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a command on Phenix refine
by Wind Sui 04 Jan '15

04 Jan '15

Dear All, I use the graphic phenix.refine to do a refinement, and Phenix informed me I need to have a command "refinement.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None". Will you please tell me by graphic phenic.refine, how can I input this command? Wind

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a question related to phenix.refine
by Wind Sui 04 Jan '15

04 Jan '15

Dear All, After I finished a refinement by Phenix.refine and I closed the Phenix software, is any method I can get the exact phenix.refine window as the moment the Phenix.refine just finished the refinement? I mean by all the documents saved automatically by the Phenix.refine after it finished a refinement, how can I get the Phenix refine window once more, for the check of Log output, Run status, Results, MolProbity, Real-space correlation, Atomic properties, and sequence check? Wind

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Fw: Reading a shelx file
by Rex Palmer 25 Dec '14

25 Dec '14

Can I read a Shelx file with Phenix and output the new pdb in Phenix format? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com

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Announcement: Membrane Protein Structures 2015 Meeting (MPS 2015)
by Nagarajan Venugopalan 22 Dec '14

22 Dec '14

Posted on behalf of the organizing committee: Registration is now open for Membrane Protein Structures 2015 Meeting (MPS 2015) Location: Argonne National Laboratory, Lemont, IL, USA Dates: April 10 - 12, 2015 Accompanying workshops: Membrane Protein Technologies Location: Argonne National Laboratory, Lemont, IL, USA Date: April 9, 2015 Meeting WEBsite: http://aps.anl.gov/mps2015. _Important dates_: _Registration deadline_: February 15, 2015 (https://www.regonline.com/mps2015) _Accommodation deadline_: March 10, 2015 (http://www.aps.anl.gov/Users/Communications/User_News/2014/MPS_hotel_info.p…) Thanks Naga -- ************************************************************************ Nagarajan Venugopalan, Ph.D. GM/CA@APS, Sector 23, X-ray Science Division Bldg 436, D005 Argonne National Laboratory 9700 S Cass Ave, Argonne IL 60439 Tel: 630-252-0669 Fax: 630-252-0667 email: vnagas(a)anl.gov ************************************************************************

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29th European Crystallographic Meeting
by Igor Sabljić 22 Dec '14

22 Dec '14

Dear Phenixbb users, I am delighted to tell you the registration for the 29th European Crystallographic Meeting is open. Just to remind you ECM29 (August 23-28, 2015) is taking place in beautiful city of Rovinj in Croatia. You can find more information on our web site, and please visit, like and share our Facebook page! I hope I will see you all there! Web: http://ecm29.ecanews.org/ Facebook: https://www.facebook.com/29thEuropeanCrystallographicMeeting?ref=hl Sincerely, Igor [1] IGOR SABLJIĆ _Social networks editor_ Ruđer Bošković Institute Division of Physical Chemistry Bijenička cesta 54, 10000 Zagreb, CROATIA http://ecm29.ecanews.org [1] Facebook [2] home [3] Links: ------ [1] http://ecm29.ecanews.org [2] http://www.facebook.com/29thEuropeanCrystallographicMeeting [3] http://www.irb.hr/eng/Research/Divisions-and-Centers/Division-of-Physical-C…

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Phenix Rosetta install
by Felipe Trajtenberg 22 Dec '14

22 Dec '14

Dear all, I am trying to build the hybrid installation between Rosetta and Phenix using the rosetta.build_phenix_interface command Phenix version: phenix-1.9-1692 Rosetta version: rosetta_2014.35.57232 I have no problem in compiling rosetta alone but when I try to build the hybrid system I get the following error: False scons: Reading SConscript files ... Running versioning script ... Done. (0.0 seconds) Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1: File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/SConstruct", line 172: main() File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/SConstruct", line 163: SConscript("SConscript", "build") File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614: return method(*args, **kw) File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551: return _SConscript(self.fs, *files, **subst_kw) File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260: exec _file_ in call_stack[-1].globals File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/SConscript", line 28: subprocess.check_call(["./update_options.sh"]) File "/home/Xtal/Phenix/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 540: raise CalledProcessError(retcode, cmd) thanks in advance Felipe

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Cross-validation when test set is miniscule
by Derek Logan 19 Dec '14

19 Dec '14

Hi everyone, Right now we have one of those very difficult Rfree situations where it's impossible to generate a single meaningful Rfree set. Since we're in a bit of a hurry with this structure it would be good if someone could point me in the right direction. We have crystals with 1542 non-H atoms in the asymmetric unit that diffract to only 3.6 Å in P65, which gives us a whopping 2300 reflections in total. 5% of this is only about 100 reflections. Luckily the protein is only a single point mutation of a wild type that has been solved to much better resolution, so we know what it should look like and I simply want to investigate the effect of different levels of conservatism in the refinement, e.g. NCS in xyz and B, group B-factors, reference model, Ramachandran restraints etc. However since the quality criterion for this is Rfree I'm not able to do this. I believe the correct approach is k-fold statistical cross-validation, but can someone remind me of the correct way to do this? I've done a bit of Googling without finding anything very helpful. Thanks Derek ________________________________________________________________________ Derek Logan tel: +46 46 222 1443 Associate Professor mob: +46 76 8585 707 Dept. of Biochemistry and Structural Biology www.cmps.lu.se<http://www.cmps.lu.se> Centre for Molecular Protein Science www.maxlab.lu.se/crystal Lund University, Box 124, 221 00 Lund, Sweden www.saromics.com

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Mac backwards compatability
by Katherine Sippel 19 Dec '14

19 Dec '14

Hi all, I was trying to be a good child and update to the latest nightly build, but I noticed that the Mac options for dev-1893 and -1894 are all listed as OS X 10.9 rather than OS X 10.6.7+. I attempted to use the OS X 10.9 installer just to see if it would work (it does not). Is phenix no longer supporting older Mac OSs? I know you have more than enough OSs to keep track of, so there is no judgement in that statement. I am just trying to figure out if I am going to have to cave and begrudgingly update my OS. Thanks, Katherine -- "Nil illegitimo carborundum"* - *Didactylos

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secondary restraint refinement
by CPMAS Chen 17 Dec '14

17 Dec '14

Dear Phenix Users, How do I force some residues in a non-helix conformation? I have a 3A data, and have the protein model refined. But in some region, 3~4 residues are in the helix conformation, and the density fit is good. Anyway, let me say this, I want to force these residues in a non-helix conformation. I tweaked the model a little bit and load them in VMD, and make sure they are not helix anymore. I turn on secondary-structure-restraint in phenix, take out the helix remarks for these residues in the def file. but once the refinement is done, they are still in a helix region (phenix automatically secondary structure analysis, or viewed in VMD). Is there a feasible way to keep them away from helix conformation? Thanks! Charles -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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number of alternate conformations allowed
by Scott Horowitz 17 Dec '14

17 Dec '14

Hi all, Does anyone happen to know the upper limit on the number of alternate conformations that phenix.refine can handle at once for a residue? From playing around with it, it seems that phenix.refine recognizes both letters and numbers in that position, but not a pound sign, so that would suggest it could at least handle 36, so long as I don't crash my computer trying that many. Is this correct, from anyone's experience/knowledge? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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