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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 11 Oct '10

11 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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maps : scattering corrections
by Lepore, Bryan 07 Oct '10

07 Oct '10

i'd like to define anomalous scattering corrections for phenix.maps, it looks like i'm not doing it right. it appears that simply pasting in various adjustments of : anomalous_scatterers { group { selection = element = Ni f_prime = 2.4 f_double_prime = -0.1 refine = *f_prime *f_double_prime # not sure about this one } in various places in maps.params mostly causes phenix.maps to report "unused parameter", e.g: maps.anomalous_scatterers.group.selection this should work, right? what am i missing here - is there a scope missing, what scope does this go in, did i miss this in the docs... -bryan

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Phenix.refine stops running in the background
by José Trincão 07 Oct '10

07 Oct '10

Hello all, I've been running phenix.refine over ssh on a remote computer, on command line. I always run it in the background (adding & to the command line). If I disconnect the ssh (or it gets disconnected) the job hangs. Any way of leaving it running even after the ssh disconnects? Thank you. Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal "It's very hard to make predictions... especially about the future" - Niels Bohr

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phenix.refine : mask
by Lepore, Bryan 07 Oct '10

07 Oct '10

i gather that the only way to define an "a priori" mask of the molecular envelope in phenix.refine is to generate Fmask and combine those in refinement - is that right? i.e. there isn't a more intuitive way using a mama mask or somesuch to keep the bulk solvent from flattening out parts you think are model, besides the model that is being refined in the first place? -bryan

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Re: [phenixbb] refine .log : loggraph flags
by Lepore, Bryan 06 Oct '10

06 Oct '10

On Wed, 6 Oct 2010, Nathaniel Echols wrote: > > loggraph [...] OR am i just missing something (CL flag, GUI...) > The GUI already does this nifty - does the entire gui have to be run? i.e. is that a "smaller" plotter you used?

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refine .log : loggraph flags
by Lepore, Bryan 06 Oct '10

06 Oct '10

[ thanks for the comments on sigma-A ] a related thread : its nice how xtriage puts loggraph specifications ($TABLE etc.) in the output. what is the source file that writes this? or is it more complicated than that? the .log can be hacked, but its a miserable thing to do. e.g. to incorporate such lines into phenix refine output - esp. a ln(sigma-A) plot - would be handy in such a format. then the course of refinement or all the dmin-dependent stats can be graphed. OR am i just missing something (CL flag, GUI...) -bryan

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refinement / alpha_beta
by Kay Diederichs 05 Oct '10

05 Oct '10

Dear Phenix developers, I'd like to refine (using phenix.refine) a _very_ incomplete model (obtained by molecular replacement with one subunit of the complete structure) against the native amplitudes, with the goal to obtain meaningful phases and figures_of_merit which should serve to find heavy atom sites in derivative datasets. If I "just refine" in phenix.refine, then the R-factors are in the 50s and the program estimates the coordinate error to be very large. Thus I would like to tell phenix.refine that the coordinates are actually quite accurate, but that a lot of the model is simply missing. I found alpha_beta free_reflections_per_bin= 140 number_of_macromolecule_atoms_absent= 225 n_atoms_included= 0 bf_atoms_absent= 15.0 final_error= 0.0 absent_atom_type= "O" method= *est calc estimation_algorithm= *analytical iterative verbose= -1 interpolation= True fix_scale_for_calc_option= None number_of_waters_absent= 613 sigmaa_estimator kernel_width_free_reflections= 100 kernel_on_chebyshev_nodes= True number_of_sampling_points= 20 number_of_chebyshev_terms= 10 use_sampling_sum_weights= True in the documentation but I have trouble understanding its meanings and defaults - but I do think this should be used. Maybe I should switch to method=calc and specify number_of_macromolecule_atoms_absent= as well as bf_atoms_absent= ? Can anyone advise me, please? thank you, Kay

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best strategy using two datasets?
by Manoj saxena 05 Oct '10

05 Oct '10

Hi , I have data 2.4 A for a protein ( Se-Met derivative) unit cell dimensions. 53.098,60.207,142.382. I have used this data to solve the partial structure with phenix.autosol and phenix.autobuild. The model from this data was then used as MR model in phaser with another data set from a crystal at 2.2 A (group P212121 ) .unit cell dimensions are 53.86,61.47,142.49. Currently my R free is 23%. My question is 1) Is there a a better way to use the two datasets. can I merge the reflection files from two datasets and does using a merged reflection file have an advantage over the strategy I used. 2) Although not directly related to phenix I was wondering can we use the merged reflection file for PDB depositions? Thanks . I will greatly appreciate any suggestions and guidance in this regard Manoj

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