- phenixbb - phenix-online.org

Phenix.refine and Unusual residues
by Haytham Wahba 28 Jun '11

28 Jun '11

Version: 1.7 Release tag: 650 Platform: intel-linux-2.6-x86_64 linux User: haytham why phenix does not recognise ACT, PO4 Sn and Br (unusual residue) as you see in this part in the Log file.. (see below) Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ACT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ACT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' SN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' SN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' SN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BR': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" SN SN E 1 " occ=0.70 residue: pdb=" SN SN E 2 " occ=0.20 --------------------------------------------------------- when i try to refine specially the Tin atom (not other, ACT,...) in coot after phenix.refine. coot display ((no restraints Found,...lablabla)) ----------------------------------------------------------- this is the PDB (what is the wrong with that) HETATM 3552 O HOH S 361 11.670 -4.327 9.559 1.00 34.14 O TER 3553 HOH S 361 HETATM 3554 OXT ACT C 1 10.133 -3.417 7.937 1.00 20.00 O HETATM 3555 C ACT C 1 9.911 -2.331 7.357 1.00 20.00 C HETATM 3556 O ACT C 1 10.897 -1.607 7.183 1.00 20.00 O HETATM 3557 CH3 ACT C 1 8.550 -1.912 6.905 1.00 20.00 C TER 3558 ACT C 1 HETATM 3559 OXT ACT C 2 10.700 -2.628 9.985 1.00 20.00 O HETATM 3560 C ACT C 2 10.962 -1.952 11.000 1.00 20.00 C HETATM 3561 O ACT C 2 11.756 -2.461 11.809 1.00 20.00 O HETATM 3562 CH3 ACT C 2 10.364 -0.601 11.240 1.00 20.00 C TER 3563 ACT C 2 HETATM 3564 SN SN E 1 6.346 -4.396 -16.894 0.70 20.00 SN TER 3565 SN E 1 HETATM 3566 SN SN E 2 6.492 -2.146 -14.779 0.20 20.00 SN TER 3567 SN E 2 HETATM 3568 SN SN F 1 10.186 0.632 6.366 1.00 30.00 SN TER 3569 SN F 1 HETATM 3570 P PO4 G 1 5.763 10.047 -3.974 1.00 30.00 P HETATM 3571 O1 PO4 G 1 6.960 10.924 -4.190 1.00 30.00 O HETATM 3572 O2 PO4 G 1 4.531 10.872 -4.101 1.00 30.00 O HETATM 3573 O3 PO4 G 1 5.758 8.978 -5.017 1.00 30.00 O HETATM 3574 O4 PO4 G 1 5.835 9.456 -2.607 1.00 30.00 O TER 3575 PO4 G 1 HETATM 3576 P PO4 G 2 9.060 -4.976 -17.812 1.00 30.00 P HETATM 3577 O1 PO4 G 2 10.418 -5.179 -18.415 1.00 30.00 O HETATM 3578 O2 PO4 G 2 8.223 -4.116 -18.710 1.00 30.00 O HETATM 3579 O3 PO4 G 2 8.412 -6.316 -17.597 1.00 30.00 O HETATM 3580 O4 PO4 G 2 9.172 -4.280 -16.485 1.00 30.00 O TER 3581 PO4 G 2 HETATM 3582 BR BR H 1 9.484 11.317 -29.959 1.00 20.00 BR TER 3583 BR H 1 END

3 2

Difference Map positive peaks in release dev-798
by Yuri 27 Jun '11

27 Jun '11

I was wondering if anything changed (weights or something) in the way the difference maps are calculated? I just ran refinement on a 1.3 structure and a hexacoordinated Mg2+ ion has significant positive density peak even at occupancy 1.0. I had not noticed that before. My ligand also does have positive peaks, but refine gives it a .91 occupancy. I wonder if I am missing some parameter cif file or some definition that would make the positive peaks decrease? Thank you -- Yuri Pompeu

3 4

NCS error in Phenix 1.7.1-743
by Ngan Nguyen Bich 26 Jun '11

26 Jun '11

Dear, Thank Nat for your quick reply, I will try the new nightly build and see what happen. I hope it will fix my problem. Ngan

1 0

Difference Map positive peaks in release dev-798
by Yuri 26 Jun '11

26 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

2 1

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

2 1

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

3 2

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 >

2 1

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

5 12

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

2 1

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

2 1

phenix.model_vs_data
by Yuri 17 Jun '11

17 Jun '11

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

1 0

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

1 0

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

4 5

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

2 1

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 >>

1 0

rosetta fragment files
by Leonid Sazanov 16 Jun '11

16 Jun '11

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

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IUCr satellitte
by Gloria Borgstahl 16 Jun '11

16 Jun '11

I am forwarding this information to you on behalf of Marc. Best regards, Gloria The Commission on aperiodic Crystals is organizing a * two days satellite meeting just after the IUCr Congress in Madrid: 'Aperiodic Crystals for Beginners', in Alcala de Henares, 31 August-1st September 2011. ** This school will present in a simple way the methods used for the structural analysis of Aperiodic Crystals*, namely incommensurately modulated phases, incommensurate composites crystals and quasicrystals. It is intended for beginners in the field and will alternate step by step lectures and tutorials. You will find more information in the attached leaflet or on the web site * **http://sig3.ecanews.org/aperbeg2011/aperbeg2011.html*<http://sig3.ecanews.org/aperbeg2011/aperbeg2011.html> Best regards Marc de Boissieu -- -- Marc de Boissieu Sciences de l'Ingéniérie, des Matériaux et des Procédés (SIMaP) Grenoble INP, CNRS, UJF 1130 rue de la piscine BP 75 38402 Saint Martin d'Hères Cedex (France) Tel 33 (0)4 76 82 67 03 Fax 33 (0)4 76 82 66 44 e-Mail: *Marc.de-Boissieu(a)simap.inpg.fr* <Marc.de-Boissieu(a)simap.inpg.fr>

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refinement of twinning dataset
by Ms Chiung-Wen Chang 15 Jun '11

15 Jun '11

hi everyone i have some issues with the refinement of my twinning dataset the dataset has 2.1 A resolution the twin fraction is around 0.43 i did not detwin and ran the refinement directly (with twinning refinement) The attached is the polygon so far the R: 0.1905 Rfree: 0.21 RMSD angles: 0.91 bonds: 0.006 clashscore: 28.176 average B: 45.8 are the clashscore and Average B in the reasonable range ? because the pattern of the polygon is looked wired what can I do more to get them better ? thanks for your help : ) Mary

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[Fwd: Re: elbow.join_cif_files error]
by Maia Cherney 14 Jun '11

14 Jun '11

Hi, I run command line elbow.join_cif_files ligand1.cif ligand2.cif ligand3.cif. As I understand, ligand1.cif and ligand2.cif are cif files present in the directory, the ligand3.cif should be made after joining the first two cifs. I get this error Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/elbow/elbow/command_line/join_cif_files.py", line 245, in <module> run(filenames, target) File "/usr/local/phenix-1.7.1-743/elbow/elbow/command_line/join_cif_files.py", line 145, in run include_commented_restraints=1, #include_commented_restraints, File "/usr/local/phenix-1.7.1-743/elbow/elbow/formats/monomer_library_cif_parser.py", line 185, in parse_cif raise RuntimeError('long tmp') RuntimeError: long tmp Maia

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Using rosetta for domain search with partial model solution
by Daniel Mattle 14 Jun '11

14 Jun '11

Dear Phenix Developers, Is there a possibility within rosetta searching only for a domain (using hhr files) while one has already a partial pdb model lacking a particular domain? I was unable to find this feature? Do you have implemented that? If this is not implemented yet, would it be possible to add this feature? Best, Daniel

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sca file & anomalous difference map: understanding the story from the scratch,
by Haytham Wahba 13 Jun '11

13 Jun '11

i am new user first Q?? with HKL2000 (with scale anomalous option: ON) the output.sca file is like that (for example): 1 -985 38.064 89.066 51.543 90.000 100.446 90.000 p21 0 0 2 3433.6 77.1 0 0 3 735.6 14.0 0 0 11 1564.7 25.4 0 0 12 5643.2 88.3 0 0 13 541.5 9.7 0 0 14 1701.0 27.4 0 1 1 2060.5 47.0 0 1 2 4115.3 75.3 4257.1 97.5 0 1 3 8782.0 280.6 7728.9 173.9 0 1 5 1760.8 28.4 1778.5 33.5 0 1 6 6650.2 122.2 6843.2 126.0 0 1 7 1935.8 36.6 1794.2 29.1 is that one is merged or unmerged????? if i compare with the output.sca with scale anomalous option (off): 0 0 2 3444.4 77.3 0 0 3 734.9 14.0 0 0 4 1705.0 27.5 0 0 5 2693.8 49.4 0 0 6 8383.1 153.9 ------------------------------------------------------- second Q? using output.sca (with scale anomalous option on) for molecular Replacment generate MR.mtz which shows F,SIGF in data labels under phenix.refine the generated (refine_data.mtz) shows: I-obs(+),SIGI-obs(+),I-obs(-),SIGI-obs(-) what is going on in first and second run? ----------------------------------------------------------------- third Q? i want to generate anomalous difference map using phenix.map but when i use output.sca (with scale anomalous option: ON) as reflections file the data label show ((i-obs,sigma)) how to convert this SCA file (if it is merged) to unmerged sca file to creat anomalous difference map for protein contains Br, Sn and Sulpher?? i want to see peaks for these 3 elements to confirm their presence. N.B: the wavelenght was 1.00900 N.B: resolution 1.78 A N.B: i use GUI phenix i am sorry for that long e-mail. thank you in advance haytham wahba biochemi UdeM Canada

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again: XDS files
by Kay Diederichs 11 Jun '11

11 Jun '11

Hi everybody, it has been possible for many years to produce MTZ files from XDS data; I do that all the time, going through xdsconv (filetype CCP4, or CCP4_F, or CCP4_I depending on what type of data one wants - see the docs). This works very well. Others use the xds/pointless/scala/truncate route or the older xds/combat route or ... - as long as it works that's fine. Thus my message was not meant to discourage people from doing that. Rather I see a new possibility to go _directly_ into Phenix, which clearly may be desirable in some cases (less programs involved means less work and maybe fewer bugs), and I wanted to describe the options. If Autosol can use unmerged data (which was new to me), then going from XDS through pointless to a unmerged MTZ file should be the easiest and best way (http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Pointless). best, Kay

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installation problem on Ubuntu
by Daqi Tu 11 Jun '11

11 Jun '11

Hi, I was trying to install the 32 bit Phenix-dev-782 or the official release 1.7.1-743 onto a virtual ubuntu 10.04 32-bit machine. Both of them failed with this error: /bin/tar: ./build/intel-linux-2.6/base/bin/wx-config: Cannot create symlink to `/net/longnose/scratch2/phenix/phenix-dev-782/build/intel-linux-2.6/base/lib/wx/config/gtk2-ansi-release-2.8': Operation not supported /bin/tar: Exiting with failure status due to previous errors /mnt/hgfs/windubuntu/phenix-installer-dev-782/bin/install-from-binary: 352: /usr/local/phenix-dev-782/build/intel-linux-2.6/base/bin/python: not found Any comments? Thanks. Daqi Tu

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low-resolution refinement
by Jennifer Weinreich 11 Jun '11

11 Jun '11

Hello, I am refining a low-resolution structure of a protein complex (4.4 Å). The structure was solved by molecular replacement using structures of individual subunits as search models. Here are some of the questions that I have (and also points raised by our reviewers.) Your thoughts and suggestions on how to proceed with this will be very much appreciated. 1) The B factors are very high (300-400). The Wilson B calculated by phenix.xtriage is ~200. Is this something I should be concerned about? 2) What is the expected (or 'acceptable') gap between R and Rfree at this resolution. (Current R = 27%, Rfree = 33%) Does this sound reasonable? 3) It has been suggested to me that I should try adding riding hydrogens during the last round of refinement (to help with geometry). Is this something I should do? And if so, should I remove them when I deposit the file to the PDB. (Hydrogens at 4.5A are probably going to raise a lot of eyebrows... 4) What is the 'acceptable' coordinate and phase errors for structures at this resolution. (They are now 1.4Å and 36˚) 5) I have been using secondary structure restraints during the refinement, which seems to work reasonably well. I also tried refinement using reference model (the structure of the individual components). But refining with reference models seems to result in high RMSD bonds/angles. Is there something I'm missing? Short of growing better crystals, are there other strategies I should be trying with the existing data? Thank you! Jenn

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