- phenixbb - phenix-online.org

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

2 2

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.

4 5

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

2 1

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

3 2

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

2 2

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

3 2

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

2 2

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

1 0

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

2 1

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

4 4

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

2 1

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.

1 0

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: >>

2 1

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

6 9

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

2 1

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

2 2

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

1 0

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

1 0

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

2 4

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

2 1

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~

3 5

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

4 6

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

3 2

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

1 0

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.

2 1