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Ligand woes
by José Trincão 05 Jul '11

05 Jul '11

Hello all, I have been having very weird problems refining a structure with several ligands. The weirdest problem is that if I try to run ligand fit giving just the name of the ligands, no problem - it finds the ligands (FAD and MTE). I save the pdb with all the ligands in and phenix.refine complains that MTE is not recognised, I have to run ready-set. I do it. Run phenix.refine again, and now it complains with the following: Number of atoms with unknown nonbonded energy type symbols: 116 "HETATM18439 C1' MTE A3003 .*. C " "HETATM18441 C2' MTE A3003 .*. C " "HETATM18443 C3' MTE A3003 .*. C " "HETATM18444 O3' MTE A3003 .*. O " "HETATM18474 N9A FAD A3005 .*. N " "HETATM18475 C8A FAD A3005 .*. C " "HETATM18476 N7A FAD A3005 .*. N " "HETATM18477 C5A FAD A3005 .*. C " "HETATM18478 C6A FAD A3005 .*. C " "HETATM18480 N1A FAD A3005 .*. N " ... (remaining 106 not shown) Any help will be greatly appreciated. Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal "It's very hard to make predictions... especially about the future" - Niels Bohr

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NCS Restraints
by Yuri 01 Jul '11

01 Jul '11

Hi Pavel, >It's rather packing.. Say, if more than one copy packs in the > asymmetric >unit then you have NCS, roughly speaking.. So is it correct to say that in cases where you have 1 molecule per ASU, there will be no NCS only crystallographic symmetry?? > In other words, if for the same enzyme one crystal goes to 3.1 and > another 1.5 A could one have significant NCS but not the other? >I'm not sure I understood this... May some one else did? I was trying to understand if this phenomenon would be noticeable depending on the resolution only... You and Nathaniel pretty much answered this now... -- Yuri Pompeu

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NCS restraints
by Yuri 30 Jun '11

30 Jun '11

Hello, I have some fundamental questions about NCS: 1- I think its somewhat of a consensus that at higher res. it should not be used to avoid missing out "real" detailed discrepancy. Is this true? 2- Should one try to use it in lower res data (3 A and worse)? 3- Is the presence of NCS macromolecule specific, or crystal specific? In other words, if for the same enzyme one crystal goes to 3.1 and another 1.5 A could one have significant NCS but not the other? Thanks or any clarification -- Yuri Pompeu

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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 27 Jun '11

27 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 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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