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Latest phenix from command line
by Graeme Winter 05 Oct '09

05 Oct '09

Hi Folks, I'm one of those people who use the command-line for everything, and I just found my "phenix mad spell" phenix.autosol sites=8 atom_type=Se infl.data=TS03_12287_free.mtz \ infl.f_prime=-9.9 infl.f_double_prime=3.9 low.data=TS03_12287_free.mtz \ low.f_prime=-3.3 low.f_double_prime=0.5 \ infl.labels='F_INFL SIGF_INFL DANO_INFL SIGDANO_INFL' \ low.labels='F_LREM SIGF_LREM DANO_LREM SIGDANO_LREM' no longer appears to work: Traceback (most recent call last): File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/command_line/autosol.py", line 585, in <module> run_autosol=run_autosol(args=sys.argv[1:]) File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/autosol/wizard_command_line.py", line 300, in __init__ self.Sorry(line) File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/autosol/wizard_command_line.py", line 1238, in Sorry raise AssertionError,e AssertionError: Sorry, unknown file or keyword: infl.data=TS03_12287_free.mtz Possibilities... (use 'phenix.autosol --help all' to get full help): general.data_quality=TS03_12287_free.mtz data=TS03_12287_free.mtz Looked at the doc and saw: MAD dataset The inputs for a MAD dataset need to specify f_prime and f_double_prime for each wavelength. You can use a parameters file "mad.eff" to input MAD data. You run it with "phenix.autosol mad.eff". Here is an example of a parameters file for a MAD dataset. You can set many additional parameters as well (see the list at the end of this document). autosol { seq_file = seq.dat sites = 2 atom_type = Se wavelength { data = peak.sca lambda = .9798 f_prime = -8.0 f_double_prime = 4.5 } wavelength { data = inf.sca lambda = .9792 f_prime = -9.0 f_double_prime = 1.5 } So I make mad.eff from information above, then -bash-3.2$ phenix.autosol mad.eff Traceback (most recent call last): File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/command_line/autosol.py", line 585, in <module> run_autosol=run_autosol(args=sys.argv[1:]) File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/autosol/wizard_command_line.py", line 155, in __init__ self.process_wizard_params(args) File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/command_line/autosol.py", line 562, in process_wizard_params self.Sorry("Unrecognized file or keyword: "+str(arg)) File "/dls_sw/apps/phenix/1.5-2c/phenix-1.5-2/phenix/phenix/autosol/wizard_command_line.py", line 1238, in Sorry raise AssertionError,e AssertionError: Unrecognized file or keyword: mad.eff As listed in the instructions. Any clues, anyone? Many thanks in advance, Graeme

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PHENIX parallel computing?
by Joe Krahn 03 Oct '09

03 Oct '09

A parallel version of PHENIX was discussed before. I know that parallelization of refinement is difficult, and probably not worth the effort when there is still a lot of function/methods work. However, running parallel independent tasks could pay off without a lot of work. For example, optimization of WXU and WXC can spawn multiple tasks with different test weights. Annealing tasks could also run multiple jobs, and pick the best result, or even merge results based on real-space fit analysis. Joe Krahn

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Does PHENIX exclude Rfree reflections in maps?
by Joe Krahn 03 Oct '09

03 Oct '09

Does PHENIX exclude R-free reflections when computing maps? IMHO, it is bad to use test reflections in maps, or anywhere else other than computing R-free, but opinions vary. If some people still want test reflections in maps, maybe it could be an option. Thanks, Joe Krahn

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installing phenix 1.5-2
by Tirumala Kumar Chowdary 02 Oct '09

02 Oct '09

Hi, My 1.5-2 build installation is failing with this error 'installing binary components making directory build-binary/intel-linux-2.6-x86_64/beryl/tmp/binary gzip: /nfs/home/chowdary/Download/phenix-installer-1.5-2/bundles/bundle-1.5-2-intel-linux-2.6-x86_64.tar.gz: invalid compressed data--format violated finding installed versions finding binary versions cat: build/intel-linux-2.6-x86_64/version: No such file or directory no pre-existing binary components detected installing new binary package configuring PHENIX components Error configuring: see /nfs/home/chowdary/Download/phenix-installer-1.5-2/build-binary/intel-linux-2.6-x86_64/beryl/log/binary.log for details' and the log file shows this error. /bin/tar: Unexpected EOF in archive /bin/tar: Unexpected EOF in archive /bin/tar: Error is not recoverable: exiting now /nfs/home/chowdary/Download/phenix-installer-1.5-2/bin/install-from-binary: line 349: /nfs/home/chowdary/phenix/phenix-1.5-2/build/intel-linux-2.6-x86_64/base/bin/python: No such file or directory. Earlier builds (1.4.175) are installing and running fine on the same machine. Help please.. Tirumal

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RESOLVE question
by Peter Grey 01 Oct '09

01 Oct '09

Hello, We use iterative cycles of manual building (coot) - refinement (phenix) - density modification to improve maps for the next building step (RESOLVE). Should we use FMODEL,PHIFMODEL from phenix or FCALC,PHIFCALC in the input to RESOLVE. MODEL structure factors are closer to experimental ones but are they better for density modification purposes ? I think that if the program uses , as in DM, only Fobs and phases to calculate the maps then PHIFCALC is better (no contribution of solvent) but if the programs calculates 2Fo-Fc maps then FMODEL,PHIFMODEL is better since it was shown that these maps are beter when bulk solvent correction is used. Could you please comment whether this reasoning is correct and give information as to which is the case in resolve. Thanks, -- Peter

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Re: [phenixbb] refining sugars
by Jose M Casasnovas 01 Oct '09

01 Oct '09

Dear Ralf. I just solved the problem with the sugar refinement. Somehow the way the BETA1-4 cif defines the link is in the reverse order to the NAG-ASN cif link (at least to way I was used to do it). In the NAG-ASN cif, residue_selection_1 in the phenix.refine input must be the NAG and residue_selection_2 the ASN, such as I was used to do in CNS. However, the BETA1-4 cifs follows the opposite way: residue_selection_1 must be the first sugar residue (linked through O4) and residue_selection_2 the second sugar (linked through the C1), which is the most distant residue to the Asn. Thanks so much for your help and to all who sent comments and suggestions. Jose M Casasnovas -- Centro Nacional de Biotecnología (lab. B16) CSIC, Campus UAM Darwin 3 28049 Madrid Spain Ph. 34 915854917(8) Fax. 34 915854506 email: jcasasnovas(a)cnb.csic.es

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Re: [phenixbb] refining sugars
by Engin Ozkan 30 Sep '09

30 Sep '09

I just answered Jose's question on this yesterday. The reason you are having trouble is that there is no NAG-NAG link. It is a BETA1-4. Read the post to see what data_link names are allowed, and use them for your sugars. Below is a copy-paste of my post from yesterday: >That's because there is no such data link as NAG-NAG-B-D. Instead, you >should use a BETA1-4 link. This is similar to what CNS used, if you are >familiar with that (I think it was B14 in CNS). >If you want to know where all the phenix link definitions are, type > >phenix.where_mon_lib_list_cif > >and read the file that's listed. > >It is good to read this to know which residue selection is selection_1 >and which is selection_2. In it you'll see this or something like this. > >data_link_BETA1-4 ># >loop_ >_chem_link_bond.link_id >_chem_link_bond.atom_1_comp_id >_chem_link_bond.atom_id_1 >_chem_link_bond.atom_2_comp_id >_chem_link_bond.atom_id_2 >_chem_link_bond.type >_chem_link_bond.value_dist >_chem_link_bond.value_dist_esd > BETA1-4 1 O4 2 C1 single 1.439 0.020 >loop_ >_chem_link_angle.link_id >_chem_link_angle.atom_1_comp_id >_chem_link_angle.atom_id_1 >_chem_link_angle.atom_2_comp_id >_chem_link_angle.atom_id_2 >_chem_link_angle.atom_3_comp_id >_chem_link_angle.atom_id_3 >_chem_link_angle.value_angle >_chem_link_angle.value_angle_esd > BETA1-4 1 C4 1 O4 2 C1 108.700 3.000 > BETA1-4 1 O4 2 C1 2 O5 112.300 3.000 > BETA1-4 1 O4 2 C1 2 C2 109.470 3.000 > BETA1-4 1 O4 2 C1 2 H1 109.470 3.000 >loop_ >_chem_link_tor.link_id >_chem_link_tor.id >_chem_link_tor.atom_1_comp_id >_chem_link_tor.atom_id_1 >_chem_link_tor.atom_2_comp_id >_chem_link_tor.atom_id_2 >_chem_link_tor.atom_3_comp_id >_chem_link_tor.atom_id_3 >_chem_link_tor.atom_4_comp_id >_chem_link_tor.atom_id_4 >_chem_link_tor.value_angle >_chem_link_tor.value_angle_esd >_chem_link_tor.period > BETA1-4 BETA_1 1 O4 2 C1 2 C2 2 C3 0.00 20.0 1 > BETA1-4 BETA_2 1 C4 1 O4 2 C1 2 C2 0.00 20.0 1 > BETA1-4 BETA_3 1 C3 1 C4 1 O4 2 C1 0.00 20.0 1 >loop_ >_chem_link_chir.link_id >_chem_link_chir.atom_centre_comp_id >_chem_link_chir.atom_id_centre >_chem_link_chir.atom_1_comp_id >_chem_link_chir.atom_id_1 >_chem_link_chir.atom_2_comp_id >_chem_link_chir.atom_id_2 >_chem_link_chir.atom_3_comp_id >_chem_link_chir.atom_id_3 >_chem_link_chir.volume_sign > BETA1-4 2 C1 1 O4 2 O5 2 C2 positiv > >Engin On 9/30/09 10:56 AM, Tirumala Kumar Chowdary wrote: > Thanks for the reply, > > here is part of the log file, which shows the parameter input for nag > refinement > > > Monomer Library directory: > "/usr/local/phenix/phenix-1.4-125/chem_data/mon_lib" > Total number of atoms: 6260 > apply_cif_link: > data_link: NAG-ASN > mod_id_1: DEL-O1 > mod_id_2: DEL-HD22 > residue_selection_1: chain C and resname NAG and resid 1670 > residue_selection_2: chain A and resname ASN and resid 670 > apply_cif_link: > data_link: NAG-ASN > mod_id_1: DEL-O1 > mod_id_2: DEL-HD22 > residue_selection_1: chain C and resname NAG and resid 1784 > residue_selection_2: chain A and resname ASN and resid 784 > apply_cif_link: > data_link: NAG-NAG > residue_selection_1: chain C and resname NAG and resid 1784 > residue_selection_2: chain C and resname NAG and resid 1785 > Number of models: 1 > Model: "" > Number of chains: 3 > Chain: "A" > Number of atoms: 5125 > Number of conformers: 1 > Conformer: "" > Number of residues, atoms: 681, 5125 > > I am presuming that it read what ever it needs to make the ASN-NAG > bonds and NAG-NAG bonds. > > what am I missing here ? > > Tirumal > > > Quoting Engin Ozkan<eozkan(a)stanford.edu>: > >> You don't need to create cif files; phenix has them. NAG is definitely >> there, and you can have two NAGs linked by any biologically-relevant >> glycosidic bond you want. You need to define the links, however. I think >> posting the cif_link.params may get you more help. >> >> Engin >> >> On 9/30/09 8:49 AM, Tirumala Kumar Chowdary wrote: >>> Hi, >>> >>> My question is related to the 'refining sugars in phenix' questions >>> that have been appearing on the bb for the last two days. >>> >>> I am trying to refine my NAGs and somehow phenix is ignoring the sugars >>> in my structure. Neither it is making a bond between my ASN and NAG nor >>> NAG-NAG bond. My nag-nag.cif and cif_link.params are read properly, >>> though. >>> >>> I am using in version 1.4.125 still. Is this the problem ? Does >>> upgrading to any of the later build will help ? >>> >>> >>> Tirumal >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >> >> >> -- >> Engin Özkan >> Post-doctoral Scholar >> Howard Hughes Medical Institute >> Dept of Molecular and Cellular Physiology >> 279 Campus Drive, Beckman Center B173 >> Stanford School of Medicine >> Stanford, CA 94305 >> ph: (650)-498-7111 >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > > > -- Engin Özkan Post-doctoral Scholar Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111

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GUI fonts
by Frank von Delft 30 Sep '09

30 Sep '09

Hi, I've just been poking around the new GUIs - neat!! But the font is absolutely enormous, which is terrifically annoying. Where do I change it? (I didn't see it in the preferences.) Cheers phx

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refining sugars
by Tirumala Kumar Chowdary 30 Sep '09

30 Sep '09

Hi, My question is related to the 'refining sugars in phenix' questions that have been appearing on the bb for the last two days. I am trying to refine my NAGs and somehow phenix is ignoring the sugars in my structure. Neither it is making a bond between my ASN and NAG nor NAG-NAG bond. My nag-nag.cif and cif_link.params are read properly, though. I am using in version 1.4.125 still. Is this the problem ? Does upgrading to any of the later build will help ? Tirumal

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N-linked glycans in phenix.refine
by Jose Casasnovas 30 Sep '09

30 Sep '09

Dear Phenix users. I am trying to refine N-linked glycans in phenix. The Asn-NAG link appears to be recognize by the program, but the NAG-NAG link is not. I guess the cif_link must be missing. Monomer Library directory: "/home/soft/phenix/phenix-1.4-3/ext_ref_files/mon_lib" Total number of atoms: 8947 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain N and resname NAG and resid 5161 residue_selection_2: chain E and resname ASN and resid 516 apply_cif_link: data_link: NAG-NAG-B-D Sorry: Missing CIF link: data_link_NAG-NAG-B-D Please check for spelling errors or specify the file name with the link as an additional argument. How can I get the required cif_link file and where to place it?? Any suggestion. Thanks. Jose

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Phenix version 1.5 Released
by Paul Adams 30 Sep '09

30 Sep '09

The Phenix developers are pleased to announce that version 1.5 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Just some of the new features in this version (1.5-2) are: - A new Graphical User Interface (accessed by typing phenix at the command line) - Two-way communication with Coot - The latest version of Phaser (2.2) - A development version of torsion angle dynamics available in phenix.refine - Real space refinement in phenix.refine - New GUIs for Autosol, AutoBuild and LigandFit wizards - A number of MolProbity and other validation tools now available - Fast loop building with phenix.fit_loops - Improved ligand geometry generation with phenix.elbow - Inclusion of Nicholas Sauter's LABELIT system for autoindexing and more For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Acting Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Patty Jimenez [ PAJimenez(a)lbl.gov ] [ 1-510-486-7963 ] --

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anomalous difference map demonstration in pymol
by crystallogrphy 30 Sep '09

30 Sep '09

Hi, I have used anomalous data to do refinement. The crystal diffracts to 3.5A. The resulting mtz file shows good anomalous density around the heavy atoms. Now I want to demonstrate the density in Pymol. Does anyone know how to generate the map use the map file in MTZ format in Pymol? Thanks!

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transfering R-free flags
by Tirumala Kumar Chowdary 28 Sep '09

28 Sep '09

Hi, I am trying to refine my model against a higher resolution file. I want to transfer my R-free flags generated by phenix.refine from the lower resolution mtz to the higher resolution file. Is there a way to transfer the R-free flags in Phenix ? If not, where can I find the mtz file from my earlier refinement with R-free flags generated ? Does phenix.refine generate this file and save it for me somewhere ? Thanks Tirumal

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NCS restraints with TLS
by Joe Krahn 28 Sep '09

28 Sep '09

I am using NCS restraints with TLS. It seems that the NCS B-factor restraints are applied to the overall B-factor, rather than just the non-TLS part. Is this correct? In my structure, the disorder varies quite a bit among equivalent molecules, and I don't get good results unless the b_factor_weight is about 1e-3 or less. I am experimenting with NCS restraints in CNS, where each pair of coordinates allows an LSQ fit of B-factor scale and offset to be excluded from the B restraints. It would probably work even better with TLS, which CNS does not have. I don't know if anyone has tried this, but I think that overall molecular B-factor differences are fairly common. Joe Krahn

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NCS averaged maps?
by Francis E Reyes 26 Sep '09

26 Sep '09

With all the recent talk about kicked and filled maps, can we have phenix output an ncs averaged map for those of us who have NCS? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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extend R-free set to higher resolution
by NATHAN THOMSEN 25 Sep '09

25 Sep '09

Is there a phenix utility to extend a phenix generated R-free set to higher resolution (while still using lattice symmetry etc.)? Thanks! Nathan Thomsen UC Berkeley

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Re: [phenixbb] extend R-free set to higher resolution
by Thomas C. Terwilliger 25 Sep '09

25 Sep '09

Hi Nathan, Yes, you can use the GUI to do this (you need a recent nightly build to do it). Just click on "Reflection file editor" and you get an option to extend a free R set, maintaining the free R set you already have. All the best, Tom T >> Is there a phenix utility to extend a phenix generated R-free set to >> higher resolution (while still using lattice symmetry etc.)? Thanks! >> >> Nathan Thomsen >> UC Berkeley >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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wxu_scale is ignored with TLS
by Joe Krahn 25 Sep '09

25 Sep '09

When using TLS, the wxu_scale is changed, even if it is given in the input file. IMHO, TLS should only modify the default value, and not a user-defined wxu_scale. Thanks, Joe Krahn

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Various problems with phenix.refine
by Joe Krahn 25 Sep '09

25 Sep '09

Here are a few problems I have found using phenix.refine 1.4: If NCS restraint selection in the .def file have newline characters, the REMARK 3 formatting is messed up. It should probably replace all white-space regions with a single space. When NCS restraints contain a residue with alternate conformations, that residue gets excluded from all equivalences, even if the selections contain ALTID to avoid the redundant atoms. If the .def file has a syntax error, phenix.refine dies with an error that the file format is not recognized. Why not print syntax errors? The optimize_wxc and optimize_wxu features are useful, but it is difficult to use the result to define an improved fixed scale on subsequent rounds, without having to optimize every time. It is not obvious whether the scale written in the log represents the new wxc_scale, or if it is a multiplier versus the current wxc_scale. The log also truncates to 2 decimal places. In my case, I only get one significant digit from scale=0.05. I propose that the optimizations write something like "Optimal wxc_scale = 0.533". The input data is written as "refine_data.mtz", not using the serial number, and there seems to be no flag to disable writing it. That means I have to force overwrite to run iterations in the same directory. If each run is in its own directory, the serial number is not very useful for filenames. So, the output MTZ should have the serial number, and you might also consider an option to disable the serial number when separate directories are used. Thanks, Joe Krahn

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specifying column labels for input MTZ file
by Tirumala Kumar Chowdary 24 Sep '09

24 Sep '09

Hi, I am trying to run phenix.refine with a sharp output MTZ file (column labels H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav). Phenix.refine stopped at 'Multiple equally suitable arrays of observed xray data found. Possible choices: sharp_sad_se_eden.mtz:FP,SIGFP sharp_sad_se_eden.mtz:Fav,SIGFav Please use refinement.input.xray_data.labels' Can someone tell me on how to use this 'refinement.input.xray_data.labels' and how to specify which column labels to use. There is nothing written in the documentation about it. Thanks Tirumal

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question about rfree flag transfer
by crystallogrphy 24 Sep '09

24 Sep '09

Hi, I have built a model against a 3.7A data set by AutoBuild. The resulting model is overall_best.pdb. The data with the rfree test flags is exptl_fobs_phases_freeR_flags.mtz Later on, I got a 3.4A data, which is isomorphous with the 3.7A data. Now I want to transfer the rfree flag from the 3.7A to 3.4A data for refinement. I know one strategy if the data file is in CNS format. That is, use DATAMAN to transfer the flags and generate new test set flags in the high resolution range: 3.7-3.4A. However, when I convert the format by phenix.reflection_file_converter, it fails: phenix.reflection_file_converter exptl_fobs_phases_freeR_flags.mtz --cns=exptl_fobs_phases_freeR_flags.cv --label="PHIM" --label="FP,SIGFP" --label="FOMM" --label="FreeR_flag" --label="FC" However, the resulting data does not have any FP, SIGFP, and FreeR flags. { file: exptl_fobs_phases_freeR_flags.cv.cns } { sg=C2 a=175.385 b=102.472 c=92.057 alpha=90 beta=111.312 gamma=90 } { source of data: exptl_fobs_phases_freeR_flags.mtz:FC } NREFlections=15307 ANOMalous=FALSe DECLare NAME=DATA DOMAin=RECIprocal TYPE=REAL END INDEx 0 0 5 DATA= 0 INDEx 0 0 7 DATA= 0 INDEx 0 0 8 DATA= 0 INDEx 0 0 9 DATA= 0 INDEx 0 0 10 DATA= 0 INDEx 0 0 11 DATA= 0 INDEx 0 0 12 DATA= 0 INDEx 0 0 13 DATA= 0 I also tried mtz2various in CCP4i, the resulting hkl file does not have rfree flags at all. Does anyone know who to convert the exptl_fobs_phases_freeR_flags.mtz into cns format or simple transfer the flags by phenix?

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supported compilers for source builds
by Ben Eisenbraun 23 Sep '09

23 Sep '09

For compiling PHENIX from source, what are the supported compilers? Are the Intel or Portland compilers supported? There are notes in the list archives about using OpenMP with gcc, and hints that the Intel compiler is supported, but I didn't see any docs on building with icc/ifort. In one email Ralf mentions that you might actually lose performance compiling your own version of Solve/Resolve because gfortran optimizes poorly, which leads me to think that the distributed binaries are using ifort for at least the Solve/Resolve bits. Did I overlook some notes on how to do this? -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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question about composite SA_omit map in phenix
by crystallogrphy 22 Sep '09

22 Sep '09

Hi, I am using molecular replacement to build a model against a 2.2A resolution data set. However, the template model only has 23% sequence identity. First, I use chainsaw in CCP4i to prune all side chain to be poly-Ala except the identical residues. Then I use AutoMR and rigid body refinement, I got Rfree=50%. The continuous electron density is not bad showing second structures. However, the model has some out-of-registration problem, for example, two proline are in a alpha-helix. In other words, it has model bias. I want to use composite SA-omit to get a less model bias map, not a simple composite omit map or a SA_omit map ommiting a part of the region. Does someone know who to do this? Thanks! Qun Wan postdoc fellow Case Western Reserve University

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heavy atom in pdb for refinement
by crystallogrphy 20 Sep '09

20 Sep '09

Hi, I have Zn atoms in my pdb for refinement. However, it failed with the following scripts. Do I have to create a libary of this heavy atom? Number of atoms with unknown nonbonded energy type symbols: 6 "ATOM 1 Zn Zn Z 1 .*. Zn " "ATOM 2 Zn Zn Z 2 .*. Zn " "ATOM 3 Zn Zn Z 3 .*. Zn " "ATOM 4 Zn Zn Z 4 .*. Zn " "ATOM 5 Zn Zn Z 5 .*. Zn " "ATOM 6 Zn Zn Z 6 .*. Zn " Time building chain proxies: 1.78, per 1000 atoms: 0.45 Here is the format of my pdb: ..... ATOM 1 Zn Zn Z 1 32.028 47.603 13.955 1.00 30.00 Zn ATOM 2 Zn Zn Z 2 29.017 71.434 8.164 1.00 30.00 Zn ATOM 3 Zn Zn Z 3 39.223 49.330 -6.810 1.00 30.00 Zn ATOM 4 Zn Zn Z 4 24.811 89.144 -4.406 1.00 30.00 Zn ATOM 5 Zn Zn Z 5 23.652 72.429 6.125 1.00 30.00 Zn ATOM 6 Zn Zn Z 6 30.132 63.054 -31.918 1.00 30.00 Zn TER 7 Zn 6 ATOM 10 CL CL L 1 20.125 63.405 10.719 1.00 30.00 CL TER 11 CL 1

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RuntimeError : min()
by RAVINDRA D MAKDE 19 Sep '09

19 Sep '09

Hi all, I will highly appreciate your help to resolve the following bugs encountered during running phenix.refine on GUI as well as on command lines. My version of Phenix and platform are: PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.4 Release tag: 3 cctbx tag: 2008_12_07_1353 Platform: mac-intel-osx osx-10.5.8 The error encountered using phenix refinement GUI (phenix.refine_gui) is as follows: A Python error was detected. This is almost certainly a bug; please send an email containing this message to phenixbb(a)phenix-online.org so we can fix it. Thanks!RuntimeError : min() argument is an empty arrayTraceback:Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Base.py", line 274, in OnBrowse self.file_text_field.SetValue(new_path) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Controls.py", line 974, in SetValue self.phil_handler.propagate_update(self.phil_def_name, new_value) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/PhilInterfaceHandler.py", line 103, in propagate_update self._update_handlers[def_name](self, def_name, value) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Extensions.py", line 28, in extract_xray_neutron_params phil_def_name = phil_object_name) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 155, in __init__ self.load_reflection_file(file_name, phil_def_name) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 159, in load_reflection_file self.hkl_server = self.hkl_handler.add_hkl_file(file_name, phil_def_name) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 66, in add_hkl_file err=sys.stderr) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_utils.py", line 393, in __init__ force_symmetry=self.force_symmetry)) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_reader.py", line 197, in as_miller_arrays base_array_info=base_array_info) File "/usr/local/phenix-1.4-3/iotbx/mtz/__init__.py", line 434, in as_miller_arrays and flex.min(column_group.sigmas()) > 0): The error encountered using phenix refinement on command line (phenix.refine coordinate.pdb reflection.mtz) is as follows: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/refine.py", line 9, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 68, in run log=log) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 231, in __init__ reflection_file_server = self.reflection_file_server() File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 566, in reflection_file_server err=self.log) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_utils.py", line 393, in __init__ force_symmetry=self.force_symmetry)) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_reader.py", line 197, in as_miller_arrays base_array_info=base_array_info) File "/usr/local/phenix-1.4-3/iotbx/mtz/__init__.py", line 434, in as_miller_arrays and flex.min(column_group.sigmas()) > 0):RuntimeError: min() argument is an empty array N.B. Earlier, I had encountered the similar error (using command line) using PHENIX version 1.3 on the same platform. Thanks in advance. Regards, Ravi Ravindra D. Makde, PhD Postdoctoral fellow, Tan lab, The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 USA

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