- phenixbb - phenix-online.org

Difference Map positive peaks in release dev-798
by Yuri 25 Jun '11

25 Jun '11

Pavel, I just ran the same job using the last official release (743). Some differences: >When the change occurred (between which version numbers)? Some where in between 743 and dev-798. >Does the peak disappear if you do the same calculation using an older > version? Yes, I see no positive or negative peaks for the Mg ion (nor my ligand). >There is no general remedy - it's all case-dependent. >Does its B-factor differ significantly from surrounding atoms? Yes, the B-factor for the ligand is 20 on average. The surrounding residues and cofactor are 10 or below. But, as I mentioned above, I see no positive peak density this time around. -- Yuri Pompeu

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NCS error in Phenix 1.7.1-743
by Ngan Nguyen Bich 24 Jun '11

24 Jun '11

Dear all, I've got a problem when rerunning the same job of my project in the new laptop. I've found that it's because of the NCS restraint groups set-up In the old computer I set two NCS restraints groups as: First group: Reference group: chain A and sidechain and resid 3:216 and not (resid 63 or resid 66 or resid 81 or resid 93 or resid 133 or resid 135 or resid 181 or resid 184 or resid 193 or resid 194 or resid 212) Second group: Reference group: chain A and backbone and resid 3:217 and not (resid 63 or resid 133 or resid 135 or resid 184) And the refine_phenix run well in the old computer, but the new laptop with the error in the end of this letter. I've found that if I delete the backbone in the second group, it runs again. So I wonder that how I could refine NCS restraint of backbone now? Thank you in advance. Ngan RuntimeError : mean() argument is an empty array Traceback: File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/libtbx/thread_utils.py", line 223, in run return_value = self._target(self._args, self._kwargs, self._c) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/libtbx/runtime_utils.py", line 58, in __call__ result = self.target() File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/phenix/refinement/runtime.py", line 68, in __call__ call_back_handler=callback) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/phenix/refinement/command_line.py", line 89, in run call_back_handler=call_back_handler) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/phenix/refinement/driver.py", line 1278, in run reference_model_manager = self.reference_model_manager) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/phenix/refinement/strategies.py", line 322, in refinement_machine monitors.collect(step = "0 :", model = model, fmodels = fmodels) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/refinement/__init__.py", line 51, in collect rigid_body_shift_accumulator = rigid_body_shift_accumulator) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/refinement/print_statistics.py", line 263, in collect ignore_side_chain = True, File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/model.py", line 971, in geometry_statistics restraints_manager = self.restraints_manager) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/model_statistics.py", line 38, in __init__ compute_gradients = True) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/restraints.py", line 66, in energies_sites normalization=False) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/ncs/restraints.py", line 686, in energies_sites self.compute_operators(sites_cart=sites_cart) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/ncs/restraints.py", line 679, in compute_operators self.operators.append(group.operators(sites_cart=sites_cart)) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/ncs/restraints.py", line 336, in operators return _operators(group=self, sites_cart=sites_cart) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/mmtbx/ncs/restraints.py", line 442, in __init__ other_sites=sites_cart.select(pair[1])) File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/cctbx_project/scitbx/math/superpose.py", line 58, in __init__ self.reference_shift = reference_sites.mean() Platform info: __FILE__ = /net/patchnose/scratch1/phenix/phenix-1.7.1-743/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Apr 28 2011 __TIME__ = 02:15:10 __i386__ __APPLE_CC__ = 5367 __GNUC__ = 4 __GNUC_MINOR__ = 0 __GNUC_PATCHLEVEL__ = 1 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __VERSION__ = 4.0.1 (Apple Computer, Inc. build 5367) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 __SSE2__ = 1 BOOST_LIB_VERSION = 1_47 PY_VERSION = 2.7.1 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 4 sizeof(std::size_t) = 4 sizeof(void*) = 4 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 16 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG os.name<http://os.name>: posix sys.platform: darwin sys.byteorder: little platform.platform(): Darwin-10.7.4-x86_64-i386-32bit platform.architecture(): ('32bit', '') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 4 Memory total: 4,294,967,296 Memory free: unknown import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = √Ö

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B-factor and phenix.refine+Occ+charge
by Haytham Wahba 23 Jun '11

23 Jun '11

June 23, 2011, 9:30 AM Dear all dimer in AU average B factor 21 resolution: 1.78 each subunit shows 2 Tin atoms in the active site B factor for 2 tin in chain A 15 and 19 but B factor for other 2 tin in chain B 30 and 41 41 for tin which is between the 2 cysteine (photo attached) (occ: 0.25) this one which i am worry about ((because the average B factor for the surrounding amino acid is 20)) and 30 of the other one near phoshate (occ: 0.70) 1- i tried to change the occupancy or refine the occupancy for tin trying to reduce B factor (41) it works (reduced to 30) but it gives me a +ve peak what could i do to solve this problem?? 2- other trial to define charge for that tin HETATM 3241 SN SN C 3 6.543 -2.139 -14.821 0.25 41.55 SN4+ but it was the same result. --- is this definetion for that charge is OK or it is not enough in PDB file --- is this way is understandable by phenix.refine? i mean does phenix differentiate in refinment between SN, SN2+ and SN4+?? N.B: protein soaked in DimethylTindiBromide Haytham Wahba Biochemistry UdeM Canada

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Re: [phenixbb] rosetta fragment files (Thomas C. Terwilliger)
by Leonid Sazanov 21 Jun '11

21 Jun '11

Hi Tom, Thanks for that! Native support for several large chains would be very useful. Leonid > Message: 3 > Date: Thu, 16 Jun 2011 13:24:55 -0600 (MDT) > From: "Thomas C. Terwilliger"<terwilliger(a)lanl.gov> > To: "PHENIX user mailing list"<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] rosetta fragment files -- adjusting residue > numbers to combine them > Message-ID:<50912.128.165.72.7.1308252295.squirrel(a)webmail.lanl.gov> > Content-Type: text/plain;charset=iso-8859-1 > > Hi Leonid and others wanting to use phenix.mr_rosetta with large chains, > > After looking at the Rosetta code and conferring with Frank DiMaio from > the Baker laboratory... > > You can paste several fragment files together to represent your entire > chain, but you need to edit all but the first one to set the position in > the sequence file that each set of fragments goes with. > > Here is a little script that will take a fragments file that you have > created that started with residue 651 and edit it in a way that you can > just add to the end of your fragments file for residues 1-650. Run it > with: > > phenix.python adjust_robetta_resid.py \ > fragments_in fragments_adjusted 651 > > -------------------------------- > # adjust_robetta_resid.py > # use: phenix.python adjust_robetta_resid.py fragments_in > fragments_adjusted 651 > # to adjust the first residue of fragments_in to be 651 > > import sys > args=sys.argv[1:] > if len(args) != 3: > print "USE: phenix.python adjust_robetta_resid.py fragments_in > fragments_adjusted<start_resno>" > sys.exit() > file_in=args[0] > file_out=args[1] > start_resno=int(args[2]) > > print "Copying %s to %s offsetting start residue number to %d" %( > file_in,file_out,start_resno) > > f=open(file_out,'w') > new_resno=0 > for line in open(file_in).readlines(): > if line.find('position:')> -1 and line.find('neighbors:')>-1: > spl=line.split() > current_resno=int(spl[1]) > new_resno=current_resno+start_resno > print "Residue %d changed to %d" %(current_resno,new_resno) > spl[1]=" %d " %(new_resno) > new_line=" ".join(spl) > else: > new_line=line > print>>f, new_line.rstrip() > > f.close() > -------------------------------- > > I will add this to phenix as "phenix.adjust_robetta_resid" as well. > > > However...there still is a problem if you have multiple chains...as > mr_rosetta has only one set of fragments files the same fragments files > are being applied to all your chains. I will add a way to specify which > fragments files go with which chains. > > All the best, > Tom T >

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scattering factors
by Goragot Wisedchaisri 20 Jun '11

20 Jun '11

Hi, I am new to Phenix but I have used Solve/Resolve in the past. I am currently using Phenix 1.6.2 and I have electron diffraction data to ~2A from a 300kV electron microscope that I would like to use Autobuild and phenix.refine to iteratively rebuild and refine my partial structure. I have a file containing electron scattering factors for 300kV EM that has been used successfully for refinement with CNS before for electron diffraction data. How can I tell Phenix to use electron scattering factors during refinement? I think currently Phenix has 4 choices for X-ray and neutron scattering factors but not for electron scattering. Is there a good way to implement electron scattering factors into phenix library? Any suggestions are welcome. George Wisedchaisri

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phenix.validate ? Or RSCC from command line?
by Francis E Reyes 20 Jun '11

20 Jun '11

Phenixers Is there a great phenix cmd line utility that computes a real space correlation for each residue given model and data? I'll take a .py if necessary. Thanks! --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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Errors in latest build dev-790
by Yuri 19 Jun '11

19 Jun '11

Dear phenixers, I ran into some errors after my last upgrade. First, I noticed that all of the data plots are gone in the GUI, instead I get a message that says :plotting disabled due to missing library. Second I was running phenix.refine and got the following message, they may be related I am not positive: AttributeError : 'RefinementStatsPlot' object has no attribute 'null_fmt' Traceback (most recent call last): File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-790/phenix-dev-790/phenix/wxGUI2/Runtime.py", line 172, in OnUpdate self.propagate_event(event, "OnUpdate") File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-790/phenix-dev-790/phenix/wxGUI2/Runtime.py", line 228, in propagate_event fn(event) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-790/phenix-dev-790/phenix/wxGUI2/Programs/Refine/Output.py", line 536, in OnUpdate self.stats_plot.update_stats(callback.data) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-790/phenix-dev-790/phenix/wxGUI2/Programs/Refine/Output.py", line 796, in update_stats stats.bs_ave) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-790/phenix-dev-790/phenix/wxGUI2/Programs/Refine/Output.py", line 809, in set_plots ax1().xaxis.set_major_formatter(self.null_fmt) AttributeError: 'RefinementStatsPlot' object has no attribute 'null_fmt' Platform info: __FILE__ = /net/anaconda/scratch1/phenix/phenix-dev-790/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Jun 17 2011 __TIME__ = 04:12:36 __x86_64__ __linux __GNUC__ = 3 __GNUC_MINOR__ = 4 __GNUC_PATCHLEVEL__ = 2 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __LP64__ = 1 __VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 __SSE2__ = 1 BOOST_LIB_VERSION = 1_47 PY_VERSION = 2.7.2 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 8 sizeof(std::size_t) = 8 sizeof(void*) = 8 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 16 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 gnu libc version: 2.5 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG os.name: posix sys.platform: linux2 sys.byteorder: little platform.platform(): Linux-2.6.18-238.12.1.el5-x86_64-with-redhat-5.6-Tikanga platform.architecture(): ('64bit', 'ELF') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 2 Memory total: 3,692,077,056 Memory free: 16,236,544 import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Å -- Yuri Pompeu

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phenix.model_vs_data
by Yuri 17 Jun '11

17 Jun '11

I just realized it is under Comprehensive Validation! -- Yuri Pompeu

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phenix.model_vs_data
by Yuri 17 Jun '11

17 Jun '11

> I would refine in parallel with and without the twin law and check > the > resulting maps and R-factors. > I had a case where the twin fraction was 0.06, which I expected to be > negotiable. When I included the twin law in refinement, my R-factors > dropped dramatically. >This is what phenix.model_vs_data does: it runs Xtriage internally and >tries all suggested twin laws, scores the results by R-factor and > prints >out the verdict: >phenix.model_vs_data model.pdb data.mtz >phenix.model_vs_data: >http://phenix-online.org/documentation/model_vs_data.htm >Pavel. Is this accomplished in polygon in the GUI? -- Yuri Pompeu

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General Questions about Joint x-ray/neutron refinement
by Louis Lazar 17 Jun '11

17 Jun '11

Developers/all: I have been running some Joint X/N jobs, and I have some questions that perhaps you can help me with. First, doing joint refinement gave a total of 53 waters (thanks to ordered_solvent=true), yet the electron density seems to show that there are several more waters that are actually present (however it should be noted that there is no nuclear density associated with those waters, and in some cases no nuclear density associated with the 53 that were chosen by ordered_solvent=true). Should I add in manually to the electron density what I believe are these extra waters, or simply ignore them? Second, when I try to real space refine any of the residues, I get an error message telling me about exploding atoms. What is the cause of this message, and is it possible to real space refine any of these residues and specifically the hydrogen atoms associated with them. Third, during the joint refinement run, I chose to refine occupancies of all atoms. This breaks down into several questions: A) Should I be refining occupancies at 2.0 A resolution (of the neutron structure; 1.05A for the X-ray)? B) How does Phenix go about refining occupancies of hydrogen/deuterium sites? C) If the resulting occupancies result in values of, for example, 60% deuterium and 40% hydrogen, am I to presume that deuterium presence is significant if the nuclear density looks "good". At what point of deuterium occupation (while examining the nuclear density), would I say that there is likely no deuterium present (or that it is insignificant)? Hopefully all of these questions make sense, and if I need to clarify anything, please let me know. Thanks so much in advance for the help, I appreciate it as always. Regards, Louis

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