June 2011 - phenixbb - phenix-online.org

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 21 Jun '11

21 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 20 Jun '11

20 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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tls group and anisotropic
by ChenTiantian 17 Jun '11

17 Jun '11

Dear Phenixers, I refined my structure with TLS, I did not mean to refine it with anisotropic strategy, but I got ANISOU record. As the manual metioned, when doing TLS refinement, It always happens like this. What does this ANISOU record mean ? Does that mean TLS is a grouped anisotropic refinement? Tiantian -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

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no density on the anchored proteins
by zhangh1＠umbc.edu 16 Jun '11

16 Jun '11

Hi, I am using phenix.refine to calculate the map of the 50S RNA (1FFK). It is weird that there is no density on the anchored proteins even for the Fc map. Following is the code I am using: phenix.refine ${f}.pdb ${f}.mtz main.number_of_macro_cycles=0 xray_data.high_resolution=${res} xray_data.r_free_flags.generate=True export_final_f_model=mtz Thanks for any advice! Hailiang

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Re: [phenixbb] rosetta fragment files -- adjusting residue numbers to combine them
by Thomas C. Terwilliger 16 Jun '11

16 Jun '11

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 >> [phenixbb-bounces(a)phenix-online.org] On Behalf Of Leonid Sazanov [sazanov(a)mrc-mbu.cam.ac.uk] >> Sent: 16 June 2011 13:11 >> To: phenixbb(a)phenix-online.org >> Subject: [phenixbb] rosetta fragment files >> >> Hi, I am trying to use mr_rosetta with phenix-1.7.1-743 and rosetta 3.2.1. All rosetta tests passed OK. >> I have several large protein chains in the starting model (already placed). >> So I had to get several pairs of fragment files from robetta server and list all of them in the script. >> Then mr_rosetta fails at the REBUILD_1 stage with the message: >> could not open file (fragment file), although file is definitely there. Is the reason that one can have only two input fragment files (3/9)? Can several fragment files be combined into two 3/9 ones? >> Thanks >> >> -- >> Dr. Leonid A. Sazanov >> Research group leader >> Medical Research Council >> Mitochondrial Biology Unit >> Wellcome Trust / MRC Building >> Hills Road >> Cambridge >> CB2 0XY >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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