April 2011 - phenixbb - phenix-online.org

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 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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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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