December 2014 - phenixbb - phenix-online.org

labelit distl_minimum_number_spots_for_indexing
by Christian Roth 22 Sep '15

22 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

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Refinement with new mtz.file
by Aleksandar Bijelic 14 Jul '15

14 Jul '15

Dear CCP4 user and experts, I refined (with PHENIX) a 3.0 A dataset obtaining Rfree of about 0.24 (with good geometry according to Ramachandran, Beta Outliers, etc.) .... Everything seems to be ok (especially in relation to the resolution) .... because the mtz.file I used was quite old and I cannot find my xscale.hkl file, I processed the data set again (this time with optimizng and polishing) and received a "better" file according to almost everything (resolution limit, I/sigma, CC(1/2), Rmeas), thus I used this new mtz.file and put it in my last refinement step (the refinement which led to the above mentioned Rfree = 0.24). Suprisingly, the refinement starts at Rwork = 0.18 and Rfree = 0.19 but ending up with 0.20 and 0.22, respectively. So I wanted to know if this is usual? I was expecting my data to become slightlly better but what is irritating me is the starting R-values of the refinement and that it get worse during refinement. Maybe I did something wrong? Is it reasonable to replace the mtz.file with a new one in the last refinement step or should I start the refinement from the scratch? In the sake of completeness, I deleted the header of the used pdb.file because of the R-flag error which occurs, since Phenix reconizes that the pdb.file was already used with other Rflags. Sorry, but I am still a beginner in this field, so I would be very grateful if somebody could explain me this situation and my mistake and if I need to start refinement from the beginning. Thank you in advance! Best Regards. Aleksandar -- ------------------------------------------- Aleksandar Bijelic, MSc. Institut für Biophysikalische Chemie Universität Wien Althanstrasse 14 A-1090 Wien Tel: +43 1 4277 52536 e-Mail: aleksandar.bijelic(a)univie.ac.at --------------------------------------------

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FEM maps
by Colin Levy 05 Jan '15

05 Jan '15

Dear All, when using FEM maps I notice that some solvent structure has clean (ish) 2Fo-Fc but not FEM density. Is this indicative of the water without FEM density being simply noise or is it more complicated than that? Many thanks, Colin Manchester Protein Structure Facility Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 c.levy(a)manchester.ac.uk<mailto:[email protected]>

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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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