- phenixbb - phenix-online.org

Re: [phenixbb] B-factors vs resolution
by miket＠chem.ucla.edu 07 Apr '11

07 Apr '11

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? -- Are the two crystals with different max resolution isomorphous? B-factors contain contributions from both dynamic and static disorder. Your difference in b-factors and resolution are both likely due to the fact that your higher-resolution data comes from a more ordered crystal, not a less dynamic protein. More ordered crystals diffract better, but if the two crystals were grown in the same conditions and the crystals are isomorphous I doubt that there is any difference in the dynamics of the molecules. If you are interested in which parts of your protein are more dynamically disordered you may want to consider (within a single dataset) which atoms have high b-factors relative to the average b-factor for all the atoms in that dataset. Mike -- 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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tools to obtain ADP?
by Jason 07 Apr '11

07 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 07 Apr '11

07 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 06 Apr '11

06 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 06 Apr '11

06 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 06 Apr '11

06 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 06 Apr '11

06 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 06 Apr '11

06 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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ICSG 2011 May 10-14, 2011, Toronto
by Thomas C. Terwilliger 04 Apr '11

04 Apr '11

Dear Colleagues, We hope that you are planning to join us in Toronto, Canada for the International Conference on Structural Genomics 2011 which will be held on May 10-14, 2011. We have an excellent scientific program prepared which includes both oral and poster presentations (please see: http://www.icsg2011.org/scientific_program.php ). Participants will also enjoy the fabulous view of the city of Toronto during the banquet to be held at the revolving 360 Restaurant at the top of the CN tower. An optional post-conference tour to Niagara Falls will also be available. We invite you to register on line by April 15, 2011 at 11:59 pm EST. A limited number of late poster abstracts will be accepted until April 12, 2011 at 11:59 pm EST In addition to the main ICSG meeting, there will be a whole day of concurrent satellite workshops (May 10, 2011) that are free for ICSG 2011 registrants, including: Small Molecule Screening Workshop- This hands-on workshop will allow participants to screen a protein of their choice for binding of selected compounds, using thermal shift assays. iSee: Interactive 3D Documents for the Dissemination of Structural Biology - This hands-on workshop will familiarize participants with the iSEE 3D graphical software which allows interactive viewing of 3 dimensional molecular structures and is currently used by journals such as Nature Structural & Molecular Biology and PLoS Biology and PLoS ONE Eukaryotic Gene Expression Systems Workshop - This workshop will provide participants with a detailed understanding of the state-of-the-art for production of eukaryotic proteins destined for biochemical, biophysical, and structural analyses.. Workshop on NMR Methods for Structural Biology- This workshop will survey technologies for structure/function investigations of proteins, developed in (or in collaboration with) structural genomics projects, that are ready for widespread use by the wider biological community. Phenix Crystallography Software Workshop - This workshop will introduce the PHENIX software for macromolecular structure determination and the core algorithms that it uses. It will provide hands-on tutorials for crystallographers of all levels. The workshop registration deadline is Monday April 11, 2011 at 11:59 pm EST Please visit http://www.icsg2011.org <http://www.icsg2011.org/> for ICSG 2011 meeting and workshop registration details and to submit your poster abstract. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee

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Re: [phenixbb] why are my B factors being "refined"
by Scott Classen 04 Apr '11

04 Apr '11

On Apr 4, 2011, at 12:50 PM, Phil Jeffrey wrote: > Average coordinate B of 100++ might suggest worse than 3.5 Angstrom data. aha! …. Yes, you are correct. : ) I'm struggling with some low res. data. Mainly doing rigid body refinement of various pieces and individual xyz for a few select loops, but NOT refining ADP. Yes, The B-factors are all exactly the same. So I guess this represents the overall B correction. Thanks, Scott

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Mac 64-bit kernel
by Joseph Noel 04 Apr '11

04 Apr '11

Nope. I've set up to always run the 64-bit kernel. I am a bit of a Mac lover so go pretty in depth with the operating system. I think Nat fixed things. For the last many latest builds, I have always installed from the source files for linux/mac to ensure I am running at maximum memory capacity. ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/noel.html Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________ On Apr 4, 2011, at 11:27 AM, phenixbb-request(a)phenix-online.org wrote: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Re: nqh_flips (Pavel Afonine) > 2. latest 64-bit command line build for Mac OSX 10.6.7? (Joseph Noel) > 3. Re: latest 64-bit command line build for Mac OSX 10.6.7? > (Engin ?zkan) > 4. Re: latest 64-bit command line build for Mac OSX 10.6.7? > (Nathaniel Echols) > 5. Re: latest 64-bit command line build for Mac OSX 10.6.7? > (Ben Eisenbraun) > 6. Re: latest 64-bit command line build for Mac OSX 10.6.7? > (Nathaniel Echols) > 7. Minor map-definition bug in 1.7 GUI (Joe Krahn) > 8. bug report- gui freezed (Kendall Nettles) > 9. Re: bug report- gui freezed (Nathaniel Echols) > 10. Re: Minor map-definition bug in 1.7 GUI (Nathaniel Echols) > 11. Re: latest 64-bit command line build for Mac OSX 10.6.7? > (Nathaniel Echols) > 12. Re: latest 64-bit command line build for Mac OSX 10.6.7? > (Ben Eisenbraun) > 13. Re: latest 64-bit command line build for Mac OSX 10.6.7? > (Ben Eisenbraun) > 14. Modeling Disordered Domains (Damian Ekiert) > 15. Re: latest 64-bit command line build for Mac OSX 10.6.7? > (Nathaniel Echols) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 02 Apr 2011 19:27:24 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] nqh_flips > Message-ID: <4D97DB0C.9020706(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Maia, > > is the affected residue(s) listed within warning message in .log file > saying that both original and flipped version do not solve the clash? If > so, you may need to have a closer look at that residue to see what's > wrong. Otherwise, we would be interested to see the details... > > Pavel. > > > On 4/2/11 6:08 PM, Maia Cherney wrote: >> Hi, >> I just noticed that the nqh flips did not happen, even though the .def >> file has nqh_flips = True. >> >> Maia > > > > ------------------------------ > > Message: 2 > Date: Sun, 3 Apr 2011 10:57:35 -0700 > From: Joseph Noel <noel(a)salk.edu> > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] latest 64-bit command line build for Mac OSX > 10.6.7? > Message-ID: <D7EFB995-80A8-4995-973B-8FFFCC07DFB4(a)salk.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I was trying to install the latest nightly build but get error (shown after my salutation) when using the recommended procedure: > > ./install --prefix=/Applications/ > > Previously, I always installed from source so I could run the 64-bit version on Mac since I have some structures that require as much memory as possible. Should I just go back to that? It does take about an hour to install on my laptop. I assume this latest 64-bit option would significantly reduce the time for installation since I wouldn't be compiling from the source. > > Cheers! > > Joe > > ========================================================================== > PHENIX Installation > > version: dev > release tag: 718 > machine type: mac-intel-osx-x86_64 > source machine type: mac-intel-osx > OS version: osx-10.6.7 > user shell: /bin/bash > destination: /Applications/ > ========================================================================= > No binary bundles found for mac-intel-osx > bundles directory contents: > bundle-dev-718-mac-intel-osx-x86_64.tar.gz > expected one of the following: > /Users/sandiegonoels/Downloads/2011-04-03/phenix-installer-dev-718/bundles/bundle-dev-718-mac-intel-osx.tar.gz > > =============================== ERROR =================================== > No binary installer found for mac-intel-osx, installation aborted > =============================== ERROR =================================== > ___________________________________________________________ > Joseph P. Noel, Ph.D. > Investigator, Howard Hughes Medical Institute > Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics > The Salk Institute for Biological Studies > 10010 North Torrey Pines Road > La Jolla, CA 92037 USA > > Phone: (858) 453-4100 extension 1442 > Cell: (858) 349-4700 > Fax: (858) 597-0855 > E-mail: noel(a)salk.edu > > Web Site (Salk): http://www.salk.edu/faculty/noel.html > Web Site (HHMI): http://hhmi.org/research/investigators/noel.html > ___________________________________________________________ > >

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latest 64-bit command line build for Mac OSX 10.6.7?
by Joseph Noel 04 Apr '11

04 Apr '11

Hi, I was trying to install the latest nightly build but get error (shown after my salutation) when using the recommended procedure: ./install --prefix=/Applications/ Previously, I always installed from source so I could run the 64-bit version on Mac since I have some structures that require as much memory as possible. Should I just go back to that? It does take about an hour to install on my laptop. I assume this latest 64-bit option would significantly reduce the time for installation since I wouldn't be compiling from the source. Cheers! Joe ========================================================================== PHENIX Installation version: dev release tag: 718 machine type: mac-intel-osx-x86_64 source machine type: mac-intel-osx OS version: osx-10.6.7 user shell: /bin/bash destination: /Applications/ ========================================================================= No binary bundles found for mac-intel-osx bundles directory contents: bundle-dev-718-mac-intel-osx-x86_64.tar.gz expected one of the following: /Users/sandiegonoels/Downloads/2011-04-03/phenix-installer-dev-718/bundles/bundle-dev-718-mac-intel-osx.tar.gz =============================== ERROR =================================== No binary installer found for mac-intel-osx, installation aborted =============================== ERROR =================================== ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/noel.html Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Minor map-definition bug in 1.7 GUI
by Joe Krahn 04 Apr '11

04 Apr '11

The new GUI has "---" in the list of map types for phenix.refine. Users expect this to mean "don't use map definition". I think there was previously a blank menu entry that worked this way. Instead, it is written to the .def file, and the job gives an error, but otherwise works OK. Thanks, Joe Krahn

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bug report- gui freezed
by Kendall Nettles 04 Apr '11

04 Apr '11

The GUI freezes when an add dialog box is open and a job ends, launching an announcement box (..coot is starting, ready set is done...etc). I can't close either box. Using phenix-1.7-650 on a mac Kendall

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phenix.maps2mtz
by Yarrow Madrona 03 Apr '11

03 Apr '11

Hello, I am running phenix-1.7-650 and would like to generate a ccp4 map for use in pymol from an mtz. I can type: phenix.maps2mtz file.mtz but I cannot figure out how to limmit the selection to a single chain (chain A). I guess you can do this in maps.params but I wanted to keep it simple without having to use the sca file. Thank you. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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"FOM" or HL coeffs from model?
by Phoebe Rice 02 Apr '11

02 Apr '11

How can I get phenix to spit out not just PhiModel but an estimated FOM or fake HL coefficients (without experimental phases - just based on how badly my model agrees with FOBS)? And I'd like the weights in their own personal mtz column(s), not just precombined in a "weighted phi" column. In case anybody cares why, I'd like to use solvent massaging and domain-wise averaging to remove bias from a low-resolution model-phased map, preferably with DM, unless anybody has a better suggestion. I did rigid body, TLS, etc on the model in phenix, so it seems like phenix has already calculated all the info I want if I could only squeeze it out. 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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phenix.reciprocal_space_arrays: a new command line tool to get Fcalc, Fbulk, Fmask, FOM, HL, and more all in one MTZ file
by Pavel Afonine 02 Apr '11

02 Apr '11

PHENIX users: just a quick notice: starting PHENIX nightly build version dev-717 and up, a new command line tool phenix.reciprocal_space_arrays will be available. This tool takes a PDB model and a data file (in most of commonly used formats: MTZ, CNS, SHELX,...) and outputs a MTZ file containing a number of arrays that are typically used in various crystallographic calculations, such as R-factors, maps, refinement targets, etc. The output arrays include: Fmodel, Fcalc, Fmask, Fbulk, FOM, resolution, HL(input original, computed from model and combined), FB_CART (overall anisotropic scale), input Fobs and Rfree-flags and more. To run: phenix.reciprocal_space_arrays model.pdb data.mtz To see the result: phenix.mtz.dump output_file.mtz Please let me know should you have any questions, suggestions or simply find a bug! Pavel.

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low resolution map weirdness with newer releases
by Scott Classen 02 Apr '11

02 Apr '11

Something changed between build 432 and 486 that made my low resolution maps look much crappier. See attached tiff. See if you can guess which map was produced by the release 486. def file looks more or less like this (from a --diff-params): refinement { crystal_symmetry { unit_cell = top secret space_group = top secret } input { pdb { file_name = "../4_23_003.pdb" } xray_data { file_name = "../4_23.sca.mtz" labels = "4_23.sca,SIG4_23.sca" high_resolution = 3.9 r_free_flags { file_name = "../4_23.sca.mtz" label = "R-free-flags" test_flag_value = 1 } } } output { prefix = "test-486" serial = 1 } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ individual_adp group_adp tls occupancies group_anomalous sites { individual = "chain A and resseq 100:107" individual = "chain B and resseq 500:507" individual = "chain E and resseq 100:107" individual = "chain F and resseq 500:507" individual = "chain C and resseq 111:117" individual = "chain D and resseq 111:117" individual = "chain G and resseq 111:117" individual = "chain H and resseq 111:117" individual = "chain C and resseq 63:68" individual = "chain D and resseq 63:68" individual = "chain G and resseq 63:68" individual = "chain H and resseq 63:68" rigid_body = "chain A" rigid_body = "chain B" rigid_body = "chain C" rigid_body = "chain D" rigid_body = "chain E" rigid_body = "chain F" rigid_body = "chain G" rigid_body = "chain H" } } main { number_of_macro_cycles = 1 secondary_structure_restraints = True random_seed = 3141766 optimize_mask = False } modify_start_model { adp { set_b_iso = 50 } } fake_f_obs { mask { ignore_hydrogens = True } } geometry_restraints.edits { excessive_bond_distance_limit = 20 } mask { ignore_hydrogens = True } simulated_annealing { start_temperature = 300 final_temperature = 200 } target_weights { wxc_scale = 0.4 } ias { b_iso_max = 60 } secondary_structure { h_bond_restraints { substitute_n_for_h = True remove_outliers = False sigma = 0.02 h_o_distance_ideal = 2.95 h_o_distance_max = 5 n_o_distance_ideal = 2.95 n_o_distance_max = 5 } }

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omit map
by intekhab alam 01 Apr '11

01 Apr '11

Hi i generated an iterative build omit map using phenix and the output fule that i got is resolve_composite_map.mtz, but i cannot open this file in coot, what modifications do ineed to open this file in coot. Regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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Bulk solvent correction
by Ina Lindemann 31 Mar '11

31 Mar '11

Hi, I am refining two crystal structures of the same protein wtih four domains and 687 amino acids. These are the last lines form my log-files after several model building steps - protein altogether fits quite well into the density. But I am confused about these logfiles: 1.Why is there such a big difference between R values with and without bulk solvent correction and anisotropic scale? Start R-work = 0.3765, R-free = 0.5498 (no bulk solvent and anisotropic scale) Final R-work = 0.3733, R-free = 0.5509 (no bulk solvent and anisotropic scale) Start R-work = 0.2356, R-free = 0.2962 Final R-work = 0.2250, R-free = 0.2939 2. (the other structure) Why does the R value without bulk solvent and anisotropic scale decrease so much but with it remains stable? Start R-work = 0.2182, R-free = 0.2856 (no bulk solvent and anisotropic scale) Final R-work = 0.4054, R-free = 0.4223 (no bulk solvent and anisotropic scale) Start R-work = 0.2157, R-free = 0.2827 Final R-work = 0.2147, R-free = 0.2816 I would be very pleased about any helpful comments. Ina Ina Lindemann Philipps-Universität Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908

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what to do with disordered side chains
by Ed Pozharski 31 Mar '11

31 Mar '11

The results of the online survey on what to do with disordered side chains (from total of 240 responses): Delete the atoms 43% Let refinement take care of it by inflating B-factors 41% Set occupancy to zero 12% Other 4% "Other" suggestions were: - Place atoms in most likely spot based on rotomer and contacts and indicate high positional sigmas on ATMSIG records - To invent refinement that will spread this residues over many rotamers as this is what actually happened - Delet the atoms but retain the original amino acid name - choose the most common rotamer (B-factors don't "inflate", they just rise slightly) - Depends. if the disordered region is unteresting, delete atoms. Otherwise, try to model it in one or more disordered model (and then state it clearly in the pdb file) - In case that no density is in the map, model several conformations of the missing segment and insert it into the PDB file with zero occupancies. It is equivalent what the NMR people do. - Model it in and compare the MD simulations with SAXS - I would assumne Dale Tronrod suggestion the best. Sigatm labels. - Let the refinement inflate B-factors, then set occupancy to zero in the last round. Thanks to all for participation, Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs

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phenix migration
by Xtal_bb 31 Mar '11

31 Mar '11

Hi guys, I have just got a brand new iMac, to replace my MacBook, in which I used to run phenix. I have installed phenix in the new iMac, and copied the directory with all the files of my previous runs. However, what should I migrate to have the projects and previous work recognized by the fresh install? Thanks for the help, ciao s -- Sebastiano Pasqualato, PhD Crystallography Unit IFOM-IEO Campus Cogentech - Consortium for Genomic Technologies via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5172 fax +39 02 9437 5990

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