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error in running autobuild
by intekhab alam 21 Feb '12

21 Feb '12

hi i am working with phenix version 1.7.1-743. after running auto mr i tried to run autobuild but it failed and generated the following message. i am unable to run autobuild now. kindly help. OError : [Errno 5] Input/output error Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/phenix/wxGUI2/Runtime.py", line 172, in OnUpdate self.propagate_event(event, "OnUpdate") File "/usr/local/phenix-1.7.1-743/phenix/wxGUI2/Runtime.py", line 228, in propagate_event fn(event) File "/usr/local/phenix-1.7.1-743/phenix/wxGUI2/Programs/Phaser/Output.py", line 194, in OnUpdate self.process_callback(callback.message, callback.data) File "/usr/local/phenix-1.7.1-743/phenix/wxGUI2/Programs/Phaser/Output.py", line 209, in process_callback print "CALLBACK: %s %s" % (str(message), str(data)) IOError: [Errno 5] Input/output erro -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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FFT map coefficients only for certain chains
by Zhang yu 20 Feb '12

20 Feb '12

Dear Phenixers, Is that possible to generate map coefficients only for certain chains? For example, I have two chains, A and B, and I would like to output a map file only contains coefficients for chain A. The "isomesh" command in Pymol could generate similar images. But my purpose is not for presentation, I need a map file only contains coefficient for certain chains. In the interface of "FFT" tool in Phenix or CCP4, there is an option to include a PDB file and define atom selections. It describe that "If a PDB is supplied, the output map will cover the model plus a buffer on all sides. The atom selection parameters can be used to specify a smaller region" . If I define the selection as chain A when I run the FFT, the output map still covers a rectangular block containing chain A, instead of regions only surrounding chain A. Thanks. Yu Zhang

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CCN Jan 2012 article : find_alt_origin_sym_mate
by Bryan Lepore 17 Feb '12

17 Feb '12

will the find_alt_origin_sym_mate article in CCN Jan. 2012 be described in any other publications? -Bryan

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MRage
by Graeme Winter 17 Feb '12

17 Feb '12

Hi Folks, Following from the newsletter article I am trying to test out phaser.MRage. I have a well solved case which I know is in the pdb and a sequence file: phaser.MRage hklin=data.mtz composition.component.sequence=sequence.pir symmetry_exploration=pointgroup mode=full search.services=ncbi composition.count=3 however it generates a second component then complains it knows nothing about this: Sorry: Molecular weight needed for component 2. Any suggestions how to get around this? Many thanks, Graeme [gw56@ws050 rage]$ phaser.MRage hklin=data.mtz composition.component.sequence=sequence.pir symmetry_exploration=pointgroup mode=full search.services=ncbi composition.count=3 ############################################################################### # MRage version 0.1.0 # ############################################################################### All configuration options: -------------------------- hklin = data.mtz labin = None resolution_cutoff = 2.5 crystal_symmetry { unit_cell = None space_group = None } mode = quick *full symmetry_exploration = *pointgroup enantiomorph dataset output { root = "mrage" max_solutions_to_write = 0 gui_base_dir = None save_aniso_data = False job_title = None } composition { count = 3 component { sequence = sequence.pir stoichiometry = 1 ensemble { coordinates { pdb = None identity = None } } model_collection { trim = False coordinates { pdb = None identity = None } } template { pdb = None alignment = None } homology { file_name = None max_hits = 3 } search { services = local ncbi max_hits = 3 } } component { sequence = None stoichiometry = 1 ensemble { coordinates { pdb = None identity = None } } model_collection { trim = False coordinates { pdb = None identity = None } } template { pdb = None alignment = None } homology { file_name = None max_hits = 3 } search { services = local *ncbi max_hits = 3 } } } queue { technology = lsf threading sge *multiprocessing pbs cpus = 1 submission_command = None qslot_cpus = 1 } packing_pool = 20 rotation_peaks_cutoff = 0.75 post_refinement_cutoff = 0.75 final_selection_cutoff = 0.75 b_factor_refinement = True significant_peak_threshold = 7.0 sculptor_protocols = 11 10 13 12 1 3 2 5 4 7 6 9 8 *all minimal template_equivalence = False exclude_pdb_ids = None simple_run { enable = False component_sequence = None template_model = None blast_services = local ncbi max_blast_hits = 3 } Sorry: Molecular weight needed for component 2.

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AutoSol with 4.2A dataset for a protein/DNA complex
by Wei Shi 17 Feb '12

17 Feb '12

Hi everyone, I have got a 4.2A SeMet MAD dataset for a protein-DNA complex. And, the native dataset for this protein-DNA complex is ~3.2A. The space group for the native and SeMet crystals seem to be different. I am not sure whether it’s possible to solve the structure with the current data I have, and wondering whether any of you have experience with working with this low-resolution data and any suggestion for me. I processed the data with XDS in space group P31, and used *.cns.hkl file from XDSCONV as an input for AutoSol and also include the sequence for protein only. The protein dimer has 418 residues and DNA is 32bp. I run Autosol with the default setting. Below is statistics I got. It seems that I didn’t get anything promising. Any comment or suggestion about what to try next? Thank you so much! Statistics: Top solution: 2 Sites: 11. Space group: P32. FOM: 0.550. BAYES-CC: 8.10. Residues: 465 Side-chains: 0. Chains: 60. Model CC: 0.67 R-work: 0.4100 R-free: 0.4569. Under Heavy-atom search and phasing: Space group # of refined sites FOM Overall score R-factor Map skew Corr. of local RMS density Solution1 P31 11 0.530 8.10+/-11.80 0.4184 -0.12 0.66 Solution2 P32 11 0.550 8.10+/-11.80 0.3881 -0.10 0.66 Best, Wei

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Comprehension of Orotidine 5'-Monophosphate Decarboxylase
by Kevin Jin 16 Feb '12

16 Feb '12

Dear all, I wrote a story for Orotidine 5'-Monophosphate Decarboxylase. http://www.jinkai.org/Enzymology.html Best, Kevin

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Re: [phenixbb] qFit error in fixing alternate conformations
by Subhani Bandara 15 Feb '12

15 Feb '12

Hi, I used qFIT to fix the alternative conformations of my protein with a chelator complex, by submitting a PDB file and a mtz file. But it gave following error. What could be the reason for this. > > ___Run time error messages (if any):___ > xyz.pdb mtz.rfl FP SIGFP > Sorry: No matching array: refinement.input.xray_data.labels=FP,SIGFP > Thanks Subhani

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Re: [phenixbb] Example datasets
by mohamed noor 15 Feb '12

15 Feb '12

Dear Phenix users Is there some examples datasets involving 3-wavelength MAD phasing available? I would like to learn from indexing to structure solution with a combination of CCP4 and Phenix if possible. Thanks.

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cbf file
by Theresa H 15 Feb '12

15 Feb '12

Hi all Is there a utility to convert cbf file from Pilatus detector to mtz in Phenix? Thank you. Theresa

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Re: [phenixbb] alternative conformation of residues
by Subhani Bandara 15 Feb '12

15 Feb '12

Hi all, I have a protein where three consecutive amino acids have alternative conformations. I edited the PDB file to have those altloc and made total occupancy of A and B to 1.00. But after refinement both A and B are overlapping and I could see the positive density for one conformation away from that (may be b'se I didn't change coordinates of B conformation). How can I move the B altloc in to the positive density. Do I have to edit the coordinates on PDB and if so how can Ido that? Thanks in advance for any help Subhani

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