March 2012 - phenixbb - phenix-online.org

links in phenix summary
by Christian Roth 04 Apr '13

04 Apr '13

Dear all, thanks to the phenix team which helped me a lot to resolve all issues regarding the correct link definitions. I have summarised a few things which one might consider if nonstandard links are necessary. Try phenix ready set to get your links out of the pdb. Do not forget to change the possible LINKR to LINK! Inspect the links and decide if they are useful! Peptide links are automatically incorporated if residues are close (inspect geo file) Non standard peptide links could be created using using an now available alpha release script: elbow.ligand_linking model.pdb Inspect the generated cif file and correct angles and incorporate dihedrals and so on if necessary. Sugar links which exists in the mon_lib.cif should be incorporated using the apply_cif link option like refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain B and resname GLC and resseq 1 residue_selection_2 = chain B and resname GLC and resseq 2 } According to the link definition the C1 oxygen of the following sugar with the higher number must be removed. The automatic incorporation of sugar links will be probably soon available in phenix. Nigel is already working on this. If one want use hydrogens in the refinement, they have to be added previously with ready_set and afterwards the OH4 sugar hydrogen has to be removed before the refinement. For links with symmetry related atoms the symmetry operator must be included in a custom bond definition efinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain A and resname HEM and resid 154 and name FE atom_selection_2 = chain A and resname MTO and resid 155 and name O symmetry_operation = -x,y,-z distance_ideal = 2.2 sigma = 0.01 } } The operator can be obtained using iotbx.show_distances your.pdb > all_distances Search for keyword "sym" or from Coot clicking on the symm option. Coot print out the operator and the translation term separately. Both has to be merged in the final operator used in phenix! Christian

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How to include restraints when refining DNA?
by Xun Lu 03 May '12

03 May '12

Dear all, I am refining a protein-DNA complex structure at 2.9A resolution. The R/Rfree is 0.2181/0.2501, which is pretty good, but I can tell that the DNA is not well refined. Some sugar puckers are not right. The distances between some base-paired bases are kind of short (~2.5A). I've tried including a reference model for the DNA, or including a cif file, and I've also tried to turn on the secondary_structure_restraints.... nothing worked. I must have not done it in a correct way. But how to do it? And how to deal with sugar puckers? In refmac, I can set the distances between bases during the refinement, so there must be a way to do it in phenix as well? Any advice is welcome. Thanks! Xun -- Department of Molecular and Structural Biochemistry North Carolina State University

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cut-out mtz edition
by Dialing Pretty 26 Apr '12

26 Apr '12

Dear All, I just cut out a fragment of chain and the corresponding electron density from the whole molecule. Will you please give me some suggestion on how to edit the attached file so that those electron density not from the protein fragment can be erased? Or do you have other methods to produce high quality figure which just shows the fragment chain and the fragment eletron density? Cheers, Dialing

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DEN refinement is crashing
by Mario Sanches 02 Apr '12

02 Apr '12

I am running phenix.refine using the graphical interface. Under "global refinement paramerters..." I am selecting "DEN". The problem is that Python crashes all the time, always at the same point (see portion of the log output below). Is it a known bug? Is DEN incompatible with some of the options in refinement? My resolution is 2.9A by the way. Thank you for your inputs. Mario Sanches ___________________________ Log output final portion: tardy dynamics: number of bodies: 3678 number of degrees of freedom: 3713 number of atoms * 3: 38220 ratio: 0.097 = 1/10.29 temperature degrees of freedom: cartesian (38220) kinetic energy sensitivity to generalized velocities: n: 3713 min: 3.61771e-06 max: 0.0300001 mean: 0.00410663 time step: 0.00100 pico seconds velocity scaling: True suppressing allowed origin shifts: False new target temperature: 2500.00 K step= 1 temperature= 2500.0 rmsd=0.0446 r_work=0.3010 r_free=0.3214 -- Mario Sanches Postdoctoral Researcher Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave Toronto - Ontario Canada M5G 1X5 http://ca.linkedin.com/in/mariosanches

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very informative - Trends in Data Fabrication
by Bosch, Juergen 31 Mar '12

31 Mar '12

really fascinating, bringing back the discussion for a repository for your collected frames. Jürgen Acta Cryst. (2012). F68, 366-376 doi:10.1107/S1744309112008421<http://dx.doi.org/10.1107/S1744309112008421> Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen B. Rupp<http://scripts.iucr.org/cgi-bin/citedin?search_on=name&author_name=Rupp,%20B.> Abstract: Physically improbable features in the model of the birch pollen structure Bet v 1d (PDB entry 3k78<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78>) are faithfully reproduced in electron density generated with the deposited structure factors, but these structure factors themselves exhibit properties that are characteristic of data calculated from a simple model and are inconsistent with the data and error model obtained through experimental measurements. The refinement of the 3k78<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?3k78>model against these structure factors leads to an isomorphous structure different from the deposited model with an implausibly small R value (0.019). The abnormal refinement is compared with normal refinement of an isomorphous variant structure of Bet v 1l (PDB entry 1fm4<http://pdb.pdb.bnl.gov/pdb-bin/opdbshort?1fm4>). A variety of analytical tools, including the application of Diederichs plots, R plots and bulk-solvent analysis are discussed as promising aids in validation. The examination of the Bet v 1d structure also cautions against the practice of indicating poorly defined protein chain residues through zero occupancies. The recommendation to preserve diffraction images is amplified. ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/

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Problems fitting NADH
by Phillip Steindel 30 Mar '12

30 Mar '12

Dear all, I'm trying to fit a NADH into a 1.7 Å structure. LigandFit worked with just the three-letter code (NAI), however phenix.refine won't work with just the model. If I use eLBOW to create restraints, meanwhile, the ligand gets distorted during refinement (non-tetrahedral phosphates, mainly). I'm not sure exactly how I'm supposed to be generating these restraints- any help is appreciated. Thank you, Phillip Steindel Theobald Lab Department of Biochemistry Brandeis University

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Re: [phenixbb] [ccp4bb] a small trick for protein and organic compound cocrystallization.
by Bryan Lepore 30 Mar '12

30 Mar '12

On Fri, Mar 30, 2012 at 3:26 PM, Jacob Keller <j-keller2(a)fsm.northwestern.edu> wrote: > What's the harm? have you seen usenet/Google groups? -Bryan

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a small trick for protein and organic compound cocrystallization.
by Kevin Jin 30 Mar '12

30 Mar '12

Dear All, Here is way I have used for protein and hydrophobic organic compound cocrystallization. Via this method, less amount of DMSO will be used to aviod protein ppt. I hope you can use for your research. http://www.jinkai.org/Xtal.html Regards, -- Kevin Jin Sharing knowledge each other is always very joyful...... Website: http://www.jinkai.org/

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Re: [phenixbb] need help for crystallization
by Kevin Jin 30 Mar '12

30 Mar '12

My pleasure ! Since this may be help for other people, I also cc it to CCP4BBS. According to your email, I guess the buffer is phosphate buffer at pH 7.4. You can do a quick buffer exchange before crystallization. Since PO4 is a competitor in this case, I will also avoid PO4 and Cocodylate buffer from screen kits. Here is what you can do, 1. concentrate your protein using an amicro centrocon with 3KD cutoff. 2. Measure how much buffer has been spin down, then add equal amount of Tris with same pH back to the top. 3. Then, spin down again. 4. Repeat several times, 5 times may be good enough. 5. Most of Phosphate buffer should be removed. That's what I used before. Let me know if it works. Best, Kevin Jin On Fri, Mar 30, 2012 at 9:40 AM, Afshan Begum <afshan490(a)yahoo.com> wrote: > > Dear Kevin > > I have seen your website and come to you to discuss my problem actually i > want to co-crystallized my enzyme with inhibitor but problem is that the > phosphate ion come to the active site and occupied the cavity and my > inhibitor not bind to the active center i purchase this enzyme from a > commercial source and they purify with phosphate buffer that's why also > phosphate is occupied the cavity how can i get ride of it from the active > center could you kindly help me regarding this i would be really thankful to > you. > > > Best Regards > > AFSHAN > =========================================== > Dr. Afshan Begum > University of Hamburg > Institute of Biochemistry and Molecularbiology > Laboratory for Structural Biology of Infection and Imflammation > c/o DESY, Build. 22a > Notkestr. 85 > 22603 Hamburg > Germany > Home phone: +49 40 22888618 > Fax: +49 40 8998-4747 > E-mail: afshan490(a)yahoo.com > -- Kevin Jin Sharing knowledge each other is always very joyful...... Website: http://www.jinkai.org/

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Re: [phenixbb] phaser_ep
by Airlie McCoy 30 Mar '12

30 Mar '12

Dear Kay, You can control the distance for the atom separation/anisotropy in Phaser with the llgcomplete.clash input parameter. By default llgcomplete.clash is zero, which means Phaser will calculate a value based on the resolution. If a value is set this will override the default. Apologies, this was not explained in the wiki, but is now! Airlie

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phaser_ep
by Kay Diederichs 30 Mar '12

30 Mar '12

Dear all, is there a way to modify the decision constants in phaser_ep? Specifically, I want to refine against heavy-atom derivative with one strong site. The resolution of the data is 3.6A; the substructure (4 sites) was solved at 8A. Upon refinement, phaser finds two more sites at distances of ~3.5A to the strongest site. Furthermore, it finds two holes at distances of ~3.5A to the strongest site. Now I would like phaser to treat the site as anisotropic. However, the distances are beyond its decision constant (~2.54A), so it chooses to add two sites to my HA model, but they refine poorly. How is the decision constant calculated? Can I influence the calculation? I found nothing in the phaser wiki. Alternatively: how can I tell phaser_ep that it should refine a given input atom anisotropically? I tried to add a ANISOU line to the PDB file but the program seems to ignore it. thanks, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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A small trick to make cover glass extremely hydrophilic for hanging drop
by Kevin Jin 29 Mar '12

29 Mar '12

Dear All, Making the surface of cover glass hydrophilic could let drop with organic solvent (MPD, etc) shrink into a ball shape, not spread out. Here is the method I used before. http://www.jinkai.org/Xtal.html Kevin -- Kevin Jin Sharing knowledge each other is always very joyful...... Website: http://www.jinkai.org/

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a strategy for endotoxin removal
by Kevin Jin 29 Mar '12

29 Mar '12

Dear All, I developed a method to remove endotoxin before and it worked pretty well. Here is the strategy for this protocol. http://www.jinkai.org/Endotoxin.html I hope it is useful. Best, Kevin -- Kevin Jin Sharing knowledge each other is always very joyful...... Website: http://www.jinkai.org/

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reference model restraints now support multiple reference model files
by Jeff Headd 28 Mar '12

28 Mar '12

Hi PHENIX users, After numerous user requests, we've added support to phenix.refine for multiple reference model input files. If you are refining a complex and have reference models for individual components, you may now input as many files as necessary. A parameter file would include: refinement { reference_model { file = "reference_A.pdb" file = "reference_B.pdb" } } Chain matching is still carried out automatically, so simply specifying the file paths is usually enough for the restraints to be generated for refinement. Details of chain matches are printed in the .log file, as well as in the reference_model scope in the .eff file. If anyone has questions, please let me know. Thanks! Jeff

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positive density around heavy metals
by Subhani Bandara 28 Mar '12

28 Mar '12

Hi everyone, I have refined a protein with a metal-chelate complex at 1.4 resolution and saw positive density around some metals that are on a two fold. I refined those chelator complexes with fixed occupancy to avoid the negative density seen around it as they are partially occupied. Also I had to avoid xyz refinement after fixing them on special position, to avoid moving away from two fold. I have attached a figure of one of those complexes. If I increase occupancy then it shows negative density. How can I get rid of this positive density. Thanks in advance for the help Subhani

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Re: [phenixbb] merging in hires data in AutoBuild
by Desiree Ho-Chi Fong, Ms 27 Mar '12

27 Mar '12

It works! Thank you. Desiree

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Generating a list of peak heights in a Bijvoet difference Fourier
by John Rose 27 Mar '12

27 Mar '12

Hi, Is there a way to get a print out of the peak positions and their heights from a Bijvoet difference Fourier map? I can generate the map and see the peals but I would like a listing also. Thanks, John Rose John Rose Ph.D. Associate Professor B204B, The Fred C. Davison Life Sciences Complex 120 Green Street Department of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602-7229 ========================================= Phone: 706-542-1750 Fax: 706-542-3077

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merging in hires data in AutoBuild
by Desiree Ho-Chi Fong, Ms 27 Mar '12

27 Mar '12

Hello all, I am using PHENIX 1.7.3-928 and I am trying to merge a high resolution native data set with a MAD data set in AutoBuild. I have run AutoBuild through the GUI as well as on the command line. Here is the command I used: phenix.autobuild data=AutoSol_run_1_/exptl_fobs_phases_freeR_flags_1.mtz hires_file=hires.mtz model=AutoSol_run_1_/overall_best.pdb rebuld_in_place=True The data file, exptl_fobs_phases_freeR_flags.mtz from AutoBuild only includes data to the resolution of the MAD data set. The higher resolution native data was not incorporated into this mtz file. Looking at the log file, the hires data was merged with expel_fobs_phases_freeR_flags_1.mtz from AutoSol (with AutoBuild after) and followed by anisotropy correction. This was then used for density modification. However, the high resolution data was never included in the mtz file for refinement in AutoBuild. My understanding is that if hires data is specified in AutoBuild, the phases would be extended and included in map calculation as well as subsequent refinement. The output exptl_fobs_phases_freeR_flags.mtz from AutoBuild would also include the hires data for subsequent refinement. Is this correct? Thank you for your help. Desiree

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R value difference in model vs data vs refinement
by Christian Roth 24 Mar '12

24 Mar '12

Dear all, I refined a structure in phenix quite good resolution (1.4 Ang.) After the last refinement I created the "table 1" to extract all data. Interestingly I got a warning due to small changes in the R values R/Rfree after Refinement. 15,46/18,16 Phenix modelvs.data gives me R/Rfree 15,34/18,07 Interestingly this is nearly exactly the value which I got after the first OHS scattering optimization from phenix R/Rfree 15,43/18,03 The differences are of course very small and negeligible, but I wonder why it happens. Esspecially taking into account that it was refined with phenix and in this case I would expect that both values match exactly. Thank you very much in advance Best Regards Christian

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sequence file for DNA-Protein complex
by Sita Ram Meena 24 Mar '12

24 Mar '12

Hello Everyone. As per my knowledge we gives the Protein sequence .SEQ OR .DAT file format having only protein sequence in Caps and no gaps now, Please suggest me how we can give a sequence file for double stranded DNA-Protein Complex for the use in Phenix autobuild. Thank you. Best Regards Sita Ram

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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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