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Question
by Louis Lazar 18 Oct '10

18 Oct '10

Hello, I am seeing an internal error while trying to conduct joint x-ray/neutron refinement, and any help with the issue below would be greatly appreciated. Thank you very much in advance: ================================ ADP refinement =============================== Traceback (most recent call last): File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/driver.py", line 1182, in run call_back_handler = call_back_handler) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py", line 735, in refinement_machine h_params = h_params) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py", line 192, in __init__ all_params = all_params) File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/refinement/adp_refinement.py", line 216, in refine_adp model.set_refine_individual_adp() File "/sware/phenix-1.6.4-486/linux64/phenix-1.6.4-486/cctbx_project/mmtbx/model.py", line 1035, in set_refine_individual_adp iselection = selection_iso.iselection()) RuntimeError: cctbx InternalError: /net/anaconda/scratch1/phenix/phenix-1.6.4-486/cctbx_project/cctbx/xray/scatterer_flags.h(417): CCTBX_ASSERT(f.use_u_iso()) failure. This error occurs during the 2nd macro cycle of refinement using this general command: phenix.refine model.pdb data_xray.hkl neutron_data.file_name=data_neutron.hkl input.xray_data.labels=FOBSx input.neutron_data.labels=FOBSn Thanks again. Regards, Louis

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real space refinement or fix rotamers
by helene.krueger＠staff.uni-marburg.de 14 Oct '10

14 Oct '10

Hi, I want to fit bad fitting residues into electron density of my 2.0 A dataset. To do so should I use the "real space" option or the "fix bad sidechain rotamers" option? or both? Thanks Helene -- Helene Köster Philipps-Universität Marburg Institute of Pharmaceutical Chemistry AG Klebe Marbacher Weg 6 35032 Marburg, Germany Phone: +49-6421-28-25908 Mail: helene.krueger(a)staff.uni-marburg.de www.agklebe.de

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How to eliminate or decrease negative electron density at ligand position
by J J 14 Oct '10

14 Oct '10

Hello everyone, I have fine electron density 2Fo-Fc around a small ligand (~20 atoms) binding to my protein (at 1sigma level, all of the ligand atoms are surround by electron density, resolution=3 angstrom). However, I also see some negative electron density Fo-Fc surrounding some of the ligand atoms. My question is should I care about these negative electron density? If I should, what should I do in order to decrease or eliminate these negative electron density? I have tried occupancy refinement. It does help to decrease the negative density. However, it also makes 2Fo-Fc weaker. Another method I tried is to use tls refinement only for the ligand. It also helped to decrease the negative electron density. But since the data resolution is only 3 angstrom, I do not know if I am even allowed to do tls refinement? Thank you all in advance. Jason University of Pittsburgh

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Average B-factors when using TLS
by Phil Jeffrey 13 Oct '10

13 Oct '10

I'm having a discussion with a colleague here about what we expect to see on a model with and without TLS being used. I had the expectation that if you'd compared both models the Biso values reported in the ATOM line for the same atom w/ and w/o TLS would be somewhat comparable. Not the same, because the ADP model is different, but similar. However in the case of the TLS-refined model the average B-factors are systematically higher over the whole structure (86 A^2 vs 69A^2 for one polypeptide chain). Is this reasonable ? Expected ? Phil Jeffrey Princeton

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Re: [phenixbb] When to freeze crystal?
by miket＠chem.ucla.edu 13 Oct '10

13 Oct '10

Just last week I had crystals on Friday, then by Monday they dissolved back into the drop. I don't really understand how or why this happens, but it does. After experiencing this and complaining about it, I heard several other similar stories from around the department. Lesson learned: if you think you have a decent crystal, freeze it. Having said this, I've also heard of good data being collected from a crystal that was over a year old. Like Bert said, I think that occasionally a crystal survives or even improves over time, but those cases are much more rare than cases where the crystal deteriorates. Do how many crystals do you have? You might try freezing some and saving the others in the drop, then you can see for yourself. Good luck, Mike ----- Original Message ----- From: "Nathaniel Echols" <nechols(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Wednesday, October 13, 2010 8:44:42 AM GMT -08:00 US/Canada Pacific Subject: Re: [phenixbb] When to freeze crystal? On Wed, Oct 13, 2010 at 4:16 PM, J J <phenix.upitt(a)gmail.com> wrote: > Hi everyone, > Sorry to ask a question that is not really related to phenix. I hope someone > here will be able to help me out. > I have a few crystals at hand right now, but I will not be able to look at > them for at least another month or so due to beamline schedule. Do you think > I should freeze them now or wait till I have my beamtime, or it is crystal > dependent? Thanks in advance. (Bert meant to send this to the list, but since he's using the wrong email address, it went to the list admin instead:) From: "Van Den Berg, Bert" <Lambertus.VandenBerg(a)umassmed.edu> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Date: Wed, 13 Oct 2010 11:27:32 -0400 Subject: Re: [phenixbb] When to freeze crystal? It is crystal dependent, but if they are big enough I would freeze them now. I have seen many crystal forms deteriorate over time and wouldn’t take the risk of that happening. It can happen though that old crystals get better (presumably due to slow dehydration of the drop), but I think these cases are fairly rare. Bert _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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When to freeze crystal?
by J J 13 Oct '10

13 Oct '10

Hi everyone, Sorry to ask a question that is not really related to phenix. I hope someone here will be able to help me out. I have a few crystals at hand right now, but I will not be able to look at them for at least another month or so due to beamline schedule. Do you think I should freeze them now or wait till I have my beamtime, or it is crystal dependent? Thanks in advance. Jason University of Pittsburgh

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Merging low resolution mtz file with high resolution sca file with phenix_reflection_file_editor
by Pei-Chun Lin 13 Oct '10

13 Oct '10

Hi, If I merge my low resolution mtz file with the high resolution sca file with phenix.reflection_file_editor GUI, is it the same as : Merge in hires data phenix.autobuild data=solve_2.mtz hires_file=w1.sca seq_file=seq.dat in Phenix Autobuild? PC

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secondary structure restraints question
by Peter Grey 12 Oct '10

12 Oct '10

Dear Phenix community, I have a very large model with many chains (due to NCS and complexity of model) where chain-id is not unique (e.g. there are several chain A) but segid is. All atom selections (for rigid body refinement, ncs restraints, tls etc...) are defined by segid. When I look at the output of phenix.secondary_structure_restraints I see that these restraints are defined by chain-id and residue number. Does this mean I must have unique chain-id names to correctly apply these secondary structure restraints or am I missing something ? Thank you for your time, Peter

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refine : annealing and bulk solvent
by Lepore, Bryan 12 Oct '10

12 Oct '10

[ phenix 1.6.4-486 ] from the program output, it appears that prior to annealing ( e.g. torsion ), a bulk solvent grid search is run using the initial model. after that ends, all the annealing steps are carried out on the model using the initially optimized bulk solvent. When annealing is done, another search is conducted on the final model. i.e. there are no bulk solvent changes during annealing. is this right? -bryan

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DNA base pairing restraints work for GC only
by Phoebe Rice 07 Oct '10

07 Oct '10

We're trying to refine a large, low-resolution protein-DNA complex structure (4A in the good direction), and we need every restraint we can get, so I'm trying to use secondary structure restraints (in addition to ncs and 3 known substructure models). I found this from the newsletter: phenix.secondary_structure_restraints model.pdb > ss.eff ran it, editted it, and plugged into the gui, where it seems to be taken into account if I also say "yes" to "find automattically". Then I ran torsion angle dynamics to see if things were restrained as requested. It only seems to be restraining G:C pairs - the ATs fly apart! The log file makes a very suspicious set of remarks under "secondary structure": No entry for base pair AT with type WWT (H=False). (repeated about the same # of times as we have AT pairs). I thought maybe it was a nomenclature problem, but if "Gd" is OK I don't see what's wrong with "Ad", and the usual suspect, the thymine methyl, stays coplanar with the rest of its base, so the program must be recognizing our base/atom names. Question 2 is that I wanted to view the restraints in pymol, but this command, also cribbed from the newsletter: phenix.secondary_structure_restraints partry1noss.pdb ss_manual.eff format=pymol > h_bonds.pml seems to overwrite the manual editing in my .eff file. Help? I'm new to phenix, so please be explicit about where I've gone wrong. thanks, Phoebe ===================================== Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alph… http://www.rsc.org/shop/books/2008/9780854042722.asp

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