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How to extend R-free set to higher resolution by new phenix-1.5.2
by Pei-Chun Lin 12 Dec '09

12 Dec '09

Hi, I know this topic was discussed before, but I am still confused and still unable to refine my map merged from hires data because phenix.refine complains "No array of R-free flags found" The command was used to generate a hires map. phenix.autobuild data=resolve_1.mtz hires_file=hires.sca \seq_file=sequence.dat maps_only=True So, now I have "exptl_fobs_phases_freeR_flags.mtz", "cycle_best_1.mtz", "overall_best_denmod_map_coeffs.mtz"...several files in my autobuild folder, How do I merge low and high resolution data by "phenix.reflection_file_editor"? What files (input and output arrays) should I choose? Detail description will be very appreciate. Thanks for answer my question. PC _________________________________________________________________ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/so…

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Side chain at special position
by Nate Nicely 11 Dec '09

11 Dec '09

I have a structure wherein the data show alternate conformations for a particular Trp side chain. The problem is that each of these conformations also occupies a special position: rotamer A clashes with rotamer A of the symmetry object, and similar for rotamer B. I'm attaching a screenshot wherein I tried to capture what's going on. The prerefined structure has a yellow carbon backbone, and you can see how refinement pushes rotamer A out of its rightful place in the map. I readjusted it and added the alternate conformation as seen in the green carbon backbone, but refinement after that just pushes apart both rotamers (not shown). I'd appreciate advice how to handle refining this structure in phenix. Thanks, Nate N

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Re: [phenixbb] structural validation and deposit format
by Pavel Afonine 11 Dec '09

11 Dec '09

On 12/11/09 12:55 PM, rui wrote: > SO in the output pdb file, there are another set of lines start with > ANISOU, what are those, should I keep those? These are ADPs - Atomic Displacement Parameters, or B-factors. They are as important as atomic coordinates (almost) stored in ATOM records -:) > I turned on the optimze_wxc and optimize_wxu flags in the GUI, it does > give better R/Rfree. Do I need to turn on every time or just use the > optimized weights, where I can find those optimized weight? In log file? Optimization of weights is usually time consuming and the default weights are just good most of the time. So I usually recommend running weights optimization as the last step to tune up your model. Of course there might be exceptions. Since optimal weight may be different from run to run, they are not stored in .def file for the next runs. Pavel.

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structural validation and deposit format
by rui 11 Dec '09

11 Dec '09

Hi, All, Sorry for this stupid question. When I tried to use phenix to validate the structure, it generate geometry outliers, model validation, real-space correlations and a phenix_map_coeffs.mtz file which I assume could be open in coot. How should I use this generated mtz file? When I open in coot, it tellls me core dump. I'm wondering if phenix will automatically do the corrections or should I look one by one in the log file and modify? It also generate a test_reduced.pdb, should I use this reduced pdb ( H added) for next round of refinement? Thanks. Is the format from phenix.refine ready for deposit?

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refinement
by r n 11 Dec '09

11 Dec '09

Hi all I do have very low resolution data (around 4 ang), what are the efficient way of doing refinement, either rigid body alone or rigidbody and tls or individual with group_adp. I did both, but not much significant changes in Rfree stays around 48/50%. Also I do have other questions 1. While doing rigid body refinement, phenix complaint about the special position and could not perform rigid body refinement, whereas individual site refinement is working fine. I do have to delete the atom in special position for rigid body refinement? Thanks

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How to reload a project into the gui
by Dirk 11 Dec '09

11 Dec '09

Hi, during a phenix refinement the gui froze and I had to kill the process. After restarting the gui the project I was working with was disappeared - all other projects are still there. Is there a way to reload the project into the gui? All files including the project folder still exists but are somehow not recognized by the gui. I'm using dev-249 64bit. Greetings Dirk

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Re: [phenixbb] How to reload a project into the gui
by Thomas C. Terwilliger 10 Dec '09

10 Dec '09

Hi Dirk, Try phenix.refine --gui Refine_xx/refine_xx.eff where xx is the run number of your refinement. That should preload all the parameters you had set at least. All the best, Tom T >> Hi, >> >> during a phenix refinement the gui froze and I had to kill the >> process. After restarting the gui the project I was working with was >> disappeared - all other projects are still there. Is there a way to >> reload the project into the gui? All files including the project folder >> still exists but are somehow not recognized by the gui. >> I'm using dev-249 64bit. >> >> Greetings >> >> Dirk >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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Are sigma cutoffs for R-free reflections cheating?
by Joe Krahn 10 Dec '09

10 Dec '09

Using a sigma cutoff in refinement is almost always a bad idea. It appears that some people still use them. The problem is that sigma cutoffs almost always improve R-factors, because it increases the denominator in the error/average equation. Some people incorrectly think that the reduced R-factor means that the cutoff was an improvement in the structure quality. The result of a sigma cutoff is that the R-factor can be made to look better than it really is. I think that this should be prevented by never excluding any R-free reflections by any sort of cutoff criteria. That keeps the R-free value unbiased. If culling R-free is required for proper error analysis, or just because the culled data are almost certainly bogus values, then the un-culled R-free could be a separate value. Now days, most people use a sigma cutoff of zero, so it is normally not a big problem. However, it appears that PHENIX still throws out many reflections where Fobs==0, which can be a significant fraction in the last shell with anisotropic data. Unfortunately, the exclusion of weak reflections depends on how amplitudes were derived. If using CCP4 Truncate, those weak reflections will be inflated a bit to a non-zero value, and a zero-sigma cutoff will have a significantly different affect. Therefore, I think that the default should be to use reflections with Fobs==0, with SigFobs > 0 as the criterion for non-absent reflections in reflection files without a missing number flag (i.e. CNS format). Joe Krahn

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cif_as_mtz : column labels
by Bryan W. Lepore 10 Dec '09

10 Dec '09

a .cif has a bunch of labels (see below). the output .mtz has three: FOBS, SIGFOBS, R-free-flags ... without getting anyones' hands dirty, are the F's merged from the four correct columns, viz. F_plus, F_minus, (and sigmas)? -bryan (for pdb code, pls. off-list) labels in .cif : _refln.F_meas_au _refln.F_meas_sigma_au _refln.F_calc _refln.phase_calc _refln.pdbx_F_plus _refln.pdbx_F_plus_sigma _refln.pdbx_F_minus _refln.pdbx_F_minus_sigma _refln.pdbx_HL_A_iso _refln.pdbx_HL_B_iso _refln.pdbx_HL_C_iso _refln.pdbx_HL_D_iso

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Clearing old NCS group definitions
by John Pascal 09 Dec '09

09 Dec '09

Hello, I am using NCS restraints in phenix.refine, and I am defining the restraints in a parameter file that I read into the GUI interface. After modifying the ncs parameters file, I see in the log file that phenix.refine has used the updated NCS groups, but also retains the old restraints settings. Therefore, the number of NCS groups doubles each time I make an edit. Is there a way to erase the previous NCS restraints? I see that the restraints are accumulating in the project_data/*.eff files. Are those read in by default on consecutive runs? I am probably missing something obvious, but I would appreciate any advice. Thanks. Best, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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