March 2012 - phenixbb - phenix-online.org

error generating output file overal_best pdb
by Andres PALENCIA 23 Mar '12

23 Mar '12

Dear Phenix users, I have been running Phenix_Autobuild successfully for the last houra. The program generates the corresponding Autobuild_run_** folders as usually, however I got an error message when the program was trying to generate the overal_best.pdb file after the Autobuild cycle 3. I copy below the error message that I got, thank you in advance for any help: OSError : [Errno 2] No such file or directory: '/user/palencia' Traceback (most recent call last): File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Home/Jobs.py", line 170, in OnTimer self.project.refresh_detached_jobs() File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Tracking.py", line 72, in refresh_detached_jobs tmp_dir = self.get_tmp_dir() File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/phenix/tracking/project.py", line 97, in get_tmp_dir os.makedirs(tmp_dir) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", line 150, in makedirs makedirs(head, mode) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", line 150, in makedirs makedirs(head, mode) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", line 150, in makedirs makedirs(head, mode) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", line 150, in makedirs makedirs(head, mode) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", line 150, in makedirs makedirs(head, mode) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", line 150, in makedirs makedirs(head, mode) File "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 2] No such file or directory: '/user/palencia' Platform info: __FILE__ = /net/anaconda/scratch1/phenix/phenix-1.7.3-928/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Dec 6 2011 __TIME__ = 04:18:10 __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_48 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-2.6.18-238.9.1.el5-x86_64-with-redhat-5.7-Final 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: 24 Memory total: 25,263,722,496 Memory free: 20,157,317,120 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 = Ã

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Rosetta and disulphides
by Morten Groftehauge 23 Mar '12

23 Mar '12

Hi phenix-bb'ers, Is there anyway to make phenix.mr_rosetta take disulphide bridges into account? It's a rather enormous restraint on conformational space after all (wait is that a constraint or restraint? I get confused). Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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about readyset
by Ming 23 Mar '12

23 Mar '12

Dear all, I was using ready set to get my pdb ready. It automatically built the ligand cif file from scratch too. And the phenix.refine was fine with the files from ready set. Then I tried another method in which I threw everything that phenix.refine needs, including pdb file, ligand cif file, ligand pdb file, mtz. And phenix.refine ran smoothly again. But the refinement results were different between these two ways. The R fac is 1% different. I think ready set is only making the phenix.refine easier by generating ligand and building H, but if I do all the work of ready set and prepare the files for phenix.refine. Aren't they supposed to give the same results back? Can anyone help me here? Thanks a lot. -- Ming

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Partially reduced disulfides
by Christopher Wanty 23 Mar '12

23 Mar '12

Hi, I have a structure that appears to have a combination of reduced and oxidised disulfides. >From previous reading on the board I've taken the strategy of dropping the disulfide detection cutoff to 0.1 then added back the disulfides as appropriate using restraints. The problem I now have is that for some of these cysteine pairs there are clearly oxidised and reduced positions in the density. Modelling altloc's for each of these works, but the occupancies do not refine as I expected; the altloc's involved in the disulfide I expected to have the same occupancy as their counterpart in the disulfide. To try to get these to match, I introduced occupancy constraint that look like: constrained_group { selection = (chain A and resseq 276 and altloc B) or (chain A and resseq 286 and altloc B) } But with that the sum of occupancies for altloc 276 (for example) is not adding to 1.00. My thought is that I need to change the occupancy constraints but I'm not sure how to make them do what I want. Any help/advice is appreciated. Regards, Chris ------------------------------------------------------- Dr. Christopher Wanty christopher.wanty(a)uwa.edu.au Research Associate Biomolecular, Biomedical and Chemical Sciences, Building M310 University of Western Australia 35 Stirling Highway Crawley 6009 Western Australia Australia

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Documentation in last Dev versions
by Alexander Batyuk 22 Mar '12

22 Mar '12

Dear developers, Is there any particular reason for missing documentation file in phenix-dev-1008 and up (it could not be found on the website as well)? dev-1005 is fine. Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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Hydrogens
by Christopher Wanty 21 Mar '12

21 Mar '12

Hi all, I've been refining with riding hydrogens, and from what I've read hydrogen contribution should be included in Fo calculation automatically for maps. What I'm seeing after refinement is a lot of little bits of green in the difference density that look like they could be explained by hydrogens. I'm working at 1.4A, attached image gives an example and shows contours at 3 sigma for difference map. Is there a setting/parameter I need to adjust to get this to work properly? Kind Regards, Chris ------------------------------------------------------- Dr. Christopher Wanty christopher.wanty(a)uwa.edu.au Research Associate Biomolecular, Biomedical and Chemical Sciences, Building M310 University of Western Australia 35 Stirling Highway Crawley 6009 Western Australia Australia

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building a peptide-like polymer with phenix.elbow
by Geoffrey Feld 21 Mar '12

21 Mar '12

Greetings, I have a co-crystal structure of a protein bound to an interesting polymer -- poly-D-g-glutamic acid (poly glutamic acid with D chirality and gamma linked, rather than alpha linked). In the structure, I have density corresponding to different links, from 1 to 6 (so far). I'd like to build a ligand that has "residues" much like a polypeptide polymer so that I can refine each residue individually (hopefully in COOT). Up till now, I've been using SMILES to generate the different length polymers so I have pdbs and cif files, and then (painstakingly) modelling them into COOT, building restraints for refinement, etc. More recently, I used maestro to build a dimer that at least has the right atom labels you'd expect for a protein. However, I can't use phenix now to generate cif files because it is confused by the GLU. Is there a way to use phenix.elbow to make a multi-residue polymer? I'm also doing some monte carlo minimizations in macromodel to generate models of the various low energy states and would like to use them as building blocks, so an easy order-of-operations would be to generate the files in macromodel and feed them in via pdbs to phenix.elbow to generate cif restraints. Any help on this would be greatly appreciated. Cheers, Geoff -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"

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a small trick for SDS-Gel storage
by Kevin Jin 21 Mar '12

21 Mar '12

Dear All, Maybe most of you already knew. I just put my understanding of SDS page gel storage here, if you want to make gel yourself and safe some money. http://www.jinkai.org/SDS_page.html If I am wrong, please let me know. Sharing knowledge each other is always joyful. -- Kevin Jin Protein crystallographer and Biopolymer chemist Personal Website: http://www.jinkai.org/

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A possible conjugative relaxase with novel fold for DNA cleavage?
by Kevin Jin 20 Mar '12

20 Mar '12

Dear All, The protein structure of Jann_2411 (PDB 3H0N) from Jannaschia sp. strain CCS1 carries a novel fold for unknown function. Zn-finger is indentified in the C-terminus. However, the N-terminus with a metal binding site presents a novel fold. As the person who solved and characterized this protein, I would like to put some further observation here for your consideration. My analysis is available here: http://www.jinkai.org/Novel_fold_3H0N.html Best regards, Kevin -- Kevin Jin Protein crystallographer and Biopolymer chemist Personal Website: http://www.jinkai.org/

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NCS operators
by Melania Strycharska 20 Mar '12

20 Mar '12

Dear all, I have a bit of a problem applying NCS to my fairly low resolution structure. If I try to look for NCS symmetry automatically - phenix doesn't find any. If I specify sections that I want to be related by NCS, the script usually crashes. I have a dimer in the asymmetric unit, however it appears that one domain is related by 3-fold symmetry while the other is related by 6 fold symmetry. I can "cheat" phenix and generate operators for each of the domains by feeding a stripped pdb file (one that contains only a dimer of one domain or the other) to phenix.simple_ncs_from_pdb and then it easily identifies the ncs operators... unfortunately the simple_ncs_from_pdb.ncs file generated that is meant to be fed into phenix.refine contains only the chain selections, not the actual operators. Is there a way to specify different NCS operators (rotational matrix and translational vector) for specific chain selections in the .eff file or under GUI? or if there isn't, how can I still take advantage of my NCS symmetry? Also, is there any obvious reason why NCS operators that I generated with Phenix do not match the operators that I found using CCP4 Lsqkab? (yes I already accounted for chain A moving onto B or chain B moving onto A) Can I choose to apply NCS symmetry to just my backbone? How would I specify that? thanks so much! Melania

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