November 2012 - phenixbb - phenix-online.org

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 30 Nov '12

30 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 29 Nov '12

29 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 28 Nov '12

28 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 28 Nov '12

28 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 27 Nov '12

27 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 26 Nov '12

26 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 21 Nov '12

21 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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