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Re: [phenixbb] phenixbb Digest, Vol 40, Issue 31
by Marjolein Thunnissen 31 Mar '09

31 Mar '09

> > Hi Marjolein, > >> I have been trying to find in the documentation if there is a way to do this >> but I have the following problem: In a recent structure we are currently >> refining we identified a spermine molecule sitting right on a >> crystallographic two-fold axis. Spermine has internal two-fold symmetry and >> it is part of extensive crystal contacts. I just wonder how to refine this >> with Phenix. In Refmac it is easy, I put the occupancies to 0.5 and the >> program ignores the clashes of the symmetry related molecule, but that >> doesn't seem to be the way that Phenix works. Can anyone give me advise on >> this? > > Supporting the occupancy trick is on my to-do list (fairly high up). > > In the meantime, could you try giving only the asymmetric unit of the > spermine? I.e. delete all duplicate atoms from your pdb file. > The restraints across the symmetry bond will not work automatically. > You have to define a "custom bond" instead, and if you also want to > restrain the angles, custom pseudo-bonds. See the > "Definition of custom bonds and angles" section. > In your case you'll have to define symmetry_operations (not shown > in the docs), e.g.: > > bond { > action = *add > atom_selection_1 = resname SPM and name C7 > atom_selection_2 = resname SPM and name C7 > symmetry_operation = -x,-y,z > distance_ideal = 1.5 > sigma = 0.01 > } > > The main difficulty will be to find the correct symmetry_operation > for each custom bond. If you send my the CRYST1 card from your > PDB file and the part with the SPM residue I could help out. > > Ralf > > > ------------------------------ Hi, The commands worked indeed the trick. Luckily it is actually not that difficult to find the symmetry operators when using coot. One just has to switch drawing symmetry atoms on and clicking on a symmetry atom, coot will tell you in the bottom line which atom it is and which symmetry operator was used to draw it... Thanks again Marjolein __________________________________________________________________________ | Marjolein Thunnissen Phone +46-(0)46-22 24584| | Associate Professor Fax +46-(0)46-22 24692| | Dept of Molecular Biophysics, Lund University http://www.mbfys.lu.se | | PO-Box 124 S-221 00 Lund, Sweden | | | |Scientific coordinator I911 (Max-lab): MAD and fixed-wavelength stations | | for macromolecular crystallography | |__________________________________________________________________________|

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Re: [phenixbb] PHENIX user mailing list <[email protected]>
by Ralf W. Grosse-Kunstleve 30 Mar '09

30 Mar '09

Hi Maia, > I have a Ca2+ ion in a special position. the ocupancy should be 0.5, as > the other half belongs to a symmetry-related molecule. However, > refinement makes the occupansy 1. What should I do to prevent this? > Should not it find automatically that? phenix.refine uses the correct symmetry factor automatically (internally). Unless you have an actual partial occupancy, the occupancy factor in the pdb file should be 1, irrespective of the multiplicity of the special position. Let me know if this doesn't answer your question. Ralf

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can I turn off TLS for subsequent rounds of refinement?
by Scott Classen 30 Mar '09

30 Mar '09

Hi all, As the TLS refinement can take a significant amount of time, I'm wondering if I can turn it off after a few rounds with it on? or will phenix.refine "see" the ANISOU records and assume I am doing anisotropic ADP? Thanks, Scott

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phenix automr
by sbiswas2＠ncsu.edu 30 Mar '09

30 Mar '09

Hi all, I tried to use phenix automr by using the gui and also I am using the latest version of phenix (courtesy of the phenix development team). I asked it to search for two molecules in the asymmetric unit but it finds just one also I am getting negative (-29) LLG value for the final solution. The map also does not look good. I also asked it to search for all possible space group, although I processed the data with P43212 phenix automr finds a different one P41212.Will fixing the space group fix the problem? Does anyone know what is going on? I tried running phaser separately through ccp4 and phaser did find two molecules although the map did not look good in this either. Shya

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Missing map for model
by Folmer Fredslund 30 Mar '09

30 Mar '09

Dear all, In phenix.refine (1.4-3) my electron density maps look weird. I get beautiful density for a helix that is missing from the current model, but absolutely horrible density for the rest of the molecule. Any ideas what is going on? Maps from automr look fine and the density modified map from autobuild also look fine, whereas the autobuild map from refinement has the same features. Any ideas what is going on? I am running all programs with default parameters. Best regards, Folmer Fredslund

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Geometry problem with the ligand
by Jhon Thomas 30 Mar '09

30 Mar '09

Hello all I am working with a 3.0 A dataset, which binds with cAMP. I have refined the dataset with phenix (TLS+Group_adp) and followed by weight optimization. Though cAMP fit well in the density, validation tools (molprobity, procheck) suggest the bond angles and bond lengths of ligand of completely refined model is very bad(100% bad). Can anyone suggest what could be the problem with model or refinement? I will appreciate the suggestions. Thanks in advance John

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weight optimization
by peter hudson 29 Mar '09

29 Mar '09

Hello all I am very new to this field. I am refining a dataset of 3.0A resolution. I want to perform the weight optimization. while weight optimisation, occupancy refinemnet is default. I donot want torefine the occupancy of any of the atoms from my model. How can i set to occupancy_refinemnet=false. I will appreciate the suggestions. Thanks in advance Peter

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Re: [phenixbb] Question about scale of ED maps from phenix vs map coeffs when displayed in COOT
by Ralf W. Grosse-Kunstleve 29 Mar '09

29 Mar '09

For phenix maps: the sum is over the entire unit cell. Ralf > Is the sum over the asymmetric unit or the portion of space that > happened to be covered by the map? The result of this calculation > depends greatly on the amount of solvent region that is included in > the sum. > > Dale Tronrud > > Ralf W. Grosse-Kunstleve wrote: > >> That was (and is) always a mystery for me: when I look at two maps (both > >> coming from phenix.refine): > >> - one is computed in COOT from phenix.refine map coefficients, and > >> - another one displayed in PyMol using X-plor formatted map. > >> > >> To make both maps looking identical I have to draw them at different > >> sigma levels, sometime very different. This is true for both fo-fc and > >> 2fo-fc maps. > >> > >> I have some ideas but no any proofs so I don't want to put my > >> speculations to the bb. So, I have no answer... May be Ralf or Paul E...? > > > > Our "sigmas scaled maps" are simply divided by the "biased standard > > deviation": > > > > sqrt(sum((value-mean)**2) / n) > > > > The mean of our maps is usually zero, as we don't usually include F000. > > > > Ralf

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Refinement error
by Katya Heldwein 27 Mar '09

27 Mar '09

Hi, I am getting the following error when I run phenix.refine. How can I get rid of it? Katya =============================== refinement start ============================== ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- show_stack(1): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/mmtbx/twinning/twin_f_model.py(1676) r_values show_stack(2): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/mmtbx/twinning/twin_f_model.py(1837) r_work show_stack(3): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/mmtbx/f_model.py(2249) __init__ show_stack(4): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/mmtbx/twinning/twin_f_model.py(1139) info show_stack(5): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/mmtbx/__init__.py(109) show_comprehensive show_stack(6): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/phenix/phenix/refinement/strategies.py(280) refinement_machine show_stack(7): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/phenix/phenix/refinement/driver.py(1121) run show_stack(8): /private/var/automount/nfs/programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/phenix/phenix/refinement/command_line.py(89) run show_stack(9): /programs/i386-mac/cciapps/2009_02_15_2320/cci_apps_sources/phenix/phenix/command_line/refine.py(16) <module> Floating-point error (Python call stack above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

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AssertionError in twin refinement...
by Francis E Reyes 26 Mar '09

26 Mar '09

====================== bulk solvent modeling and scaling ====================== |--(resolution: 2.00 - 23.08 A; n_refl. = 24304)------------------------------| | | | r_work= 0.2462 r_free= 0.2706 ksol= 0.32 Bsol= 47.55 scale= 1.149 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (-2.11,5.80,-3.69,0.00,-0.00,-0.00); trace/3= -0.00 | | | | maximum likelihood estimate for coordinate error: None A | | x-ray target function (twin_lsq_f) for work reflections: 0.346916 | | twin fraction: 0.03 twin operator: k,h,- l | | -----------------------------------------------------------------------------| ================== ordered solvent: location/analysis/update ================== Start model: number = 165 b_iso_min = 37.62 (limit = 1.00) b_iso_max = 70.26 (limit = 50.00) b_iso_mean = 49.33 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 1.00) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = 2.45 (limit = 1.80) dist_sol_mol_max = 4.94 (limit = 6.00) Filtered: number = 71 b_iso_min = 37.71 (limit = 1.00) b_iso_max = 49.89 (limit = 50.00) b_iso_mean = 45.14 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 1.00) occupancy_max = 1.00 (limit = 1.00) dist_sol_mol_min = 2.45 (limit = 1.80) dist_sol_mol_max = 3.99 (limit = 6.00) Traceback (most recent call last): File "/usr/local/phenix-1.3-final/phenix/phenix/command_line/ refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/ command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/ driver.py", line 1081, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/ strategies.py", line 364, in refinement_machine log = log) File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/solvent/ ordered_solvent.py", line 159, in __init__ use_kick_map = self.params.use_kick_maps).peaks_mapped() File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/solvent/ ordered_solvent.py", line 332, in find_peaks log = self.log) File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/find_peaks.py", line 85, in __init__ symmetry_flags = maptbx.use_space_group_symmetry) File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/twinning/ twin_f_model.py", line 2244, in electron_density_map "m_gradient") AssertionError phenix version is 1.3 final. Ideas? thanks! FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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