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phenix.ligand_identification problem
by Andrzej 29 Jun '11

29 Jun '11

Dear All, I'm having problem with running ligand_identification script. All well up to the point where the ligand library is created and then for each ligand following error is displayed: Running job sequence 13, ligand 14, in /share/scratch/an... Sorry, resolve was not able to finish on the first cycle I suspect it has something to do with resolve size but there is no keyword like resolve_size for ligand_identification. I've tested my input files with 1.7.1-743 and dev-738 release - same results. Thanks in advance for the support! Regards, Andrzej -- Dr. Andrzej Lyskowski (andrzej[.]lyskowski[(a)]acib[.]at) ACIB Austrian Centre of Industrial Biotechnology GmbH Petersgasse 14, A-8010 Graz, Austria http://acib.at/ c/o IMB Institute of Molecular Biosciences, University of Graz Humboldtstraße 50,III/194, A-8010 Graz, Austria http://strubi.uni-graz.at/ +43 316 380 1993 tel +43 316 380 9897 fax

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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

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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

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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

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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

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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 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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