 0.42 A From refmac5: estimated overall coordinate error: ESU based on R value: 0.427 A ESU based on Free R value: 0.293 A ESU based on maximum likelihood: 0.239 A I am wondering why they are different. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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General Question !!!
by john kryst 01 Aug '07

01 Aug '07

Hi all !! Please bare with me.. one general very basic question. Do we use electrostatic charges in x-ray refinement. regards John

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AutoSol problem
by Ben Eisenbraun 31 Jul '07

31 Jul '07

Hi- One of my users is running the Linux 64-bit version of Phenix-1.3b and they are getting the following message at the end of their logfile: ************************************************************ Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked ************************************************************ The solve part of Phenix looks like it built correctly: $ ls -l phenix-1.3b/build/intel-linux-2.6-x86_64/solve_resolve/exe/ -rwxr-xr-x 1 sbgrid sbgrid 1561344 Jun 27 16:55 extract_segment -rwxr-xr-x 1 sbgrid sbgrid 1561344 Jun 27 16:55 extract_segment_pair -rwxr-xr-x 1 sbgrid sbgrid 3483160 Jun 27 16:55 resolve -rwxr-xr-x 1 sbgrid sbgrid 3483576 Jun 27 16:55 resolve_extra_huge -rwxr-xr-x 1 sbgrid sbgrid 3483256 Jun 27 16:55 resolve_giant -rwxr-xr-x 1 sbgrid sbgrid 3482968 Jun 27 16:55 resolve_huge -rwxr-xr-x 1 sbgrid sbgrid 1768392 Jun 27 16:55 resolve_pattern -rwxr-xr-x 1 sbgrid sbgrid 1768392 Jun 27 16:55 resolve_pattern_extra_huge -rwxr-xr-x 1 sbgrid sbgrid 1768392 Jun 27 16:55 resolve_pattern_giant -rwxr-xr-x 1 sbgrid sbgrid 1768392 Jun 27 16:55 resolve_pattern_huge -rwxr-xr-x 1 sbgrid sbgrid 1547840 Jun 27 16:55 segment_library -rwxr-xr-x 1 sbgrid sbgrid 1575648 Jun 27 16:55 side_chains -rwxr-xr-x 1 sbgrid sbgrid 1566208 Jun 27 16:55 side_chains_update -rwxr-xr-x 1 sbgrid sbgrid 5327984 Jun 27 16:55 solve -rwxr-xr-x 1 sbgrid sbgrid 11331152 Jun 27 16:55 solve_extra_huge -rwxr-xr-x 1 sbgrid sbgrid 6529136 Jun 27 16:55 solve_giant -rwxr-xr-x 1 sbgrid sbgrid 7729424 Jun 27 16:55 solve_huge -rwxr-xr-x 1 sbgrid sbgrid 11393392 Jun 27 16:55 solve_mx $ file phenix-1.3b/build/intel-linux-2.6-x86_64/solve_resolve/exe/solve phenix-1.3b/build/intel-linux-2.6-x86_64/solve_resolve/exe/solve: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.4.0, statically linked, for GNU/Linux 2.4.0, stripped We do have a standalone Solve install with its corresponding SOLVEDIR, etc, environment variables. Could that be confusing Phenix? I have the complete logfile, but it's rather long. If it would help, it can be made available. Any ideas on what I should do to troubleshoot this? Thanks. -ben -- Ben Eisenbraun Structural Biology Grid http://sbgrid.org/

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TEST - please ignore
by Luca Jovine 31 Jul '07

31 Jul '07

Sorry, just re-testing whether my e-mails to phenixbb are still vanishing into nowhere...

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A question about AutoBuild
by Marcelo Carlos Sousa 30 Jul '07

30 Jul '07

We have solved (in part) a structure by Molecular Replacement. The protein is a homodimer with 360 amino acids per chain (one dimmer per asu). The model was pretty good for the last 220 amino acids or so but appears to be wrong for the first 140 so I deleted them and refined using phenix to an R free of ~ 0.38. As I was about to start model building in O I thought I would give the phenix autobuild a try. The resolution is 2.5 Å and the map shows buildable features for the missing domain. I ran the autobuild wizard with RESOLVE building “in- place” to extend the current model. However the program seemed unable to add fragments of secondary structure (even as alanines) to the model. The question is: is the building “in-place” restricted to “growing” the current model from the ends? Marcelo

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part II. A question about autobuild
by Marcelo Carlos Sousa 30 Jul '07

30 Jul '07

I also noticed that water molecules are assigned to the buildable parts of the map.

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R-factor problem !!!
by john kryst 30 Jul '07

30 Jul '07

Hi all !! I am using phenix.refine to refine my 3.2 A structure. Also i use xtal_pdbsubmission utility in CNS to generate pdb file which is submission ready format. Please note no refinement in CNS only formating. Phenix.refine gave a R and Rfree of 0.1929 & 0.2512 ( rmsd bonds = 0.006) respectively. When i format in CNS it gave R and Rfree 0.2282 & 0.2794 ( rmsd bonds= 0.010865 ). Am i doing any mistake ?? As for as i know we cant generate a submission ready PDB format from phenix.refine. Is it possible to implement it, which will be very helpful for all of us. Thanks in advance for your inputs regards John

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problems with clashes
by Lari Lehtio 30 Jul '07

30 Jul '07

Hi, I nowadays use phenix.refine almost always in the first stages of the refinement and later usually move to refmac. Now I have two modest resolution structures which behave much better in phenix than in refmac. In addition to the more tedious deposition (I guess), I have a problem with clashes. When I analyse the structures with molprobity, I get much better clashscores with refmac refined files. Is there a way to increase the restraint for these contacts or should I just keep decreasing the wxc_scale (from the default)? Rmsds reported by refmac (0 cycles) for bonds and angles are already lower than what I'm used to. B-factors on the other hand seem to be less restrained in phenix. ~Lari~ _______________________________________ Lari Lehtiö Structural Genomics Consortium Medical Biochemistry & Biophysics Dept. Karolinska Institute Stockholm, Sweden _______________________________________

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Re: [phenixbb] ramachanran plot refinement or restraint?
by Ralf W. Grosse-Kunstleve 27 Jul '07

27 Jul '07

Hi Jianghai, > I tried "discard_psi_phi=False" in phenix.refine. There is only > slightly improvement in the R, Rfree, and ramachandran plot (about > 0.2% less disallowed residues, wxc_scale=0.2). A structure > optimization (wxc_scale=0) with the phi-psi restraints has a bigger > impact (about 2% less disallowed residues) with about 2% higher > Rfree. Thanks for your feedback! > What do you think is a good value for wxc_scale in a low-resolution > refinement? This is a tough one to answer. wxc_scale reflects how much you trust your data to guide you to the best model. That depends on many influences. I think the best - although expensive - approach is to simply try a range of values. Note that the esd on the psi-phi restraints are just someone's (?) best guesses. It may be worth playing with these values as well. For that, copy the data_link_TRANS, data_link_PTRANS, data_link_CIS, and data_link_PCIS blocks from mon_lib_list.cif to a new files, change the values, then specify the file on the phenix.refine command line. (You may want to double-check in the .geo file that your new values are actually used.) > What is the difference between wxc_scale=0 and > phenix.geometry_minimization? Should basically be the same, but in phenix.refine you can override parameters like discard_psi_phi. phenix.geometry_minimization doesn't allow you to do this (it is one of those many little things I never got to). Ralf

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Re: [phenixbb] ramachanran plot refinement or restraint?
by Ralf W. Grosse-Kunstleve 26 Jul '07

26 Jul '07

Hi Jianghai, > I am refining a low resolution huge protein structure. There are > about 20% residues in the disallowed region of ramachandran plot. Is > there a way in phenix.refine to refine the phi, psi angles to get a > better ramachandran plot? or a phi, psi restraints in refinement? If you add discard_psi_phi=False to the phenix.refine command line the psi and phi dihedral angles are restraint according to the CCP4 monomer library definitions in mon_lib_list.cif (run phenix.where_mon_lib_list_cif to get the full path name). Look for data_link_TRANS and data_link_CIS, scroll down to _chem_link_tor.value_angle, to see the restraint definitions. We don't have much experience using the phi, psi restraints. If you don't mind, please let us know how it goes! Ralf

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ramachanran plot refinement or restraint?
by Jianghai Zhu 26 Jul '07

26 Jul '07

Hi, I am refining a low resolution huge protein structure. There are about 20% residues in the disallowed region of ramachandran plot. Is there a way in phenix.refine to refine the phi, psi angles to get a better ramachandran plot? or a phi, psi restraints in refinement? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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problems in installation of phenix
by tara kashav 25 Jul '07

25 Jul '07

Dear all, I am trying to install phenix but getting following error. My system specifications are: 2.6.5-1.358 i686. Can anyone suggest me how to troubleshoot and install the program. Traceback (most recent call last): File "/usr/local/phenix-1.3b/phenix/wxGUI/wxPhenix.py", line 11, in <module> import wx File "/usr/local/phenix-1.3b/build/intel-linux-2.6 /base/lib/python2.5/site-packages/wx-2.8-gtk2-ansi/wx/__init__.py", line 45, in <module> from wx._core import * File "/usr/local/phenix-1.3b/build/intel-linux-2.6 /base/lib/python2.5/site-packages/wx-2.8-gtk2-ansi/wx/_core.py", line 4, in <module> import _core_ ImportError: libXfixes.so.3: cannot open shared object file: No such file or directory Thanks, Tara Kashav, Dr. S. Gourinath's Lab, Lab No 430, School of Life Sciences, Jawaharlal Nehru University, New Delhi - 110067

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Re: [phenixbb] How to keep a custom bond planar ?
by Ralf W. Grosse-Kunstleve 24 Jul '07

24 Jul '07

Hi Mathieu, Also sorry for the late reply. > How can I define a plan or some dihedral ?? Sorry, this is not implemented (not hard, but never got to it). > Or as in the ligand .cif I defined a plan > LIG plan-2 C1 0.020 > LIG plan-2 C2 0.020 > LIG plan-2 C3 0.020 > > I could add the atoms NZ and CE of the lysine to the plan-2. You can define the bond, angles, dihedrals, chiralities and planarities with a cif link. Currently we don't generate such links automatically (it is in the works). To get a start, copy one of the links from the mon_lib_list.cif file; the command phenix.where_mon_lib_list_cif will give you the absolute path. Give the cif link a unique name and modify it for your situation. Then use "apply_cif_link" as described in the phenix.refine documentation, e.g. at the CCI Apps download page (http://www.phenix-online.org/download/cci_apps/). Let me know if you need more specific help. Ralf

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Re: [phenixbb] handling of alternate conformations
by Ralf W. Grosse-Kunstleve 24 Jul '07

24 Jul '07

Hi Ulrich, Sorry for the late reply. I was out of town for a week. > My first question is whether NCS constraints are also applied to alternate > conformations. Should be, but is not heavily tested. All NCS restraints are listed in the .geo file created by phenix.refine (assuming write_geo_file=True, which is the default). Look for the long lists following "NCS restraint group". Do your alternative conformation atoms appear in these lists? > My second question concerns the atom count of the conformers, where the > parts with non-alternating conformations seem to be included as well. Pavel's explanation from last week is correct. Internally a "conformer" is always a complete chain. The bond, angle, dihedral, chirality, and planarity restraints are determined independently for each conformer. This generates duplicate restraints which are checked for consistency and then reduced again. Ralf

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handling of alternate conformations
by Ulrich Baumann 16 Jul '07

16 Jul '07

Dear Phenix experts, we encounter the following "problem" when trying to refine alternating conformations: we have a complex with 4 chemically different polypeptide chains in the asymmetric unit, composition A3B3CD. For chains C and D we see additional density, which appears to belong to three alternating conformations which can be thought as rigid-body motions (for the whole chains C and D, let's call these conformers 1,2 and 3, but we label them conventionally in the file with the prefix A,B,and C) with roughly estimated occupancies of about 0.3, 0.3 and 0.4 (we can really see most of them). A and B have no visible alternating conformations (occupancies set to 1.0). From the atom count it appears that phenix reads in three conformers called A,B and C with A: A3B3C(1)D(1), B: A3B3C(2)D(2) and C: A3B3C(3)D(3). Phenix.refine says it has these 3 conformers: conformer A A:2700 atoms, conformer B:2700 atoms, common with A 2100, conformer C:2700 atoms, common with A 2100, common with B 2100. Refinement yields an R/Rfree of about 0.210/0.325. If we treat the three conformers of polypeptide chains C and D as independent chains with occupancy each 1.0 (this is possible 'cos there are no repulsive contacts between them, fortunately), we get R/Rfree of 0.243/0.291 and phenix applies NCS restraints to all chains. The resolution is about 2.9 A. We use phenix.refine from the CCI_APPS, version 2007-03-26-1903, SUSE Linux. My questions is: is the difference due to the lack of NCS between conformers or are the occupancies mistreated somwhow? I am asking because I would not consider the whole A3B3C(x)D(x) particle as a conformer but only chains C and D ...... Is there a possibility to apply NCS restraints to conformers? Many thanks in advance, Ulrich

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How to keep a custom bond planar ?
by Coincon Mathieu 16 Jul '07

16 Jul '07

Hi, I defined a bond (and angles) between my ligand and the NZ of a lysine in a file (bond.def). ..-C2-.. | -CE-NZ = C1-C3-.... This is a double bond. Everything work good except for the planarity of the lysine's atoms. For the bond I wrote in my bond.def: bond { action = *add atom_selection_1 = chain D and resname LIG and name C2 atom_selection_2 = chain A and resname LYS and resid 66 and name NZ distance_ideal = 1.340 sigma = 0.02 } For an angle: angle { action = *add atom_selection_1 = chain D and resname LIG and name C3 atom_selection_2 = chain D and resname LIG and name C2 atom_selection_3 = chain A and resname LYS and resid 66 and name NZ angle_ideal = 120.000 sigma = 3 } How can I define a plan or some dihedral ?? Or as in the ligand .cif I defined a plan LIG plan-2 C1 0.020 LIG plan-2 C2 0.020 LIG plan-2 C3 0.020 I could add the atoms NZ and CE of the lysine to the plan-2. Thanks by advance. And by the way phenix (with coot) is GREAT (I did my apo-enzyme in four days !!!!) -------- Mathieu Coicon PhD Student Biochimie Universite de Montreal (+1)514-343-6111 #5352

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Phaser
by john kryst 13 Jul '07

13 Jul '07

Hi all !!! Is it possible to fix one domain and search for the second one in phaser !!! What are the keywords to use for that. I have a protein with two domains. It i give both the domains together it is not finding the solution. If i give only one domain it is giving the solution and the R and Rfee is 28 and 33. But it is not finding the second one. Thanks in advance for your suggestions.. regards John

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Refinement use of Friedel pairs
by Mark A Saper 11 Jul '07

11 Jul '07

I am refining a structure containing SeMet with data collected at peak wavelength. Provided I give the f' and f'', will phenix.refine calculate F+ and F- structure factors and use the provided FOBS+ and FOBS- ? CNS does this. Refmac only uses f' and I get >6 sigma Fo-Fc peaks on the Se. Thanks for your help. _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

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setting resolution for 2 datasets in AutoSol
by Thomas C. Terwilliger 09 Jul '07

09 Jul '07

Hi Luca, It's easiest to do this in 2 steps: 1a. You can set the resolution separately for each dataset in the AutoSol Wizard. In the GUI, just go through each dataset and set the overall resolution to your desired values as you go. Ignore the density modification and building that occurs in this run. 1b. Then you'll get an output exptl_fobs_phases_freeR_flags_2.mtz or equivalent that is phased to the resolution you specified, but that has all the data (with no phases) to higher resolution. 2. Now run the AutoBuild wizard, and set the resolution to your high-resolution limit. That should use the phases you generated, and include the high-res data for density modification and refinement. Equivalently, you can run AutoSol at low resolution then run AutoBuild at higher resolution by supplying an input_hires_file with the hires data. A key point here is that the building in AutoSol is just a preliminary build...the building in AutoBuild is the real thing. You can also run 2 datasets and set the resolution for each in a script. Here is a script to read in 2 SAD datasets and solve them together as one, setting the resolution of phasing to 3 A for the first and 2.9 for the second, cat two_datasets.inp input_seq_file seq.dat resolution 2.9 # Resolution expt_type sad input_file_list se.sca ############## NEW DATASET ################ run_list start # run "start" method. run_list read_another_dataset # starting a new dataset here resolution 3.1 # Resolution input_file_list br.sca Let me know if that does not do it! -Tom T >> From: lp212(a)mole.bio.cam.ac.uk >> Date: July 9, 2007 3:38:28 PM PDT >> To: phenixbb(a)phenix-online.org >> Subject: script for Zn and Se phasing >> Hi, >> I have collected two peak datasets on two different crystals, for a protein that contains zinc: >> 1. peak dataset at the Zn edge (lambda=1.285A, 2.5A reso) >> 2. peak dataset at the Se edge (lambda=0.98A, 2.8A reso) >> The protein has 2 Zn and 11 SeMet, and 4/au. When I input both >> datasets in the AutoSol GUI, Hyss finds correctly 8/8 Zn sites, and ~34/44 Se sites, but only when I cut back the resolution (4.2A for Zn, and 4.7A for Se). What I can't figure out is how to tell the Autosol GUI to use a low-res cutoff for finding the sites, and then use all the data for model building. Could someone please explain how to do this in the GUI, or send me a script? >> Thanks a lot! Apologies if this is trivial... >> Luca >

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Re: [phenixbb] depositing phenix-refined coordinates
by Ralf W. Grosse-Kunstleve 05 Jul '07

05 Jul '07

Hi Enrico, > However, I would be very grateful if someone could point me to the topic > already posted in the message below by Dr. Scott few days ago, > exactly at: > "a quick description for depositing phenix-refined coordinates?", > though the full message contained very interesting points I would > love to hear about We don't have a dedicated deposition tool yet, sorry. But we are actively working with the PDB on this. In the meantime, the .pdb files produced by phenix.refine are the best starting point. > (I also performed refinement by refmac/phenix, and observed kind of a > similar trend for those numbers). It may be because we are reporting mean deviations instead of root-mean-square deviations. This is kind of an oversight on our part and will be changed in the next version. Ralf

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CCI-Apps Verisons vs. Phenix Versions
by Schubert, Carsten [PRDUS] 05 Jul '07

05 Jul '07

Hi, Quick question about versions of CCI-Apps as standalones and in phenix. How does once decide which version of the CCI-Apps is more current? I have not looked in depth, but is there a equivalent build tag for the CCI-Apps in phenix as the one for the CCI-Apps. Currently I am assuming that the CCI-Apps are alway more up to date, but that may not hold true for the upcoming phenix 1.3 release. Thanks Carsten

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some general refine questions
by William Scott 04 Jul '07

04 Jul '07

Hi folks: With the helpful advice of the phenix crew, I've re-refined 2goz, an entry in the pdb in which I used refmac5 the first time around. There was a small error in the pdb: One nucleotide (C8 in chain A) was rotated 180 degrees about the glycosylic bond from where it should have been. The net result is one oxygen atom was in the wrong place in the structure, and this was apparent within the difference Fourier. After I rotated the base and re-refined in refmac, the Rfactor and other stats remained essentially unchanged (so this fix has nothing to do with the following): My refinement results in Refmac: REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.241 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1503 ; 0.009 ; 0.021 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2331 ; 1.676 ; 3.000 Then I refined in phenix. I get REMARK Final: r_work = 0.1737 r_free = 0.2224 bonds = 0.003 angles = 0.745 So the working and free R factor are both lower, and the geometry is substantially tighter. If I relax the weights in phenix, even to get rms bonds of around 0.006, the free-R goes up, which tells me this is not something I am justified in doing. Phil Evans once told me that anything tighter than about 0.01 (conservatively) was science-fiction, in that this is within the error of the idealized libraries for bond lengths. Other people have asked me about this too, and I didn't know how to reply. Is bonds = 0.003 angles = 0.745 realistic, or have I done something wrong? Even if I do structure idealization in Refmac, I can't get the rms bonds below about 0.005 (and my understanding is that it uses the same monomer library). Why is the weight multiplied by 0.5 by default? Since changing that to 1.0 slightly increases freeR, I assume it is the default for some reason. All the best, Bill PS: Could someone point me to a quick description for depositing phenix-refined coordinates? (The latest phenix installer seems to have omitted the docs.) William G. Scott contact info: http://chemistry.ucsc.edu/~wgscott

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Re: [phenixbb] sugar links in phenix.refine
by Ralf W. Grosse-Kunstleve 04 Jul '07

04 Jul '07

Almost, but you need a separate scope (thing between braces) for each link, e.g.: refinement.pdb_interpretation.apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resid 900 residue_selection_2 = chain A and resname ASN and resid 329 } refinement.pdb_interpretation.apply_cif_link { data_link = NAG-NAG-b-D residue_selection_1 = chain A and resname NAG and resid 901 residue_selection_2 = chain A and resname ASN and resid 900 } Or alternatively: refinement.pdb_interpretation { apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resid 900 residue_selection_2 = chain A and resname ASN and resid 329 } apply_cif_link { data_link = NAG-NAG-b-D residue_selection_1 = chain A and resname NAG and resid 901 residue_selection_2 = chain A and resname ASN and resid 900 } } Ralf

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Re: [phenixbb] Multivariate Z score L-test
by Claudia Scotti 29 Jun '07

29 Jun '07

Thank you so much. I'll try all the space groups and see what happens. Many thanks again, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 ---------------------------------------- > Date: Fri, 29 Jun 2007 07:35:22 -0700 > From: PHZwart(a)lbl.gov > To: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Multivariate Z score L-test > > Hi Claudia, > > This could indicate that tyour data is actually P 2 1 1, P 1 2 1 or P > 1 1 2 or P 21 1 1, P 1 21 1, P 1 1 21. Try processing that data in > those spacegroups and see if that makes any difference. You might end > up havig to refine your structure in all spacegroups to find out which > possibility is the best. > > It could also indicate that the quality of your data is not very good, > either due to suboptimal data processing or because of bad diffraction > (or both). > > HTH > > Peter > > > 2007/6/29, Claudia Scotti : > > > > Dear List, > > > > I'm only at my third structure (a scFv antibody fragment) and I'm disturbing about a dataset that is giving problems at the refinement stage: it gets stuck at about Rcryst= 0.36 and Rfree=0.44. > > > > I've tried data processing with several softwares (Mosflm, XDS, Denzo) and the result is consistently P222, unit cell 69x79x90, 90, 90, 90. The data are anisotropic, with limits at 2.3 and 2.8 A. I cut the data at 3.0 A. > > Matthews coefficient suggests two molecules per asu. > > No NCS is detected by self-rotation and a native Patterson detects a small peak (10% of origin peak) at 0.19, 0.34, 0.5. > > MR using several softwares (AmoRe, Molrep and Phaser) and several models all agree that the best space group is P21212, though the systematic absences are not perfectly consistent. > > > > When refining, refinement gets stuck as I mentioned above. > > > > I've run Phenix x-triage and the results include this line (see below): "It could be worthwhile considering reprocessing the data". I was wondering if the Multivariate Z score L-test: 6.305 might suggest how to reprocess the data. > > > > Sorry for the probably trivial question and for probably missing important data. > > > > Thanks a lot for any help and suggestions, > > > > Claudia > > > > ------------------------------------------------------------------------------- > > Twinning and intensity statistics summary (acentric data): > > > > Statistics independent of twin laws > > - /^2 : 1.827 > > - ^2/ : 0.838 > > - : 0.649 > > - , : 0.417, 0.242 > > Multivariate Z score L-test: 6.305 > > The multivariate Z score is a quality measure of the given > > spread in intensities. Good to reasonable data is expected > > to have a Z score lower than 3.5. > > Large values can indicate twinning, but small values do not > > neccesarily exclude it. > > > > > > No (pseudo)merohedral twin laws were found. > > > > > > Patterson analyses > > - Largest peak height : 11.094 > > (correpsonding p value : 1.080e-01) > > > > > > The largest off-origin peak in the Patterson function is 11.09% of the > > height of the origin peak. No significant pseudotranslation is detected. > > > > The results of the L-test indicate that the intensity statistics > > are significantly different then is expected from good to reasonable, > > untwinned data. > > As there are no twin laws possible given the crystal symmetry, there could be > > a number of reasons for the departure of the intensity statistics from normality. > > Overmerging pseudo-symmetric or twinned data, intensity to amplitude conversion problems > > as well as bad data quality might be possible reasons. > > It could be worthwhile considering reprocessing the data. > > ----------------------------------------------------------------------------------------------- > > > > Claudia Scotti > > Dipartimento di Medicina Sperimentale > > Sezione di Patologia Generale > > Universita' di Pavia > > Piazza Botta, 10 > > 27100 Pavia > > Italia > > Tel. 0039 0382 986335/8/1 > > Facs 0039 0382 303673 > > > > _________________________________________________________________ > > Express yourself instantly with MSN Messenger! Download today it's FREE! > > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb _________________________________________________________________ With Windows Live Hotmail, you can personalize your inbox with your favorite color. www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-us&ocid=TX…

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Multivariate Z score L-test
by Claudia Scotti 29 Jun '07

29 Jun '07

Dear List, I'm only at my third structure (a scFv antibody fragment) and I'm disturbing about a dataset that is giving problems at the refinement stage: it gets stuck at about Rcryst= 0.36 and Rfree=0.44. I've tried data processing with several softwares (Mosflm, XDS, Denzo) and the result is consistently P222, unit cell 69x79x90, 90, 90, 90. The data are anisotropic, with limits at 2.3 and 2.8 A. I cut the data at 3.0 A. Matthews coefficient suggests two molecules per asu. No NCS is detected by self-rotation and a native Patterson detects a small peak (10% of origin peak) at 0.19, 0.34, 0.5. MR using several softwares (AmoRe, Molrep and Phaser) and several models all agree that the best space group is P21212, though the systematic absences are not perfectly consistent. When refining, refinement gets stuck as I mentioned above. I've run Phenix x-triage and the results include this line (see below): "It could be worthwhile considering reprocessing the data". I was wondering if the Multivariate Z score L-test: 6.305 might suggest how to reprocess the data. Sorry for the probably trivial question and for probably missing important data. Thanks a lot for any help and suggestions, Claudia ------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws - /^2 : 1.827 - ^2/ : 0.838 - : 0.649 - , : 0.417, 0.242 Multivariate Z score L-test: 6.305 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data is expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not neccesarily exclude it. No (pseudo)merohedral twin laws were found. Patterson analyses - Largest peak height : 11.094 (correpsonding p value : 1.080e-01) The largest off-origin peak in the Patterson function is 11.09% of the height of the origin peak. No significant pseudotranslation is detected. The results of the L-test indicate that the intensity statistics are significantly different then is expected from good to reasonable, untwinned data. As there are no twin laws possible given the crystal symmetry, there could be a number of reasons for the departure of the intensity statistics from normality. Overmerging pseudo-symmetric or twinned data, intensity to amplitude conversion problems as well as bad data quality might be possible reasons. It could be worthwhile considering reprocessing the data. ----------------------------------------------------------------------------------------------- Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/

2 1

sugar links in phenix.refine
by Jianghai Zhu 21 Jun '07

21 Jun '07

Hi, How does phenix.refine handle the sugar links in refinement? I suppose phenix.refine will automatically recognize NAG and MAN. Will it recognized NAS-ASN, beta1-4, alpha1-4, etc linkages between sugars? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

2 1

'Tasks' tab missing from 1.3b GUI and HL coefficients from a model
by Stephen Graham 21 Jun '07

21 Jun '07

Hi all, I recently (well, yesterday) installed the latest beta of phenix and everything is working great from the command line (which is how I use phenix 99.9% of the time). However, I fired up the GUI and found that the 'Tasks' tab appears to be missing from the 'Strategy Interface'. Is this a bug, a manifestation of an installation problem, or a feature? And... I was trying to use the GUI for prime-and-switch phasing to improve the maps for a partly-refined MR solution. What is the recommended path for creating HL coefficients from a model (from simulated annealing in phenix.refine) so that I can use the GUI's resolve 'prime-and-switch' strategy? Or is there an even better way of removing model bias and density-improving a big, low-res, MR-solved structure with 4-fold NCS in phenix? Thanks, Stephen -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

5 5

harmonic restrains in phenix.refine
by Bjørn Pañella Pedersen 21 Jun '07

21 Jun '07

Hi all, Is it possible to use harmonic restrains in phenix.refine, in a manner similar to CNS v1.2? I have searched the phenix.refine documentation and the web, but can't find anything. I use version 2007_04_06_1210 of phenix. Thanks! -Bjørn -- Bjørn Pañella Pedersen Ph.D Student, MSc Department of Molecular Biology Office: +45 89425021 University of Aarhus Lab: +45 89425010 Gustav Wieds Vej 10c Email: bpp(a)mb.au.dk DK-8000 Aarhus C Lab WWW: http://www.bioxray.dk Denmark

2 1

SAD + MR
by Lucas Bleicher 19 Jun '07

19 Jun '07

I have a dataset from a Cs-soaked crystal, and the protein has a domain solved in the PDB. The problem is that the map obtained just with the experimental phasing is not so easily interpreted, and the domain is just about 25% of the whole protein. Inspection of the map generated by MR suggests that it's a good solution, with residues fitting reasonably well on the density. Given the new features on Phaser 2.0, which I suppose is included in Phenix 1.3b, can anyone suggest a protocol to profit from both things (anomalous scattering + good search model)? Thanks in advance, Lucas ____________________________________________________________________________________ Novo Yahoo! Cadê? - Experimente uma nova busca. http://yahoo.com.br/oqueeuganhocomisso

3 2

Death by Big-ass structure&[email protected]
by Kate Kavanagh 13 Jun '07

13 Jun '07

Hi Peter, The reindexing works fine but when I try to convert back to R3:H all atoms with ANISOU records are given B-factors of -79.86: ATOM 1 N MET A 1 16.402 60.069 44.768 1.00-78.96 N ATOM 2 CA MET A 1 16.316 58.621 44.978 1.00-78.96 C ATOM 3 CB MET A 1 17.622 57.922 44.573 1.00-78.96 C ATOM 4 C MET A 1 15.966 58.300 46.432 1.00-78.96 C ATOM 5 O MET A 1 16.196 59.115 47.326 1.00-78.96 O ATOM 6 N PHE A 2 15.408 57.114 46.661 1.00-78.96 N ATOM 7 CA PHE A 2 15.047 56.686 48.013 1.00-78.96 C ATOM 8 CB PHE A 2 13.750 55.866 48.016 1.00-78.96 C ATOM 9 CG PHE A 2 13.323 55.436 49.391 1.00-78.96 C ..... And since TLS refinement has been used, all protein atoms have ANISOU records. Any suggestions? Kate

3 2

Re: [phenixbb] [ccp4bb] DANO from PDB
by Peter Zwart 07 Jun '07

07 Jun '07

Hi Santosh, Here is an alternative to methods mentioned earlier. If you get the latest version of the cctbx or cci_apps (from www.phenix-online.org) you will find a new application named phenix.xmanip (or mmtbx.xmanip if you only download the cctbx). xmanip has some useful features, one of them is that one can provide pieces of python code to the interface that will be executed. You have full access to all cctbx methods available. Please find below an example parameter file that perform structure factor calculation (in less than 90 lines of code and input) that includes elements with f" and f' not being equal to zero (you have to set the values of f" and f' yourself rather then rely on lookup tables by wavelength) and allows you to set bulk solvent parameters such as ksol, bsol and the overall anisotropic B of the data (B_cart). Save the text below (between the hash-es in a file named params.def , change the unit cell and sg parameters, the input pdb file and f" and f' value dictionary to suit your needs: ( like fp_dict = { "S": 0, "C": 0 } fdp_dict = { "S": 0, "C": 2.8 } for instance } You can fool around with solvent density, solvent B, overall scale factor and overall anisotropic B value and resolution (d_min). Then run phenix.xmanip params.def and get a file named xmanip.mtz that will contain your error free data. If you want, you can add uniform or Gaussian errors yourself. Since xmanip is fairly new, you will find a bug in the current release that somehow appears when you do not read in any external xray data. This happens however right after the mtz file in question has been written out. This will be fixed in the forthcoming release (soonish). Let me know if anything is unclear or if you have trouble running it. HTH Peter Zwart ################################################################### xmanip { input { unit_cell = "80.127 80.127 71.582 90.00 90.00 120.00" space_group = R3:H model { file_name = tst.pdb } } parameters { action = reindex manipulate_pdb *manipulate_miller manipulate_miller { task = get_dano get_diso lsq_scale sfcalc *custom None output_label_root = "Imock" custom{ code = """ #------------------------------------------------------- # This you can change if desired # # Dictionary for fp and fpp values fp_dict = { "Zn": -0.189 } fdp_dict = { "Zn": 4.898 } # final resolution of the data d_min = 2.0 # anisotropic B value b_cart = [ 0, 0, 0, 0, 0, 0 ] # solvent parameters k_sol = 0.35 b_sol = 45.0 # overall scale k_overall = 1.0 #------------------------------------------------------- # below this point, things should be more or less okai # from mmtbx import f_model from cctbx.xray import observation_types #loop over all scatterers in the xray structure #print >> out, dir(xray_structure) scatterers = xray_structure.scatterers() for atom in scatterers.as_1d(): if fp_dict.has_key( atom.element_symbol() ): atom.fp = fp_dict[ atom.element_symbol() ] if fdp_dict.has_key( atom.element_symbol() ): atom.fdp = fdp_dict[ atom.element_symbol() ] #the changes have been made to fp and fdp #Now we have to do some trickery to get some fobs with bulk solvent #contribution ... #First make a 'fake' set of f_obs fake_f_obs = abs(xray_structure.structure_factors( d_min = d_min, anomalous_flag = True ).f_calc()) # make a 'fake' set of free flags fake_free_flags = fake_f_obs.generate_r_free_flags(fraction = 0.1, max_free = 99999999) fmodel = f_model.manager( xray_structure = xray_structure, r_free_flags = fake_free_flags, target_name = "ls_wunit_k1", f_obs = fake_f_obs, b_cart = b_cart, k_sol = k_sol, b_sol = b_sol, overall_scale = k_overall ) # now get the final values of F+ and F-. # Note the abs to get amplitudes only result = abs( fmodel.f_model() ).set_observation_type( observation_types.amplitude() ) # you want make this into intensities? result = result.f_as_f_sq() # lets leave the intensities alone for now, and just make 'mock' sigmas # to statisfy certain programs. # Don't forget to set the observation type! sigmas = result.data()/100.0 result = result.customized_copy(data = result.data(), sigmas=sigmas).set_observation_type(result) #By default, a parameter named result is passed back to the xmanip #routines and will be written to the final mtz file """ } } } output { logfile = "xmanip.log" hklout = "xmanip.mtz" xyzout = "xmanip.pdb" } } ################################################################### Santosh Panjikar wrote: > Hi all, > > Does anybody have a program which can calculate anomalous differences or > F+ and F- from a refined structure at given wavelength and resolution ? > > Thanks > Santosh > > > Santosh Panjikar, Ph.D. panjikar(a)embl-hamburg.de > Staff Scientist > EMBL Hamburg outstation http://www.embl-hamburg.de/~panjikar/ > DESY, Notkestrasse 85 Tel.:+49-40-89902-141 > 22603, Hamburg, Germany Fax: +49-40-89902-149

1 0

removing Van der Waals repulsion between two atoms
by Miguel Ortiz-Lombardía 06 Jun '07

06 Jun '07

Dear all, I've a question regarding phenix.refine. Is it possible in phenix.refine to remove repulsion between a couple of atoms to see to what distance they refine when unrestrained? I'm thinking in something like what in CNS/XPLOR one would do by setting: igroup interaction (selection1) (selection2) weights * 1 vdw 0. elec 0. end end I've been searching the web for a solution to this question, but haven't come up with anything. Sorry if I missed it! I would appreciate your help. Cheers, Miguel -- correo-e: ibdeno(a)gmail.com ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens

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Re: [phenixbb] how to add phase info to the autosol wizard
by Thomas C. Terwilliger 05 Jun '07

05 Jun '07

Hi again Chuanbing, I'm sorry, I mean 1.3b-d5 (d4 is just about to be released). -Tom T Hi Chuanbing, It will be available in version 1.3b-d4 which has yet to be released (or even built)...it takes a little time between the time I have put the code in and the time that it gets to you, unfortunately! -Tom T > Dear Tom, > > Thank you very much! It's expected! > I am using the Version 1.24.1b, is version 1.3 the next version you > mentioned? > > Chuanbing > > > > On 6/5/07, Tom Terwilliger <terwilliger(a)lanl.gov> wrote: >> >> Hi Chuanbing, >> >> I have added this to the AutoSol wizard >> (input_phase_file=my-phases.mtz) and the next version of PHENIX will have >> it. >> >> -Tom T >> >> At 01:51 AM 5/31/2007, CB Bian wrote: >> >Dear all, >> > >> > I am trying to add phase info from externally calculated >> > phases to the autosol wizard with S-SAD data. But I can not find the option to do it in the running. Can someone help me? >> > >> > >> >Thanks in advance >> > >> >Chuanbing >> > >> >-- >> >ChuanBing Bian, Ph.D Student >> >Structural biology group >> >State Key laboratory of Structural Chemistry >> >Fujian Institute of Research on the Structure of Matter, >> >Chinese Academy of Sciences >> >155 Yang Qiao Xi Lu, Fuzhou, Fujian 350002 P. R. China >> >E-mail: >> ><mailto:[email protected]>cbbian(a)gmail.com >> ><mailto:[email protected]> cbbian(a)fjirsm.ac.cn >> >Tel:(office)+86-591-8370-5814 >> ><http://protein.fjirsm.ac.cn/>http://protein.fjirsm.ac.cn >> >_______________________________________________ >> >phenixbb mailing list >> >phenixbb(a)phenix-online.org >> >http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> >> >> >> Thomas C. Terwilliger >> Mail Stop M888 >> Los Alamos National Laboratory >> Los Alamos, NM 87545 >> >> Tel: 505-667-0072 email: terwilliger(a)LANL.gov >> Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org >> ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu >> TB Structural Genomics Consortium web site: >> http://www.doe-mbi.ucla.edu/TB >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> >> >> >> Thomas C. Terwilliger >> Mail Stop M888 >> Los Alamos National Laboratory >> Los Alamos, NM 87545 >> >> Tel: 505-667-0072 email: terwilliger(a)LANL.gov >> Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org >> ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu >> TB Structural Genomics Consortium web site: >> http://www.doe-mbi.ucla.edu/TB >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > > > > -- > ChuanBing Bian, Ph.D Student > Structural biology group > State Key laboratory of Structural Chemistry > Fujian Institute of Research on the Structure of Matter, > Chinese Academy of Sciences > 155 Yang Qiao Xi Lu, Fuzhou, Fujian 350002 P. R. China > E-mail: cbbian(a)gmail.com cbbian(a)fjirsm.ac.cn > Tel:(office)+86-591-8370-5814 > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

2 1

Re: [phenixbb] how to add phase info to the autosol wizard
by Tom Terwilliger 05 Jun '07

05 Jun '07

Hi Chuanbing, I have added this to the AutoSol wizard (input_phase_file=my-phases.mtz) and the next version of PHENIX will have it. -Tom T At 01:51 AM 5/31/2007, CB Bian wrote: >Dear all, > > I am trying to add phase info from externally calculated > phases to the autosol wizard with S-SAD data. But I can not find > the option to do it in the running. Can someone help me? > > >Thanks in advance > >Chuanbing > >-- >ChuanBing Bian, Ph.D Student >Structural biology group >State Key laboratory of Structural Chemistry >Fujian Institute of Research on the Structure of Matter, >Chinese Academy of Sciences >155 Yang Qiao Xi Lu, Fuzhou, Fujian 350002 P. R. China >E-mail: ><mailto:[email protected]>cbbian(a)gmail.com ><mailto:[email protected]>cbbian(a)fjirsm.ac.cn >Tel:(office)+86-591-8370-5814 ><http://protein.fjirsm.ac.cn/>http://protein.fjirsm.ac.cn >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

3 2

secondary structure restraint
by Jianghai Zhu 05 Jun '07

05 Jun '07

Hi all, I am refining a low resolution structure (~3.8 A). For some of the domains in the structure, we already have high resolution structures. Despite of some conformational changes in some loops, the core structures should be the same. I am wondering if it is possible to restrain the secondary structures in phenix.refine. Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

3 7

phenix.refine crashed
by Jianghai Zhu 05 Jun '07

05 Jun '07

Hi, In my refinement phenix.refine crashed with the following errors. ================================ xyz refinement =============================== Traceback (most recent call last): File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/ refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ command_line.py", line 78, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ driver.py", line 1310, in run log = log) File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ strategies.py", line 733, in refinement_machine h_params = h_params) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/ minimization.py", line 136, in __init__ ignore_line_search_failed_step_at_lower_bound = True)) File "/nfs/home/jzhu/cci_apps_sources/scitbx/scitbx/lbfgs.py", line 242, in run log) File "/nfs/home/jzhu/cci_apps_sources/scitbx/scitbx/lbfgs.py", line 121, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/ minimization.py", line 369, in compute_functional_and_gradients u_iso_refinable_params = u_iso_refinable_params) File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/ minimization.py", line 224, in compute_target sf_v3d_sel = sf_v3d.set_selected(self.hd_selection, [0,0,0]) RuntimeError: scitbx Internal Error: /net/sharptail/scratch1/rwgk/ auto_build/sources/scitbx/include/scitbx/array_family/boost_python/ flex_wrapper.h(473): SCITBX_ASSERT(a.accessor() == flags.accessor()) failure. What happened here? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

2 1

Re: [phenixbb] elbow.builder
by William Scott 04 Jun '07

04 Jun '07

Problem solved: The OS X pre-compiled distribution comes with an executable gamess.Mar242007R1.x but the shell script seems to require gamess.00.x so in /usr/local/gamess I did this: sudo ln -s gamess.Mar242007R1.x gamess.00.x and benzene is as one would expect. BTW, when I run this under tcsh, I get a more informative error message -- it says it can't find gamess. Under zsh, it just says "Failed to read coordinates. Aborting optimisation." Anyway, it all works now. Thanks. Bill On Jun 3, 2007, at 3:08 PM, Peter Zwart wrote: > gamess is installed right? > > P > > > > 2007/6/3, William Scott <wgscott(a)chemistry.ucsc.edu>: >> actually, "small distortions" was too optimistic: >> >> http://chemistry.ucsc.edu/~wgscott/temp/benzene.png >> >> >> >> >> On Jun 3, 2007, at 2:33 PM, William Scott wrote: >> >> > Hi folks: >> > >> > I've been playing around a bit with elbow.builder, and found the >> > following: >> > >> > -------------- >> > >> > >> > elbow.builder --opt --smiles c1ccccc1 >> > >> > gives me a nice, flat, hexagonal benzene >> > >> > elbow.builder --gamess --smiles c1ccccc1 >> > >> > gives me a benzene that is slightly bent out of plane and has other >> > small distortions with respect to 6-fold symmetry. >> > >> > Is this a problem with elbow, a problem with gamess, or a Jahn- >> > Teller effect? >> > >> > >> > ------------ >> > >> > >> > >> > Also, I noticed elbow.doc requires a mozilla or netscape >> > executable. Since both of these are obsolete, maybe a firefox >> > executable should be an option? On OS X, "open" should open a URL >> > in the user's favorite browser, but it doesn't seem to work right >> > with Safari (which stupidly opens a Finder window of the directory >> > containing the html file). My workaround was to make a shell >> > script called "mozilla" that invokes Camino: >> > >> > #!/bin/zsh -f >> > /usr/bin/open -a Camino "$@" >> > >> > HTH someone. >> > >> > ------------------ >> > >> > >> > Bill >> > >> > >> > >> > >> > William G. Scott >> > >> > contact info: http://chemistry.ucsc.edu/~wgscott >> > >> > >> > >> > >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

2 2

elbow.builder
by William Scott 03 Jun '07

03 Jun '07

Hi folks: I've been playing around a bit with elbow.builder, and found the following: -------------- elbow.builder --opt --smiles c1ccccc1 gives me a nice, flat, hexagonal benzene elbow.builder --gamess --smiles c1ccccc1 gives me a benzene that is slightly bent out of plane and has other small distortions with respect to 6-fold symmetry. Is this a problem with elbow, a problem with gamess, or a Jahn-Teller effect? ------------ Also, I noticed elbow.doc requires a mozilla or netscape executable. Since both of these are obsolete, maybe a firefox executable should be an option? On OS X, "open" should open a URL in the user's favorite browser, but it doesn't seem to work right with Safari (which stupidly opens a Finder window of the directory containing the html file). My workaround was to make a shell script called "mozilla" that invokes Camino: #!/bin/zsh -f /usr/bin/open -a Camino "$@" HTH someone. ------------------ Bill William G. Scott contact info: http://chemistry.ucsc.edu/~wgscott

1 1

Binary file not executable during installation?
by lkemp＠mrc-lmb.cam.ac.uk 01 Jun '07

01 Jun '07

Hello BB I am trying to install Phenix on Suse 9.3. I went for the 2.6 version as i got this: 2.6.11.4-21.17-smp i686 when i typed uname. However it required libtermcap.so.2 so i switched to the 2.4 version as suggested on a previous BB query. This however also goes wrong: This time the binary.log file says that python in /common is not executable I checked and this was due to the need for libstdc++.so.6. I made a softlink directing this to the .5 version but it doesnt like this. Does anyone have any ideas??? Thank you in advance for any help Lauris

2 1

AssertionError & TLS
by Kanchan Anand 01 Jun '07

01 Jun '07

Hello everybody, I am a new user of Phenix and presently trying to refine 3.6 A data of a protein-RNA complex. whenever i add tls into my .def file for the next run, i get this problem: Traceback (most recent call last): File "/data/software/phenix-1.3b/phenix/phenix/command_line/refine.py", line 5 , in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/data/software/phenix-1.3b/phenix/phenix/refinement/command_line.py", li ne 78, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/data/software/phenix-1.3b/phenix/phenix/refinement/driver.py", line 130 8, in run log = log) File "/data/software/phenix-1.3b/phenix/phenix/refinement/strategies.py", line 887, in refinement_machine h_params = h_params) File "/data/software/phenix-1.3b/mmtbx/mmtbx/refinement/adp_refinement.py", li ne 160, in __init__ tools.split_u(fmodel.xray_structure, tls_selections, offset) File "/data/software/phenix-1.3b/mmtbx/mmtbx/tls/tools.py", line 468, in split _u assert (u_iso < 0.0).count(True) == 0 AssertionError I have downloaded the new 1.3b version and without tls the program runs fine! could you please help Thanks in advance Regards kanchan

1 0

textal problem
by Daniele de Sanctis 31 May '07

31 May '07

Dear all, I'm running textal.build to build a model in a 3.2 A map, and I'm using the option --input_model and --sequence. It seems to run ok until finishing the lookup but then i got the error message: doing sequence alignment against: ../pippo.seq sh: Syntax error: Bad fd number error: [Errno 2] No such file or directory: 'phentx-lookup-correct.pdb' indeed the file is not there, but i guess that is not there because o the previous Syntax error. any clue? thanks d -- Daniele de Sanctis, PhD Homo sum humani nil alienum a me puto ______________________________________________________________ phone ++ 351 21 4469 662 fax ++ 351 21 4433 664 e-mail de.sanctisd(a)gmail.com, sanctis(a)itqb.unl.pt Mailing address: ITQB, Av. República, Apartato 127 2781-901 Oeiras Portugal

1 0

Re: [phenixbb] how to add phase info to the autosol wizard
by Tom Terwilliger 31 May '07

31 May '07

Hi Chuanbing, I'm sorry, that option isn't there yet! It is one that is on my list of to-do's. -Tom T At 01:51 AM 5/31/2007, CB Bian wrote: >Dear all, > > I am trying to add phase info from externally calculated > phases to the autosol wizard with S-SAD data. But I can not find > the option to do it in the running. Can someone help me? > > >Thanks in advance > >Chuanbing > >-- >ChuanBing Bian, Ph.D Student >Structural biology group >State Key laboratory of Structural Chemistry >Fujian Institute of Research on the Structure of Matter, >Chinese Academy of Sciences >155 Yang Qiao Xi Lu, Fuzhou, Fujian 350002 P. R. China >E-mail: ><mailto:[email protected]>cbbian(a)gmail.com ><mailto:[email protected]>cbbian(a)fjirsm.ac.cn >Tel:(office)+86-591-8370-5814 ><http://protein.fjirsm.ac.cn/>http://protein.fjirsm.ac.cn >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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how to add phase info to the autosol wizard
by CB Bian 31 May '07

31 May '07

Dear all, I am trying to add phase info from externally calculated phases to the autosol wizard with S-SAD data. But I can not find the option to do it in the running. Can someone help me? Thanks in advance Chuanbing -- ChuanBing Bian, Ph.D Student Structural biology group State Key laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences 155 Yang Qiao Xi Lu, Fuzhou, Fujian 350002 P. R. China E-mail: cbbian(a)gmail.com cbbian(a)fjirsm.ac.cn Tel:(office)+86-591-8370-5814 http://protein.fjirsm.ac.cn

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Re: [phenixbb] Death by Big-ass structure
by Petrus H Zwart 30 May '07

30 May '07

Hi Ulrich, Frank, Ralf has just placed a new version of cci_apps on our download sites (www.phenix-online.org). It contains a new application named phenix.xmanip (or mmtbx.xmanip if you only download the cctbx). It is basically a rewritten version of the reindex.py script I once wrote as an example jiffy. xmanip can read in various reflection files or mtz/cns data columns which subsequently can be used in reindexing or other tasks. The parameter file I send Frank a couple of days ago should still work, even though some rearrangements have been made . Typing phenix.xmanip reindex.def should do the trick. Other options are available as well. One could - generate map coefficients from a model (plain FC,PHIC, or sigmaA style maps if observed data is available) - get anomalous / isomorphous differences - scale two datasets together - generate symmetry mates of a model - the 'custom' option allows you to pass in a snippet of python code and have it executed. One has access to all datasets and molecular model read in. You could for instance add two datasets or multiply them if it makes you happy. Full documentation is under way. If you have any question, please let me know. Peter

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Re: [phenixbb] phenix.refine questions: weights, docs, etc.
by Ralf W. Grosse-Kunstleve 29 May '07

29 May '07

Hi Dale, > The sets of parameters that can be refined simultaneously is a result of the > choice of optimization method, not the choice of the function being optimized. > The crucial difference is how the second derivatives are handled. In the > methods used in Phenix and CNS the seconds derivatives of all parameters are > assumed to be equal and uncorrelated. This is true only for the first iteration of a minimization in a phenix macro cycle. After that the L-BFGS method builds up an approximation of the second derivative information. > To ensure that this assumption is true > only parameters of the same category can be varied in a single cycle. This > means that the coordinates can be varied, but the B factors and scale factors > have to be held fixed. When the B factors are varied the coordinates and > scale factors must be constant. When the scale factors are varied everything > else must be fixed. > > Other refinement programs use second derivatives in a more explicit way > than Phenix and do vary more types of parameters in a single cycle. Shelxd is > the most powerful and, by default, varies all parameters of all classes each > cycle. Refmac, to the best of my knowledge, refines both coordinates and ADPs > together, but does refine TLS parameters in a separate step. As far as I know, Shelx doesn't use second derivatives at all. Shelx is shaped completely by the least-squares approach, using the Jacobian. You couldn't plug another target function into Shelx as you can do in the common macromolecular programs. I.e. there is in fact a link between the minimization method and choice of the target function. REFMAC uses a block-diagonal approach that only takes the correlations of the parameters of one atom into account. phenix approximates these with the L-BFGS method. We have not actually tried to refine coordinates and B-factors simultaneously since we've been too busy with other priorities. In theory it should be possible, but I'm sure it will take a lot of fine-tuning. > Since all the parameters of our models are correlated with one another, it > is better to refine as many of them at once as possible. Implementing > the join refinement of all these kinds of parameters is difficult, so to save > programmers' time approximations are sometimes made. We'll spend the time when we find it. :-) But I don't expect spectacular gains, no matter how long we beat on the second derivatives. Ralf

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phenix.refine questions: weights, docs, etc.
by Frank von Delft 29 May '07

29 May '07

Hi, four questions on phenix.refine: 1) What's the reason for refining bss, xyz and adp in separate cycles? CNS does that too while refmac (I believe) refines them simultaneously. I suspect I missed something, but I thought the power of ML refinement is that no refinable parameters are held constant if they're not supposed to be. (At least, wasn't that the big deal in Sharp when it came out?) 2) How does one figure the right restraint weights? (wxc and wxc). In refmac, I've always calibrated the weight with rmsd(bonds), tightening it until rmsd(bonds) is ~0.018 (or below for lower reso); invariably this is where Rfree will decrease furthest and smoothly as well (i.e. without that silly rise at the end.) With phenix.refine I'm finding that I only get Rfree to drop monotonously when I tighten the weights (both wxc and wxu) so much that rmsd(bonds) goes down to ~0.002. Would there be a different way to do this? 3) There isn't currently torsional refinement, is there? For high-temperature simulated annealing, I mean. I'm having the same weight-adjustment question for SA, except is harder to fiddle with because jobs take so long, but with torsional that becomes moot. Or should one always put very tight weights on for SA? 4) Is there good documentation for all the loads and loads of keywords? The names themselves are just descriptive enough to be interesting, but obviously not enough to be informative if I don't just want the black box. Nice program, though, got to say... phx.

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Death by Big-ass structure
by Frank von Delft 25 May '07

25 May '07

Hi, we get the memory error below for a structure of 30603 atoms 273217 reflections 2.1A H3 193.868 193.868 352.223 90.00 90.00 120.00 10x NCS Anything I said? It's not THAT large a problem, I'd have thought, or should we go to the rhombohedral setting instead? (Hmmmm, this rings a bell, wasn't there a posting about this 3 days ago? Nothing in the archives, was it CCP4bb?) Cheers phx Traceback (most recent call last): File "/usr/local/phenix/phenix-1.26b/phenix/phenix/command_line/refine.py", line 5, in ? command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix/phenix-1.26b/phenix/phenix/refinement/command_line.py", line 75, in run refine_object.run( File "/usr/local/phenix/phenix-1.26b/phenix/phenix/refinement/driver.py", line 1236, in run log = log) File "/usr/local/phenix/phenix-1.26b/phenix/phenix/refinement/strategies.py", line 273, in refinement_machine log = log) File "/usr/local/phenix/phenix-1.26b/phenix/phenix/refinement/weight_xray_chem.py ", line 111, in __init__ self.fmodel_copy = self.fmodel.deep_copy() File "/usr/local/phenix/phenix-1.26b/mmtbx/mmtbx/twinning/twin_f_model.py", line 1003, in deep_copy map_types = self.map_types File "/usr/local/phenix/phenix-1.26b/mmtbx/mmtbx/twinning/twin_f_model.py", line 888, in __init__ self.update_f_mask() File "/usr/local/phenix/phenix-1.26b/mmtbx/mmtbx/twinning/twin_f_model.py", line 1370, in update_f_mask self.f_mask_array = mask.structure_factors( self.miller_set ) File "/usr/local/phenix/phenix-1.26b/mmtbx/mmtbx/masks.py", line 103, in structure_factors flex.grid(fft_manager.m_real()).set_focus(fft_manager.n_real())) MemoryError

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Re: [phenixbb] Question about restraints in individualB-factor re finement
by Schubert, Carsten [PRDUS] 25 May '07

25 May '07

Thanks Pavel,Nigel: so it looks as if neither approach works and I would need to split the ligands into seperate PDB files for a truly independent B-factor refinement. Thanks for the hint about the non-bonded interactions. That was useful. Cheers Carsten -----Original Message----- From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]]On Behalf Of Pavel Afonine Sent: Friday, May 25, 2007 12:51 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Question about restraints in individualB-factor refinement Hi Carsten, for the refinement of b-factors there is no difference between two options. We use the sphere b-factors restraints which are calculated based on interatomic distances and the information about alternative conformations is not used at that point. However if you refine the coordinates, the difference is significant: if you refine it as two separate residues then they will "see" each other for non-bonded interactions term calculation and hence will be pushed apart. Please let me know if you still have questions! Pavel. Schubert, Carsten [PRDUS] wrote: Hi, I have a question about the handling of restraints in the individual B-factor refinement routine. What I'd like to do is to refine a ligand, which can be present in 2 or more different conformations/orientations in its binding site. I'd like to use B-factor refinement on the various instances of the ligand, which one is the most relevant one, assuming that the most relevant conformation/orientation is associated with the lowest B-factor (Validity of that assumption set aside ...) My question is now is there any difference in the restraints applied to the b-factors in the scenarios where A) the ligand is modeled as alternate conformations i.e. ATOM 2724 C01AINH I 1 27.808 26.376 23.301 0.50 27.77 I C ATOM 2733 C01BINH I 1 30.898 22.496 17.340 0.50 22.15 I C ... vs. scenario B) where the same ligand is modeled as 2 different residues ATOM 2724 C01 INH I 1 27.808 26.376 23.301 0.50 27.77 I C ATOM 2733 C01 INH I 2 30.898 22.496 17.340 0.50 22.15 I C .... Basically, what I am trying to achieve is to uncouple the B-factor refinement of each individual instance of the ligand from its other instance(s). Are there any hidden pitfalls between these 2 scenarios I should be aware of? Many thanks for any input. Cheers Carsten _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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Question about restraints in individual B-factor refinement
by Schubert, Carsten [PRDUS] 25 May '07

25 May '07

Hi, I have a question about the handling of restraints in the individual B-factor refinement routine. What I'd like to do is to refine a ligand, which can be present in 2 or more different conformations/orientations in its binding site. I'd like to use B-factor refinement on the various instances of the ligand, which one is the most relevant one, assuming that the most relevant conformation/orientation is associated with the lowest B-factor (Validity of that assumption set aside ...) My question is now is there any difference in the restraints applied to the b-factors in the scenarios where A) the ligand is modeled as alternate conformations i.e. ATOM 2724 C01AINH I 1 27.808 26.376 23.301 0.50 27.77 I C ATOM 2733 C01BINH I 1 30.898 22.496 17.340 0.50 22.15 I C ... vs. scenario B) where the same ligand is modeled as 2 different residues ATOM 2724 C01 INH I 1 27.808 26.376 23.301 0.50 27.77 I C ATOM 2733 C01 INH I 2 30.898 22.496 17.340 0.50 22.15 I C .... Basically, what I am trying to achieve is to uncouple the B-factor refinement of each individual instance of the ligand from its other instance(s). Are there any hidden pitfalls between these 2 scenarios I should be aware of? Many thanks for any input. Cheers Carsten

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probable RTFM question
by William Scott 17 May '07

17 May '07

Howdie: I just used phenix.geometry_minimization to try to see the effect of deleting some disulphide bonds in a protein structure. Is there a way to do the equivalent of CNS's model_anneal (i.e., simulated annealing with just a model)? It wasn't apparent from reading the phenix.refine docs. Thanks. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/

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