- phenixbb - phenix-online.org

tools to obtain ADP?
by Jason 06 Apr '11

06 Apr '11

Hi, Is there a convenient tool to obtain ADP for each chain or ligand or a selective group? phenix.model_vs_data only gives an averaged ADP for everything and it takes really long. Thanks. ====================== Jason Structural Biology Department University of Pittsburgh ======================

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Question about anisotropic refinement
by Louis Lazar 06 Apr '11

06 Apr '11

I have several structures that I am refining (~1.05A), and I have a question about anisotropic refinement. I have read a couple things about whether or not to refine waters anisotropically, as opposed to hydrogen, which I never refine anisotropoically. I am wondering what the general consensus is on it, and if anyone has anything from the archives (I'm having trouble searching through) or papers that I should read, please don't hesitate to let me see them. Thanks very much in advance Regards, Louis

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Ligand conformations.
by Yuri 06 Apr '11

06 Apr '11

Has anyone ever reported seeing 2 different binding confromations for a ligand that was soaked vs. the same ligand co-crystallized? -- Yuri Pompeu

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How to fix c-beta deviation?
by Jason 06 Apr '11

06 Apr '11

Hi, I have tried to regularize my protein structure in coot and use ramachandran restrain to improve statistics (and then release them). However, I can not make the c-beta deviation be zero. Is there some special way to improve c-beta deviation? Thanks. ====================== Jason Structural Biology Department University of Pittsburgh ======================

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B-factors vs resolution
by Yuri 06 Apr '11

06 Apr '11

I am refining a 1.3 A structure the maps look great and I notice the main chain B factors are all around 7~12. I have refined the same enzyme at resolution 2.2 A and the B factors here were around 25~30. The question that comes to mind is: Usually one will describe ordered parts of a protein vs disordered parts based on B factors. Is the higher resolution protein more ordered and that may have contributed to its stronger diffraction? Or are the B factors values artifacts of refinement? -- Yuri Pompeu

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why are my B factors being "refined"
by Scott Classen 05 Apr '11

05 Apr '11

Hello Phenix community, I'm currently using nightly build 718, but this behavior is exhibited since sometime in the 1.6.xx releases too. I've turned off ADP refinement (only doing rigid_body refinement) and set the b_iso specifically as such: modify_start_model { selection = None adp { atom_selection = None randomize = None set_b_iso = 55 convert_to_isotropic = None convert_to_anisotropic = None shift_b_iso = None scale_adp = None } Yet the output PDB file has all b-factors in the 100s. Whazzup with that? Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 sibyls.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Modeling Disordered Domains
by Damian Ekiert 05 Apr '11

05 Apr '11

Perhaps inspired by the fierce debate on this BB and elsewhere about how to model disordered side chains, I would like to present the following scenario (my current refinement project): The structure was solved by molecular replacement, is 3.25Å resolution, and ~70% solvent. I have 6 copies of a large complex in the AU (~100kDa per protomer). Only one copy is fully ordered. In the other 5 copies, a entire domain (~25kDa) is largely disordered (some have patchy residual density, but not readily interpretable). Altogether, this means that I am missing ~20% of the total protein in the AU. It seems that how you model this much "missing" material could have a significant effect on the final refined model. This is something we have observed a number of times, so I am wondering if anyone can suggest ways to deal with this aside from just leaving the domains out entirely. In this case, the missing domain is connected by two short hinges that restrict the rotational degrees of freedom considerably (you can think of the missing domains as a door--it can only pivot about the hinge, can't be flipped upside-down or sideways, etc., and is anchored close to the door frame). Additionally, crystal packing and steric constraints restrict the "sweep" of the missing domains to further pinpoint their location. Is it worth trying to model this? My impression from some earlier posts was that most people were content for disordered regions to be modeled as bulk solvent (rather than fiddling with masks to also cover the expected location of protein, etc.), but I wonder if you may actually substantially improve the model when this much protein is disordered. I guess I am imagining something analogous to a rigid body fit to the mean position of the disordered domains and a TLS-like ADP description of the motion (with a very large magnitude to account for the large displacement), but I am open to suggestions. On a final note, regarding those pesky missing side chains: any thoughts on trying to employ a "Ringer"-like approach to model some of these (Fraser, et al., Nature 2009, 462(7273):669-673)? Is this practical (maybe this would add to many additional parameters)? Best, Damian Ekiert

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Re: [phenixbb] occupancy on a special position
by Maia Cherney 05 Apr '11

05 Apr '11

Hi, I have a water on a two fold axis, I gave it occupancy 0.50, but the program makes it 1.0. I know this was discussed before, but we have to abide by the PDB rules, that is to have this occupancy =0.5. Could you please, fix this problem. Maia

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Question about structure quality
by Jason 05 Apr '11

05 Apr '11

Hi, I have a refined structure with phenix. The resolution=3.8 angstrom. Molprobity analysis shows following. Can anyone tell me if the structure is acceptable or I need to do something to improve it before going to publication? Thanks. Poor rotamers20.95%Goal: <1%Ramachandran outliers6.15%Goal: <0.2%Ramachandran favored80.13%Goal: >98%Cβ deviations >0.25Å23Goal: 0Residues with bad bonds: 0.00%Goal: 0%Residues with bad angles:0.75% -- ====================== Jason Structural Biology Department University of Pittsburgh ======================

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download Phenix in Windows vista platform
by Bhuiya, Mohammad 05 Apr '11

05 Apr '11

-------- WARNING: At least one of the links in the message below goes to an .exe file, which could be malicious. To learn how to protect yourself, please go here: http://www.lbl.gov/cyber/services/suspicious-links.html -------- Hi I am a new user in Phenix mailing list. I want to download Phenix in Windows Vista platform to refine structure. I selected 32-bit (Windows XP or newer) [download .exe <https://www.phenix-online.org/download/phenix/nightly/send_octet_stream.cgi…> ] and run it (Phenix version 1.7). I got a new windows with command line (c:/.) UnZipSFX 5.50 of 17 february, by Info-ZIP (ZIP-Bugs(a)list.wku.edu <mailto:[email protected]> ). Replace cci_apps_sources/antlr3/antlrconfig.h.in? [y]es, [n]o, [A]ll------------ I don't know what I should do to install the program, though I used yes/all but it doesn't work. I will appreciate if you help me to install Phenix in Windows Vista platform. Thank you. Wadud

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