- phenixbb - phenix-online.org

parameters for averaged kick maps
by Jose M de Pereda 04 Dec '12

04 Dec '12

Dear all, I would like to compare averaged kick maps obtained using different “kick sizes”. Is it possible to define the kick size and the number of kicks in phenix.refine and/or phenix.maps? In phenix.refine, the “ordered_solvent” section has keywords to control the generation of kick maps: kick_map { kick_size = 0.5 number_of_kicks = 100 } But, it seems to me that these can not be used during the generation of maps or maps’ coefficients. Related with this issue, does phenix.refine always use the same kick size or does it adjust it ad hoc (e.g. based on ML error estimates)? Thanks a lot, Jose -- ------------------------------------------------------------ Jose M de Pereda, PhD Instituto de Biologia Molecular y Celular del Cancer (IBMCC) Spanish National Research Council - University of Salamanca Campus Unamuno s/n E-37007 Salamanca, Spain Phone: +34-923-294817 Fax: +34-923-294795 http://xtal.cicancer.org/ ------------------------------------------------------------

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table 1
by So Jay 03 Dec '12

03 Dec '12

Hi, I was using generate table 1 utility in phenix-1.8.1-1168. The data was processed with HKL2000 and model was refined using Autobuster. In the table I find two entries for Multiplicity and R-sym were blank.I was wondering if there is any particular reason for this. ThanksJay

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Similar 2Fo-Fc maps, very different e/A^3 levels (absolute levels)
by Sam Stampfer 03 Dec '12

03 Dec '12

Dear Phenix group, I am trying to decide which electron density map to use for rebuilding my structure in Coot. Both 2Fo-Fc maps appear quite similar at the 1 sigma level but the absolute electrons per cubic Angstrom (e/A^3) is very different. When contoured at 1.00 rmsd in coot, these are the e/A^3 levels (Coot calls them absolute levels): Map #1 2Fo-Fc: 0.0044 e/A^3 Map #2 2Fo-Fc: 0.0832 e/A^3 Map #1 was generated using a twinning operator that is typically required for this crystal form. Map #2 was generated without the twinning operator and it tends to have slightly better 2Fo-Fc density, and there is a bit more density (or noise?) in the Fo-Fc map. The structure was refined in Phenix and gave a similar Rfree regardless of whether a twinning operator was used. What does it mean to have this 20-fold difference in electrons per cubic Angstroms for my maps? Which map should I use? Thanks for your help! -Sam PS: The Fo-Fc map in Map#2 also contours at a much higher absolute e/A^3 level.

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pseudotranslation and twinning problem
by Rajeshwer Sankhala 03 Dec '12

03 Dec '12

I am new to crystallography. I have collected data for 26 kDa protein with a maximum resolution of 2.25A in I 41 space group. I have a poor model for molecular replacement (~15-20% identical). When i did xtriage run, it suggested -h,k,-l twinning law and indicated about pseudo-translation. Now when i am running Phaser for molecular replacement i am getting very low LLG (less than 100) and TFZ score (5-6). Can anyone suggest which parameters or setting i should use to improve my LLG score and get a best model for refinement. Thanks Raj

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dev-1227: problem reading in tls parameters from refmac or tlsmd
by Boaz Shaanan 02 Dec '12

02 Dec '12

Hi, In the TLS pulldown I tried to upload tls parameters from either refmac (.tls) or tlsmd (.tlsin) through the 'load' button, according to the suggestion in this section, but it complains about wrong format of the file. Am I doing something wrong? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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Specify particular columns from data files on the command line
by Brad C. Bennett 30 Nov '12

30 Nov '12

Hi all (again)- I'm trying to run DEN refinement in Phenix from the command line. How do I specify certain columns from multiple data files (in my case, 2 MTZ files) to be used? For example, the Rfree flags from one and the hkl data from the other. Thanks! Brad C. Bennett Research Associate- Mark Yeager Lab University of Virginia Molecular Physiology and Biological Physics 320 Snyder Building 480 Ray C. Hunt Drive Charlottesville, VA 22908 Email: bcb3b(a)virginia.edu Lab phone: 434-243-2520

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DEN refinement
by Morten Groftehauge 30 Nov '12

30 Nov '12

Hi guys, Two quick questions about DEN refinement: 1) If gamma refines to 0 does that mean that I should run DEN refinement again with the output model? Or should I do a refinement and then another DEN? Since gamma = 0 the refinement should be allowed a possibility of moving the structure further towards the reference restraints in my mind. 2) If gamma refines to 1 it means that my reference model is inappropriate, right? Not really much of a question, I know. And I know that DEN refinement is in beta but it would be nice if you outputted the optimal gamma and weight for the refinement to the GUI. Actually it would be nice if the did that for geometry weights and xray weights too when one optimizes them. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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Error starting Phenix on Linux
by Brad C. Bennett 30 Nov '12

30 Nov '12

Hi all- After installing the latest version and release of Phenix (1.8.1-1168) onto our Linux workstation and setting the environment for bash, I get the following error upon trying to launch Phenix from the command line: ImportError: libjpeg.so.62: cannot open shared object file: No such file or directory I've never seen this before (previous versions of Phenix have run fine on this machine) and don't know what this file is exactly and where it should be located. Anyone come across this and know if there is a fix (or if I'm just doing something stupid!). Thanks! Brad C. Bennett Research Associate- Mark Yeager Lab University of Virginia Molecular Physiology and Biological Physics 320 Snyder Building 480 Ray C. Hunt Drive Charlottesville, VA 22908 Email: bcb3b(a)virginia.edu Lab phone: 434-243-2520

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Call for submissions for the Computational Crystallography Newsletter (CCN) January 2013
by Nigel Moriarty 30 Nov '12

30 Nov '12

Folks Calling for articles and short communications of interest to structural biologists. The deadline for publication in the January 2013 issue is 31 December, 2012 but if you can send me drafts before the 15th of December we can get started on generating proofs. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and the template are available at www.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty, PhD Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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choosing Rfree set with NCS and twinning
by vincent Chaptal 30 Nov '12

30 Nov '12

Dear phenixbb, I am using the "reflection file editor" in phenix 1.8.1-1168 to generate my test set (with the GUI). I have NCS so I ticked the box "assign test set in thin resolution shells". I also have twinning, and want to have my Rfree not biased by twin related reflections. I guess the option "use lattice symmetry to generate test set" is the one I should use for this purpose? I couldn't find much information online about this option. No log file has been generated so I can't check what happened. I am supposing xtriage is ran in the background and if a twin law is found, then used to generate the test set. My output from xtriage is: Statistics depending on twin laws ----------------------------------------------------------------- | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ----------------------------------------------------------------- | -k,-h,-l |PM| 0.249| 0.272| 0.246| 0.200| ----------------------------------------------------------------- And indeed if I check in mtzdmp the output mtz, reflections in the test set are related by (-k, -h, -l); disclaimer: I only checked in the plane (h,k,0). I would like to be sure my Rfree is generated correctly. Alternatively, what would happen when multiple twin laws are available? Is the most probale used? Is it possible to specify the editor which law to use? Thank you for your help. Vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr

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DNA double helix with many molprobity bad clashes
by Benda, Christian 30 Nov '12

30 Nov '12

Hi, I am refining a protein-DNA complex at around 3 A with a standard b-form dsDNA. R-factors are around 24/20 (kinda low for the resolution). Originally, I placed the DNA using coot and now, after several rounds of refinement in phenix, I get a long list of bad clashes from molprobity validation (in phenix) that covers the whole length of the DNA and almost exclusively lists hydrogens from the ribose moiety (whether or not in contact with protein). My question is, - why is phenix.refine not taking care of these clashes (i.e. optimizes the structure such that they go away)?. Am I giving experimental contribution to high a weight (I have "optimize x-ray/stereochemistry" checked)? - if so, can I (and how) restrain geometry for the DNA a little more but leave the protein alone (and does that make sense)? thanks for any help Christian

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phenix.erraser error
by Russell Chan 29 Nov '12

29 Nov '12

Hi, I'm currently trying to use the new command, phenix.erraser, to refine my RNA structure. I generated a ccp4 map and removed the R-free flags, however it generates an error after its starts its first round of minimization. The command I use is: phenix.erraser <mypdb>.pdb <mymap>.ccp4 The error generated is: ################################### Starting SWA_rebuild_erraser.py... Output pdb will be...precursor_chi_erraser.pdb Create temporary directory /home/Russ/Desktop/erraser_test/precursor_chi_erraser_temp/... fixed_res_final in Rosetta pdb file = [] cutpoint_final in Rosetta pdb file = [1, 2, 3, 4, 12, 15, 19, 20, 21, 25, 30, 37, 38, 49, 54, 58, 68, 69, 72, 79, 83, 84, 105, 108, 109, 122, 124, 125, 130, 133, 134, 137, 140, 143, 146, 158, 160, 161, 168, 170, 176, 179, 187, 189, 201, 204, 205, 216, 217, 228, 237, 239, 241, 245, 246, 268, 269, 273, 279, 283, 292, 293, 302, 305, 309, 311] extra_res_final in Rosetta pdb file = [] Starting whole-structure minimization 1... ******************* ERROR ENDING *************** Command 'phenix.python /home/sbgrid/programs/x86_64-linux/phenix/1.8.1-1168/phenix-1.8.1-1168/phenix/phenix/erraser/full_struct_slice_and_minimize.py -binary_name linuxgccrelease -map /home/<Russ>/Desktop/erraser_test/erraser_map.ccp4 -map_reso 2.0 -new_torsional_potential True -pdb minimize_0.pdb -out_pdb minimize_1.pdb > minimize_1.out 2> minimize_1.err' returned non-zero exit status 1 ******************* ERROR ENDING *************** Any help would be greatly appreciated! Thanks, Russell

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Re: [phenixbb] [COOT] CCP4 - Coot in Applications
by Nathaniel Echols 28 Nov '12

28 Nov '12

---------- Forwarded message ---------- From: Paul Emsley <pemsley(a)mrc-lmb.cam.ac.uk> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Cc: Date: Wed, 28 Nov 2012 17:08:50 +0000 Subject: Re: [phenixbb] [COOT] CCP4 - Coot in Applications On 28/11/12 15:03, Antony Oliver wrote: > > Ok - annoying thing…. > > 1) using /Applications/coot.app/Contents/Resources/script to launch Coot from the command line (terminal window) works IF you don't have X11 open already. > 2) if you DO have X11 open, coot pretty much always crashes with the aforementioned "invalid window errors". It is not clear to me if you are, or are not using Bill Scott's binary... (it's the one I recommend for Macintosh). Paul.

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Re: [phenixbb] [COOT] CCP4 - Coot in Applications
by Antony Oliver 28 Nov '12

28 Nov '12

Ok - annoying thing…. 1) using /Applications/coot.app/Contents/Resources/script to launch Coot from the command line (terminal window) works IF you don't have X11 open already. 2) if you DO have X11 open, coot pretty much always crashes with the aforementioned "invalid window errors". >>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorIllegalArgument: CGSGetSurfaceBounds >>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. >>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorIllegalArgument: CGSBindSurface: Invalid window 0x8da >>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorIllegalArgument: CGSBindSurface: Invalid window 0x8da >>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorIllegalArgument: CGSBindSurface: Invalid window 0x8da Ideas and suggestions welcome. I guess I could make sure that X11 is not running each time I invoke a script or run coot from the command line - but it's not exactly ideal. --> NB: Running Mac OS X, 10.7.5 - Lion. Please excuse the cross bulletin board posting, but I really do use quite a range of software across all program suites - and this method of delivering coot causes problems for many of the plugins/scripts (phenix and buster for example). With thanks, Antony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oliver(a)sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Nov 27, 2012, at 11:32 AM, Antony Oliver wrote: > Thanks Charles - that seems to work..! > > Tony. > > --- > Dr Antony W Oliver > Senior Research Fellow > CR-UK DNA Repair Enzymes Group > Genome Damage and Stability Centre > Science Park Road > University of Sussex > Falmer, Brighton, BN1 9RQ > > email: antony.oliver(a)sussex.ac.uk > tel (office): +44 (0)1273 678349 > tel (lab): +44 (0)1273 677512 > > On Nov 26, 2012, at 10:19 AM, Charles Ballard wrote: > >> You could give >> >> /Applications/coot.app/Contents/Resources/script >> >> a go. >> >> Charles >> >> On 23 Nov 2012, at 12:20, Antony Oliver wrote: >>

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coordinate refinement and maps
by Subhani Bandara 27 Nov '12

27 Nov '12

Hi all, I am refining a protein with metal-ligand complexes. Is it possible to refine only y coordinates for an atom (on two fold) while keeping X and Z fixed using Phenix? Also is there a way to calculate something like anomalous difference-difference map (Anomalous Fobs - Anomalous Fcalc) to identify any additional atoms bound at metal sites. Thanks in advance for the help! Subhani

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cif file for modified peptide
by Feldkamp, Michael Dennis 27 Nov '12

27 Nov '12

I would like to generate a cif file for a peptide that is FITC labeled at the N-terminus and also contains an unnatural amino acid (dichloro phenylalanine). I've used phenix.elbow in the past to generate cif files for small molecule ligands but when I've run it I only get a cif file for the FITC. Any insight would be greatly appreciated, Michael Feldkamp

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MR_Rosetta prerefine
by Heather Condurso 26 Nov '12

26 Nov '12

Dear all, I am using mr_rosetta to run prerefinement of various starting models that all have pretty low sequence homology to my protein of interest (~15%). I ran it using the simple script from the manual: phenix.mr_rosetta \ seq_file=seq.dat \ search_models=coords1.pdb \ run_prerefine=True \ number_of_prerefine_models=1000 Its working fairly well, but obviously taking a long time to make 1000 models. Is there a log or score file somewhere that lists all of the rosetta scores as it is running? Right now all the pdb files in each different run have the format S_"original model name"__0001.pdb no matter what run it resulted from. Is there a way to make it unique for example with the actual run number in place of 0001? This makes it difficult to compare files in pymol. Thanks, Heather Condurso UF-Department of Chemistry condurso(a)ufl.edu

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Difficult MR with TNCS
by Ian Slaymaker 25 Nov '12

25 Nov '12

Dear Phenix Community, I am having difficulties solving a protein-DNA complex structure and was hoping for some ideas or strategies. My data diffracts to 3A and depending on how I index my data fits well into I4 or P4. I have also been exploring everything in lower space groups. My MR model has 64% identity to my unsolved protein. The crystal protein is 24kD and runs as a monomer or sometimes a dimer. Xtriage strongly suggests that there is tNCS due to a strong patterson peak at 0.5, 0.5. 0.5. Using the phaser GUI, when I search around P4, I get very promising statistics (TFZ = 20's and LLG ~2000), and oddly, in these cases phaser places two subunits on top of each other (despite default packing limitations) with the protein beta sheet cores overlapping, and rotated 180 degrees of each other. The density looks believable, but obviously something is very wrong. The crystal packing would be feasible if another subunit were placed, but I have been able to coax phaser to find a complete solution. It would rather place it overlapping than in available spaces. My questions: 1) does this suggest that there is some form of twinning going on? 2) sometimes phaser (phenix GUI) tells me it is adjusting for tNCS and sometimes it says its NOT (even when there is an even number of subunits being searched for), is this a bug or deliberate? 3) I have tried using phaser from the command line in MR_AUTO mode with the keywords TNCS_USE ON TNCS PATT PERCENT 88 TNCS_NMOL 2 or 4 but dont see any indication that the TNCS adjustments are being made and I have not been able to repeat my phaser GUI results this way. 4) What is a good strategy for tackling this particular problem? Right now I am just chugging through my list of possible space groups, compositions and resolution ranges, but need to look through each possible solution individually because of the misleading statistics and so is very inefficient and time consuming. Thank you for any help or comments. Ian

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Re: [phenixbb] Question about refinement group definition
by Shota Nakamura 20 Nov '12

20 Nov '12

中村昇太 Pavel Afonine <pafonine(a)lbl.gov>: >Hi Carsten, > >some keywords have type "multiple" and some not. In your example, >rigid_body has type multiple, that is you can specify as many of them as >you want: > >rigid_body = chain A >rigid_body = chain B >rigid_body = chain C > >and that means you will be refining three rigid bodies. Same applied to >tls, and many others. > >anisotropic is not multiple, so it can be only one. I recall I had >reasons to make it this way when implementing it but it was long long >time ago, so I forgot what it was. > >To see all attributes for all parameters: >phenix.refine --show-defaults=all.all > >which will yield a long hard to digest list. > >Pavel > >On 11/20/12 6:25 PM, Schubert, Carsten [JRDUS] wrote: >> Hello all, >> >> I have a question about the parameter definition for refinement groups (hope I picked the right term here). How does the definition and handling of refinement groups vary from the "refine.sites.rigid_body" scope to the "refine.adp.anisotropic" scope? For instance: >> >> refine { >> strategy = *individual_sites individual_sites_real_space *rigid_body \ >> *individual_adp group_adp tls *occupancies group_anomalous >> sites { >> individual = None >> torsion_angles = None >> rigid_body = chain A >> rigid_body = chain B >> } >> adp { >> individual { >> isotropic = None >> anisotropic = chain A >> anisotropic = chain B >> >> } >> >> would refine chains A and B as separate rigid groups, whereas only chain B would be refined anisotropically. >> Is this an intended behavior? >> >> BTW "anisotropic = chain A or chain B" refines both chains as expected. >> >> Cheers, >> >> Carsten >> >> >> _______________________________________________ >> 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

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radiation damaged residues occupancy refinement
by Mikalai Lapkouski 20 Nov '12

20 Nov '12

Hello, I have a 1.2A model with the signs of radiation damage, judged by the negative peaks around the carboxyls (atoms CD, OE1 and OE2) of glutamates probably due to decarboxylation. I wan to refine occupancy of those atoms to account for negative density. What is the proper way of doing it? I tried to set the occupancy for those atoms 0.8 and refine individually. But obviously occupancies for those atoms are individually refined to different values which I dont think is the right way. Is there a way of how to refine occupancies for those atoms so that they remain identical after refinement (say all have 0.6)? Or is there another procedure of how to deal with refinement of radiation damaged side-chains? Any suggestions, please? Thank you Nick

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Job history recovery
by Damian Niegowski 20 Nov '12

20 Nov '12

Hello all, I have run into a problem with the Job History tab in the GUI. For one project there is a listing of 16 jobs but when I try going into Job History there is nothing. The .phenix directory for that project is present and all other directories of the individual jobs are there. Is there a way to "restore" the job history from existing parameter files? Regards, Damian Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegowski(a)ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39

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Refining Anomalous Groups
by Brennan Bonnet 20 Nov '12

20 Nov '12

Hi All, I am trying to use phenix.refine to refine partially occupied xenon sites using the Anomalous Groups selection under "Refinement settings". My list of anomalous scatters initially consisted of 22 peaks as located by HySS. Some of these were removed as they originated from S atoms from Met and Cys residues and a few others were removed after previous refinement steps due to having zero occupancy. My remaining sites consist of my xenons (hopefully) and other metals such as Mg or Zn which are mixed in and look like partially occupied xenon sites. My problem is that when I try to define the 11 remaining sites for the "refine anomalous groups" selection the software complains: Invalid combination: F-obs not anomalous, but refinement of 11 f_double_prime values requested (11 scatterers): Please provide anomalous reflection data or fix all f_double_prime values (see refinement.refine.anomalous_scatterer.group input blocks) I can't figure out exactly what I need to change to make it work and can't find a guide anywhere. Do I need to provide additional data or is the syntax for the sites incorrect maybe? Please help! ~Brennan~

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Phaser
by Morten Groftehauge 19 Nov '12

19 Nov '12

Hi guys, I was trying out the new Parallel Phaser (dev-1214) and using a model prepared by Rosetta covering 25% of the total structure (32% identity to the homology model), NCS = 2. 5 models actually but not really relevant since the program spontaneously stopped running after a couple of hours (I love what it's supposed to do though!). My question is about the log however. In the Parallel Phaser log it says: Expected LLG and Resolution Limits ---------------------------------- Expected LLG target: 120.00 Expected LLG achieved: 120.0 Resolution of All Data: 2.38 Resolution limited by eLLG target: 4.83 This resolution WILL NOT be used as the default The expected LLG achieved is greater than 120 (eLLG target) but when I tried to recreate that run in the regular Phaser-MR I get this message in the log Expected LLG and Resolution Limits ---------------------------------- Expected LLG target: 120.00 Expected LLG achieved: 49.7 Resolution of All Data: 2.38 Resolution limited by eLLG target: 2.38 This resolution WILL NOT be used as the default The expected LLG achieved is less than 60 (half eLLG target) FTF rescoring WILL be performed due to low expected LLG signal Deep search will be performed from the start I think the second result looks more realistic (unfortunately) but I still don't understand why the difference? Cheers, Morten PS Seems like there's a memory leak in 1214 and 1207 when I run the Phaser step of MR_Rosetta. Does this sound right? Definitely in 1207 but it seems like it's still there in 1214. -- Morten K Grøftehauge, PhD Pohl Group Durham University

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SASTBX server
by Tanner, John J. 19 Nov '12

19 Nov '12

I apologize if this is an inappropriate post for phenixbb… Has anyone had trouble with the SASTBX server lately? I have been getting this error since Friday when calculating shapes and P(r). Server error! The server encountered an internal error and was unable to complete your request. Error message: Premature end of script headers: cctbx_web.cgi If you think this is a server error, please contact the webmaster<mailto:[email protected]>. Error 500 sastbx.als.lbl.gov<http://sastbx.als.lbl.gov/> Fri Nov 16 07:56:37 2012 Apache/2.2.17 (Unix) PHP/5.3.4

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fwd: West Coast Protein Crystallography Workshop
by Nathaniel Echols 18 Nov '12

18 Nov '12

(There will probably be several people from our group attending this year.) ---------- Forwarded message ---------- From: "Williams, John Charles" <jwilliams(a)coh.org> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Cc: Date: Sun, 18 Nov 2012 08:15:19 -0800 Subject: West Coast Protein Crystallography Workshop All, Wayne Hendrickson will be the keynote speaker for the West Coast Protein Crystallography Workshop, scheduled for March 17th - March 20th at the Monterey Plaza and Spa. Registration will open up Dec 1st. Hope to see you there! Best, John Williams WCPCW Organizer

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v1.8.1 installation hangs
by Alex Theodossis 17 Nov '12

17 Nov '12

Hi, I'm attempting to install the latest version of phenix on mac 10.5.8, using the command line installer. Installation proceeds well until towards the end, where it hangs on: precompiling .py files I can leave it for up to an hour without any further progress, but upon typing: ctrl+c The installation comes back to life and proceeds to completion. Can anyone advise as to what might be causing this and on how reliable this installation is going to be? Thanks in advance.

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Alternate conformation occupancies sum more than 1
by Mikalai Lapkouski 15 Nov '12

15 Nov '12

Hello, I was refining the 1.2 A structure. After refining occupancies there are several residues with alternate conformers for which the sum of the occupancies is greater than one. For example: GLY A 197 O Occupancy sums to 1.14 MET B 17 CB Occupancy sums to 1.03 TYR B 142 CD1 Occupancy sums to 1.04 TYR B 142 CZ Occupancy sums to 1.01 GLY B 197 O Occupancy sums to 1.23 The density is defined nicely for them, do you know what can be the problem of why the sum could be more than 1? Thank you Mikalai

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Restraints file for a new amino acid residue
by Agnes Thiane Pereira Machado 14 Nov '12

14 Nov '12

Hi We are trying to refine a protein structure with a (covalently) modified residue. The colosest discussion to our problem is: http://www.phenix-online.org/pipermail/phenixbb/2010-August/015629.html We ran: phenix.elbow --residue SSC ourmodel.pdb And read the due cif file at phenix refinement. The residue by itself is OK, but we were not able to perform the peptide bond between C and N. How to complete the .cif file such that it has due restraints for the peptide bond with this modified residue? Agnes

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Off topic: Anomalous signal
by ash.k＠aol.com 14 Nov '12

14 Nov '12

Dear all, I am sorry for this off topic question in the bb. I have good looking but poorly diffracting (3.8-4 A) crystals of SeMet derivative. Mass spec confirmed that Se incorporation is 100% and I got a very good energy scan for Se too. I properly selected the peak, inflection and remote wavelengths for the data collection. But, I do not see anomalous signal in the data collected. Processing in HKL2000 does not show any resolution dependance of Chi square and also xtriage says that the anomalous resolution limit is only up to 8-9A. Is it something usual for the kind of diffraction I am getting or something else is going on? I have 5/200 methionine residues in the sequence. Worst case I can think of is that all the Met side chains are disordered ! Any help would be highly appreciated.. AK

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den_refine on cluster
by Michael Thompson 13 Nov '12

13 Nov '12

Hi All, Apologies if this is a naive question, but I would like to run DEN refinement and I notice the documentation says that it runs optimally on a machine with at least 30 processor cores. Is there any way to run DEN refinement on a SGE cluster as a batch job using something like run_command="qsub" as can be done with autobuild, etc.? Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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Simulated anneal
by Qiang Chen 13 Nov '12

13 Nov '12

Hi all, I have a 3.05Å structure. I refine it to Rwork=25.2 Rfree=28.81. I use Molprobity to check the structure. The clash score is 100th and Molprobity score is 99th. I was suggested to run simulated anneal to help reduce Rwork and Rfree. I tried Cartesian and Torsion and different seed. The best result I got is: torsion anneal, start_temp=2500,final_temp=300, random_seed=4250146. The Rwork:25.8, Rfree=31.2. I checked the new model and found that some places in a domain were not correctly traced. The density for that domain is not good and have several flexible loops. My question is: does simulated anneal always work and reduce Rwork/Rfree? At the final stage of refinement, does it necessary to use simulated anneal again? Thanks! yamei The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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phenix.pdbtools - renumber specific chains
by Antony Oliver 12 Nov '12

12 Nov '12

Apologies if this has been covered before - but can someone point me to a way of renumbering only specific chains (i.e. F, G, H etc). I have tried using phenix.pdbtools with either selection = "chain F or chain G or chain H" or keep "chain A or chain B or chain C or chain D" - but in both cases phenix renumbers every single residue! With thanks, Antony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oliver(a)sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512

3 3

Setting up MR_Rosetta
by Julio Lenin 08 Nov '12

08 Nov '12

Hello guys, I am currently trying to setup MR_Rosetta but I am running into some trouble. When I run the tutorial for Defensin HNP-3 from the GUI I always get an error during the ... process (see image at this dropbox link). I know that my path for phenix and rosetta are correct since I can run the phenix_regression.wizards.test_command_line_rosetta_quick and phenix_regression.wizards.test_command_line_rosetta_quick test_rosetta_rebuild. If I try to trace down the error, I can only get the same info that I got from the GUI error message (vide supra). As additional info, here are somme details of my setup: MacBookPro 4,1 running OS 10.6.8 Core2Duo 2.5 Ghz 6 Gb RAM Rosetta 3.2 compiled with flags bin mode=release Phenix 1.8.1-1168 And my input settings for the GUI run (dropbox) Now, this might just be confusing but there was one command line test that my setup failed: phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta The error is kinda cryptic (see dropbox copy of the error) but it seem to be a discrepancy in the scoring results not a missing program or any other kind of misconfiguration. Of course, I might be wrong. Any advice? Best regards. -- Lenin Domínguez-Ramírez "And for all the current and rather silly emphasis on structural biology,understanding enzymes means understanding catalysis and catalysis is concerned with kinetics, not structure: as Jeremy Knowles aptly remarked, studying the photograph of a racehorse cannot tell you how fast it can run." Cornish-Bowden, 1995 Lenin Domínguez-Ramírez, PhD "What are we to think of an organism that loses practically all of its cellular water at ordinary temperatures and pressures and ceases to metabolize, but upon being rehydrated resumes all of the characteristics it previously exhibited?...we should be reluctant to call such an organism dead (unless we are willing to entertain the possibility of its resurrection) because it resumes an active life upon simple restoration of water."

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Sugar refine in phenix
by Jan van Agthoven 05 Nov '12

05 Nov '12

Hi everyone, This is a basic question. I would like to refine the sugar ends of my protein. The sugar polymers are made of NAG and BMA and whenever I use phenix.ready_set and subsequently phenix.refine it results in a structure of disconnnected sugar monomers. Indeed the cif file generated by phenix.ready_set does'nt give any geometry constraints for connecting the monomers. How do create a cif file that tells phenix.refine how to refine the sugars? Thanks, Jan

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ligand fitting, density and refinement
by Terwilliger, Thomas C 02 Nov '12

02 Nov '12

Hi Huaidong, I'm not quite sure exactly what you did...could you possibly elaborate a little? My confusion comes from two things. First, this phrase: "did the refinement with the output files from ligandfit", is confusing to me because I would not think that you would want to use any output files from ligandfit except for the ligand PDB file. Second, I agree, I can't see why ligandfit would find good density for your ligand if it is not present in a difference map calculated from the original data. All the best, Tom T ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of 张怀东 [zhanghuaidong(a)hust.edu.cn] Sent: Thursday, November 01, 2012 8:11 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Ligandfit_SigmaF_obs Hi,Tom T We followed the instruction after the ligandfit, and did the refinement with the output files from ligandfit. The electron density for the ligand is clear, but in the refinement with the original mtz file, the density is not there. So how to explain the difference? Is this a bug? Thanks! Huaidong > -----原始邮件----- > 发件人: "Terwilliger, Thomas C" <terwilliger(a)lanl.gov> > 发送时间: 2012年11月1日星期四 > 收件人: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> > 抄送: > 主题: Re: [phenixbb] Ligandfit_SigmaF_obs > > Hi Ed, > > Yes, good point. I will be changing the way the wizards read in and store reflection data (sometime soon I hope!) and at that point this should be moot because the wizards won't write out dummy intermediate files. > > All the best, > Tom T > > ________________________________________ > From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Ed Pozharski [epozh001(a)umaryland.edu] > Sent: Thursday, November 01, 2012 9:44 AM > To: PHENIX user mailing list > Subject: Re: [phenixbb] Ligandfit_SigmaF_obs > > On Thu, 2012-11-01 at 14:23 +0000, Terwilliger, Thomas C wrote: > > The sigma values are not useful, and are just set to 1.0 in that file. > > Tom, > > I've seen this issue before, and I am just wondering what could be the > rationale to reset sigmas to 1.0? Seems like one would have to code for > this to happen, and even if the sigma values are not used for map > generation, why isn't the column simply omitted but instead replaced > with obviously incorrect values? > > Ed. > > -- > Oh, suddenly throwing a giraffe into a volcano to make water is crazy? > Julian, King of Lemurs > > _______________________________________________ > 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 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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Ligandfit_SigmaF_obs
by 张怀东 01 Nov '12

01 Nov '12

Hello, I am a newcomer. I need help. I have done phenix.ligandfit, and the result contained a mtz file named resolve.mtz. While sigma_F_obs in the file are all 1.0. Is there something wrong with the file? Is this a bug? Could I do phenix.refine with the resolve.mtz added R_flag, next? sincerely, Huaidong Zhang

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refining with f' and f" values
by Subhani Bandara 01 Nov '12

01 Nov '12

Hi Everyone, I have a structure with heavy metals which I would like to refine anomalous scattering factors. I could get the f' and f" values from Autosol, when I gave the atom name and wavelength. But when I ran refinement with anomalous scattering giving .mtz file and pdb file from pHENIX refinement I got the error "Invalid combination-F-obs not anomalous, provide anomalous reflections or fix all f" values. Then I used reflection file editor of GUI to create a mtz file that has anomalous data using the original reflection file and the mtz file of refinement. But still it gives an error. I must be doing something wrong, but cannot figure out what that is. Thanks in advance for any help. Subhani

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Rwork Rfree Bonds Angles
by Hexi Zhang 01 Nov '12

01 Nov '12

Dear All, During Phenix refinement, it request the Rwork and Rfree graduately decrease (at least no increase). But there is no request that the Bonds (should be RMS?) and the Angles (should also be RMS?) should graduately decrease. Am I right? I am looking forward to getting your reply. Hexi

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"H" atom refining occupancy with previous altconf residue in sequence
by Alexander Scouras 31 Oct '12

31 Oct '12

After a series of residues (1+) with alternate conformations, the H atom of the next residue seems to lock its occupancy to that of the final conformation of the previous residue. Hence I'm getting several H's with 0.1-0.5 occupancy on single conformation residues, where the entire rest of the residue has occupancy 1. This happens after every altconf series, and showed up in two separate structures I've worked on this week. Within a series of 2+ residues with altconfs, the H's refine correctly with their altconf groups. So it isn't just that all subsequent residue's H's are getting overridden. This behavior seems to have started with 1.8.1-1168, or at least previous refinements of the same structure didn't do this. 64 bit build on Retina MBP running OS X 10.8.2. I couldn't google any reference to this behavior, so assuming it's a new bug I can send along source files. Below I've pasted a couple residues from one of my PDBs. I added a ***** to mark the offending H with the wrong occupancy. -Alex Scouras ATOM 668 N CMET A 29 -17.970 6.464 59.720 0.21 10.72 N ANISOU 668 N CMET A 29 1641 1300 1133 -328 -379 -50 N ATOM 669 CA CMET A 29 -17.578 5.189 60.316 0.21 9.05 C ANISOU 669 CA CMET A 29 1545 882 1012 -248 -350 -140 C ATOM 670 C CMET A 29 -17.248 5.317 61.797 0.21 7.83 C ANISOU 670 C CMET A 29 1363 666 947 173 -134 166 C ATOM 671 O CMET A 29 -17.496 4.395 62.578 0.21 7.92 O ANISOU 671 O CMET A 29 1187 751 1071 371 -145 338 O ATOM 672 CB CMET A 29 -16.376 4.609 59.573 0.21 9.09 C ANISOU 672 CB CMET A 29 1561 834 1059 -243 -283 -203 C ATOM 673 CG CMET A 29 -16.681 4.210 58.145 0.21 9.05 C ANISOU 673 CG CMET A 29 1529 756 1154 -28 -331 -235 C ATOM 674 SD CMET A 29 -18.049 3.042 58.009 0.21 13.05 S ANISOU 674 SD CMET A 29 2356 1325 1279 -218 -284 -50 S ATOM 675 CE CMET A 29 -17.505 1.757 59.124 0.21 12.06 C ANISOU 675 CE CMET A 29 1866 1485 1232 -630 -667 420 C ATOM 676 H CMET A 29 -17.333 6.878 59.318 0.21 12.87 H ATOM 677 HA CMET A 29 -18.320 4.557 60.216 0.21 10.86 H ATOM 678 HB2CMET A 29 -15.671 5.275 59.551 0.21 10.91 H ATOM 679 HB3CMET A 29 -16.069 3.819 60.044 0.21 10.91 H ATOM 680 HG2CMET A 29 -16.916 5.004 57.640 0.21 10.86 H ATOM 681 HG3CMET A 29 -15.894 3.794 57.761 0.21 10.86 H ATOM 682 HE1CMET A 29 -18.164 1.059 59.140 0.21 14.48 H ATOM 683 HE2CMET A 29 -16.666 1.409 58.813 0.21 14.48 H ATOM 684 HE3CMET A 29 -17.401 2.130 60.002 0.21 14.48 H ATOM 685 N MET A 30 -16.667 6.445 62.187 1.00 6.77 N ANISOU 685 N MET A 30 1361 564 647 -30 -56 18 N ATOM 686 CA MET A 30 -16.416 6.699 63.606 1.00 7.66 C ANISOU 686 CA MET A 30 1362 946 601 -42 -173 2 C ATOM 687 C MET A 30 -17.759 6.724 64.367 1.00 7.62 C ANISOU 687 C MET A 30 1310 944 641 -9 -24 -22 C ATOM 688 O MET A 30 -17.852 6.212 65.486 1.00 9.05 O ANISOU 688 O MET A 30 1571 1151 718 84 98 231 O ATOM 689 CB MET A 30 -15.620 7.987 63.790 1.00 7.65 C ANISOU 689 CB MET A 30 1299 894 714 26 -120 -166 C ATOM 690 CG MET A 30 -14.229 7.965 63.231 1.00 8.62 C ANISOU 690 CG MET A 30 1464 1072 741 31 -163 -10 C ATOM 691 SD MET A 30 -13.130 6.745 64.006 1.00 9.04 S ANISOU 691 SD MET A 30 1555 961 919 105 -180 -94 S ATOM 692 CE MET A 30 -12.812 7.527 65.563 1.00 9.77 C ANISOU 692 CE MET A 30 1540 1284 889 150 -190 -62 C ATOM 693 H MET A 30 -16.395 7.062 61.653 0.21 8.12 H ***** ATOM 694 HA MET A 30 -15.872 5.965 63.962 1.00 9.19 H ATOM 695 HB2 MET A 30 -16.099 8.709 63.352 1.00 9.18 H ATOM 696 HB3 MET A 30 -15.550 8.173 64.739 1.00 9.18 H ATOM 697 HG2 MET A 30 -14.278 7.758 62.284 1.00 10.35 H ATOM 698 HG3 MET A 30 -13.831 8.840 63.354 1.00 10.35 H ATOM 699 HE1 MET A 30 -12.228 6.968 66.079 1.00 11.73 H ATOM 700 HE2 MET A 30 -12.397 8.378 65.406 1.00 11.73 H ATOM 701 HE3 MET A 30 -13.644 7.648 66.026 1.00 11.73 H

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Re: [phenixbb] Troublesome molecular replacement
by Yuri 29 Oct '12

29 Oct '12

Nat, Just a few simple thoughts: --1) Are you certain about the space group, and did you try letting --Phaser pick one for you? (It sounds like you did, but I can't tell --from your description.) I searched for a solution in all possible space groups in P 4. I thought I was certain of the space group, but maybe not... --2) How much refinement did you run to get an R-free of 42$, and did --you already try running AutoBuild with rebuild-in-place turned off? --Refinement alone may not have the radius of convergence you need. True, I only did a couple of rounds of rebuild/refine --3) What is the sequence identity? My model is a point-mutant of the crystal. --4) Are you using the latest version of Phenix? Phaser has had TNCS --support for almost a year now but I keep hearing from people who are --using ancient versions... I am using the latest official PHENIX built. --- -- Yuri Pompeu

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Troublesome molecular replacement
by Yuri 29 Oct '12

29 Oct '12

Dear community, I recently collected on a crystal that diffracted pretty well to 2.0 A. It indexes and scales fairly well in P 4 21 2 with cell dimensions 100, 100, 200. This would predict 4 molecules/ASU. I found a MR solution in P 41 21 2 but it does not refine very well Rfree =42%. Xtriage detects strong peaks at 0,0,0.25 for Translational NCS. Any suggestions on how to go about this one? Thanks -- Yuri Pompeu

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autobuilding homomers
by Ingemar Andre 29 Oct '12

29 Oct '12

I have a question about the proper procedure for building homomers. My test case is a trimeric coiled-coil with 3-fold symmetry (trimer in assymetric unit). My input model is a trimer with three chains (A,B,C) with identical sequence. If I run phenix autobuild (rebuild_in_place=False) with this model I get a structure with decent R/Rfree. However, there are some issues: 1) Helix 1 consists of chain A in the output structure. There is a jump in the sequence number for chain A at the end. However, disregarding this chain break the full sequence is correct for helix 1. 2) Helix 2 consists of chain B + C in the output structure. The chain B has the correct sequence for helix 2. Chain C has partly the right sequence for helix 2. 3) Helix 3 consists of chain C in the output structure. Chain C has partly the correct sequence for helix 3. Lots jumps in the sequence numbering. GIven that I know its has three subunits with identical sequences I gather it should be possible to have autobuild generate structures with three chains with identical sequences. I have tested a few things. With and without giving it the sequence file corresponding to the sequence of a monomer. With and without enforcing ncs based on the input model (find_ncs=False input_ncs_file=find_ncs.ncs_spec). I am never able to build sequence-symmetric structures with rebuild_in_place=False for any homomer I have tried to build. I have limited experience with phenix so it is likely I am missing something obvious. In any case, I would appreciate your input on this. Best regards, Ingemar

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Parallella
by Morten Groftehauge 27 Oct '12

27 Oct '12

Hi guys, So the Parallella project seems like it is going forward (with the smaller processor first off) http://www.kickstarter.com/projects/adapteva/parallella-a-supercomputer-for… I figure that phenix would have problems with low amount of RAM but are there other reasons that Phenix and Parallella might not play well together? Supposedly ships in May, btw. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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HYSS and Xtriage general questions
by Heather Condurso 26 Oct '12

26 Oct '12

Dear all, I am currently solving a structure using anomalous data from a Se-Met derivative. I collected a SAD set recently and am trying to use HYSS to find the sites. I am still not 100% sure which space group it is, but I am fairly confident that it is P43212/P41212. I have scaled the data with HKL and gave the resulting sca files to Xtriage. The recommended resolution cut off from Xtriage is 4.0 with the optimistic cut off at 3.6A. The anomalous signal is 0.15. I am hoping this data is good enough, but am also trying to get better data. In the meantime I am chugging along with the data I have. I have tried the fast version of HYSS with all of the higher P4 space groups varying the resolution and number of sites. I often find that for a given sca file the resolution given is important with 4.0A giving 1 site and 3.6A giving 24 out of 24 but with a cc of ~0.2. However, when I look at the sites and maps it seems a bit odd that all of sites lie in nearly a plane. So here are! a few questions: 1. My cell is rather large with dimensions of 132, 132, 195. Does expected CC for a good solution differ based on the size of the cell or the total number of expected sites? I expect 4 chains each with 6 sites. 2. Is it likely that I will find a solution with the anomalous signal only going to 4.0A? Are there other parameters that may clue me in as to whether or not it may be possible with this data? My data is also anisotropic. Does that play a role in finding a solution? I have other data sets, but in those the mosaicity varies outside the ideal range. In this set the mosaicity varies between 0.2 and 0.5 when I integrate the images without fixing the mosaicity. 3. I've also tried to use the full search, but I'm not sure if it is working or not. I am using the GUI with version 1.7.3-928 on a Mac running OS 10.6.8. I just realized now that this is not the latest version and I can try it on another machine that I know is running 1.8.1-1168. None the less, the run status window only shows that it is running, but the log display only shows the initial search parameters, not what it is currently doing. I also tried using different rescoring and the log display is blank. Does this mean it isn't doing anything? Or should I be more patient? Some of these have been running for days.... I appreciate any advice you may have to help me along! Heather Condurso UF-Department of Chemistry condurso(a)ufl.edu

2 1

adding some user-defined graphical objects in a PDB file (and displaying them)
by Francois Berenger 25 Oct '12

25 Oct '12

Hello, For some new project, I'd like to be able to generate things and store them in PDB format. For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and "line width" would be nice. Is there some official recommended way of doing this? Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case. I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation. My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround. My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera. Thanks a lot for your suggestions, Francois.

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Re: [phenixbb] Table 1 stastics
by Kay Diederichs 25 Oct '12

25 Oct '12

Dear all, I just want to point out that one possible source of discrepancy between I/sigma reported by a data processing program, and I/sigma reported by a program that uses the relevant cctbx routine is the following: that cctbx routine calculates the variance of merged data as max("internal variance", "external variance") which is different from what the data processing programs do (they calculate the "internal variance" - I hope I didn't get it the wrong way round). SHELXC and SHELXL also calculate the variance of the merged data like the data processing programs do. I dislike this "feature" of cctbx but I do not know if phenix.table_one actually uses this routine for this purpose. thanks, Kay P.S. you can find the discussion over at the cctbx mailing list; see e.g. http://phenix-online.org/pipermail/cctbxbb/2012-September/000530.html and other posts. On 10/18/2012 09:08 PM, phenixbb-request(a)phenix-online.org wrote: > Date: Thu, 18 Oct 2012 08:07:44 -0700 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Table 1 stastics > Message-ID: > <CALeAa1NDDy7=ZCUqThgun+k-Si7-Gf920ROvuYwpPgsShAhHVQ(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Thu, Oct 18, 2012 at 7:53 AM, Andrew Waight<waight(a)msg.ucsf.edu> wrote: >> Thanks for Phenix! Anyway quick question, I tried out the "generate >> Table1" utility for fun and noticed that my I/SigI and completeness do not >> match what is found in my XSCALE file. >> ... >> How does Phenix compute these parameters? Obviously my I/sigI has gotten >> much better (1.59 versus 0.85) but the scaling statistics should be the >> correct ones. > > It computes these statistics directly from the reflection data you > provide, not the log file. (The reasoning being that since these are > the data that Phenix actually uses, the statistics calculated from > them are more accurate and relevant than whatever the scaling program > thinks.) My guess is that some of the internal processing accounts > for the difference - could you please send me the data file? > > FYI, the plan for the future is to recalculate all of these statistics > from unmerged data rather than rely on parsing data processing > logfiles, which obey no standard format and are subject to change > without notice. > > -Nat > -- 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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Problem with elbow
by Subhani Bandara 25 Oct '12

25 Oct '12

Dear all, I am using the PHENIX version 1.8.1-1168 and need to get the pdb file and the cif file for the metal-chelate complex Gd-DTPA for refinement of a structure. I got the pdb file and the cif file for a dimer of the complex. Then I edited those to contain only one metal chelator complex and used as inputs in elbow. I have attached the pdb file and the cif file I used as inputs. I gave cif file as chemical file type with pdb file as initial geometry and ran elbow. Then I used pdb file only or cif file only as inputs separately. Every time it ended with the error “Failed to determine the bonding of a fragment of the molecule” Also I tried using smile string C(CN(CC(=O)[O-])CC(=O)[O-])N(CCN(CC(=O)[O-])CC(=O)[O-])CC(=O)[O-].[Gd+3]and pdb file as inputs. Then it runs without an error, but it outputs cif and pdb files containing only Gd. How can I get the cif file for the metal-chelate complex? I want to use the metal-chelate complex as one entity in the refinement, so that it will have the correct geometry of the chelator. Thanks Subhani

2 1

1.8.1 1168
by Colin Levy 25 Oct '12

25 Oct '12

Hi all, I have just updated to the latest version of Phenix 1.8.1 1168 but I now appear to have lost the ability to drag and drop files between different windows. Running on a mac 10.7.5 OSX. Thanks Colin Manchester Protein Structure Facility MIB 1.025 Tel 0161 306 5185 c.levy(a)manchester.ac.uk<mailto:[email protected]>

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question du jour: monomer libs where?
by Patrick Loll 24 Oct '12

24 Oct '12

Where does PHENIX find the monomer libraries? Here's why I ask: I submit a refinement job for a peptide containing a mix of D- and L-amino acids. The program seems to have no problem with D-versions of Glu, Asn, or Phe (DGL, DAS, or DPN), but it flags the atoms in a D-ornithine (ORD) residue as having unknown nonbonded energy type symbols. Curiously, when I look in the relevant directories in ...Contents/phenix-1.8.1-1168/chem_data/chemical_components I can find cif files corresponding to ALL of these D-amino acids, including ORD (...chemical_components/o/data_ORD.cif). Files are also present for DGL, DAS, and DPN. However, these files don't contain all of the information I'm accustomed to seeing in monomer libraries (e.g., explicit bond lengths & angles), so I'm not sure if the same information is somehow encoded differently (via the idealized coordinates, perhaps?), or if I'm barking up the wrong tree. So: Are these the actual monomer libraries that phenix.refine consults? And in this case why doesn't phenix.refine recognize ORD? Or are the true monomer libraries hiding elsewhere? As always, thanks, Pat ps the directory structure I'm describing is under OS X 10.7.5 --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pjloll(a)gmail.com pat.loll(a)drexelmed.edu pat.loll(a)drexel.edu

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some basic questions about phenix autobuild and phenix.refine
by Niks 24 Oct '12

24 Oct '12

Dear All, I have recently started using PHENIX so I am a beginer in PHENIX field. I am getting better statistics (Rfactor/Rfree) as compared to REFMAC so having strong inclination to continue with PHENIX but there are some discripancies I found when comparing with CCP4 programs.Therefore i I have some basic questions which I request you to throw some light and wisdom. 1) I have solved my structure using AutoMR and got two files MR.1.mtz and MR.1.pdb as output with high LLG of 8236.889. When going for AutoBuild afterwards it uses output pdb (MR.1.pdb) which is fine but uses MR.1.mtz as map coefficient. Shouldnot it uses original mtz from scala? 2) Same in Phenix.refine when going after Autobuild finishes and it asks for refining the model it uses same AutoMR output mtz (MR.1.mtz). As I was suggested by many that we should use original mtz coming from scala for Refinement to reduce model bias. shouldnot phenix.refine use Original mtz file here too? 3) After going for AutoBuild after AutoMR, even when I unselect "Place Waters" options in parameters for Refinement, I see output pdb file with waters added to it. I do not want waters to be added till I refine my model to the best , but Autobuild option comes out with waters added. Is there anyway I can have autobuilt pdb without waters added? 4) Another question that troubling me most that in Phenix.refine even if I use original mtz which clearly specifies resoultion range from 127.488-2.5A my refined pdb files comes out with Resolution range used for refinement as 37.8-2.5A. I have tried to input low resolution range as 127.488 but deafult is always 37.8 selected. My data may be very poor in lower resolutions than 37.8A but my completeness is also going down (65.5% as opposed to 79.8% in REFMAC). Can I select my refinement using my specified values of Resolution from mtz file coming out from SCALA? Sorry for the lengthy mail and many questions. Thanks and regards Nishant PhD Student, C/O Dr. C. G. Suresh, National Chemical Laboratory, Pune, India -- "The most difficult phase of life is not when No one understands you;It is when you don't understand yourself"

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