March 2019 - phenixbb - phenix-online.org

Map Segmantation
by Yangqi Gu 22 Mar '19

22 Mar '19

Hi Everyone, I have a naive question about segmentation. I have a low resolution map of a filament (~20 A) and I know the helical symmetry. I have monomer sequence but no structure. I am wondering if I could segment the filament and obtain the monomer density? Does segment_and_split_map work on the low resolution case? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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How to get command line of operation run through gui?
by Ahmad Khalifa 20 Mar '19

20 Mar '19

I'm trying to box out a cryo-em map and used the option "padding=" as per the documentation, but received error interpreting command line argument. is the documentation outdated? Regards.

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mmCIF for deposition
by Patrick Loll 19 Mar '19

19 Mar '19

Hi all, Following the instructions given here: https://www.phenix-online.org/documentation/overviews/xray-structure-deposi… I’m attempting to use mmtbx.prepare_pdb_deposition to insert sequence information into the mmCIF that contains the model coordinates. Unfortunately, the program fails with an error (shown below). The sequence file is FASTA format, and contains an entry for each of the (4) chains in the AU, i.e. >A MSEQNCE… >B MSEQNCE… etc. Any bright ideas? ============this is what happens (vide infra)==================================== [PJL-iMac:blahblah/PJL_final] loll% mmtbx.prepare_pdb_deposition filename.cif seq_name.fasta Starting mmtbx.prepare_pdb_deposition on Mon Oct 1 11:16:23 2018 by loll =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, filename.cif Found sequence, seq_name.fasta Processing PHIL parameters: ------------------------------------------------------------------------------- No PHIL parameters found Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = “filename.cif" } default_model = “filename.cif" sequence_files = "seq_name.fasta" default_sequence = "seq_name.fasta" } Starting job =============================================================================== Validating inputs Using model: filename.cif Using sequence: seq_name.fasta Creating mmCIF block for sequence Traceback (most recent call last): File "/Applications/phenix-1.14-3260/build/../modules/cctbx_project/mmtbx/command_line/prepare_pdb_deposition.py", line 9, in <module> run_program(program_class=prepare_pdb_deposition.Program) File "/Applications/phenix-1.14-3260/modules/cctbx_project/iotbx/cli_parser.py", line 71, in run_program task.run() File "/Applications/phenix-1.14-3260/modules/cctbx_project/mmtbx/programs/prepare_pdb_deposition.py", line 98, in run alignment_params=self.params.mmtbx.validation.sequence.sequence_alignment) File "/Applications/phenix-1.14-3260/modules/cctbx_project/iotbx/pdb/hierarchy.py", line 1190, in as_cif_block_with_sequence assert len(chain.residue_groups) + chain.n_missing_start + chain.n_missing_end == len(sequence) AssertionError (gouts of smoke, terrified squealing) The ‘No PHIL parameters found’ message is concerning, but the program clearly seems to be finding the input file names. Suggestions welcome. Thanks, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology 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 pjl28(a)drexel.edu

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FEM by using FoFc map
by Danilo Belviso 18 Mar '19

18 Mar '19

Dear all, I am interested in fitting a ligand in the case of a structure where water molecules have been already placed. I know that this is not the standard procedure, but these water molecules are quite sure. To do this, I used ligand fit procedure with command "lig_map_type = *fo-fc_difference_map fobs_map pre_calculated_map_coeffs" command. At the end, the procedure provides ligands with low CC (0.4-0.55). So, I would try ligand fitting by using FEM of Fo-Fc. The rationale is that FEM of Fo-Fc could help (likely) ligand fitting, by consider the presence of water molecules at the same time (Fo-Fc should be 0 where water molecules are placed). Maybe nothing will change, but I would try. I calculated FEM by using phenix.fem start_FEM.pdb start_FEM.mtz input.xray_data.label='FOFCWT' and also by using phenix.fem start_FEM.pdb start_FEM.mtz maps.map_coefficients_label='FOFCWT PHFOFCWT' file_name_prefix='FEM_map' where start_FEM.pdb and start_FEM.mtz are the pdb and mtz resulting from the refinement with water. However, by checking the the fem maps by coot, I notice that fem is completely different from Fo-Fc and it is not the expected feature-enanched Fo-Fc. Is the procedure and keywords correct to perform FEM calculation of Fo-Fc? Do you have any suggestions? Thanks Danilo -- Dr. Belviso Benny Danilo, PhD Istituto di Cristallografia (IC) Consiglio Nazionale delle Ricerche (CNR) via Amendola 122/o, 70126 Bari - Italy Tel ++39 080 5929273 Fax ++39 080 5929170 mail: danilo.belviso(a)ic.cnr.it web: users.ba.cnr.it/ic/crisdb00

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UK Open Research Data Task Force weblink to Report, Case studies and Minister’s response
by John R Helliwell 18 Mar '19

18 Mar '19

Dear Colleagues, Thankyou for asking about the weblink to the case studies. The UK Open Research Data Task Force weblink to Report, Case studies and Minister’s response is here:- https://www.gov.uk/government/publications/open-research-data-task-force-fi… Best wishes, John

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UK Open Research Data Task Force Final Report
by Jrh Gmail 17 Mar '19

17 Mar '19

Dear Colleagues, The UK Open Research Data Task Force Final Report is here:- https://assets.publishing.service.gov.uk/government/uploads/system/uploads/… This will be of general interest. As well as contributing to the general report I wrote the crystallography case study. Best wishes, John Emeritus Professor of Chemistry John R Helliwell DSc_Physics Chairman of IUCr Committee on Data

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completeness issue
by yong zhou 17 Mar '19

17 Mar '19

Dear Pavel, Thanks for your reply. The output file is attached. Please check. Look forward to the reply. Best regards Yong Zhou ________________________________ From: Pavel Afonine <pafonine(a)lbl.gov> Sent: Tuesday, March 12, 2019 6:47 PM To: yong zhou; phenixbb(a)phenix-online.org Subject: Re: [phenixbb] completeness issue Can you send the file to me off-list? I'll have a closer look once I have the file. Pavel On 3/11/19 16:10, yong zhou wrote: Hi, Recently I deposited a structure to PDB. However, I was told there is a large difference between reported (77.89%) and calculated (88.36%) values for data completeness. In order to confirm the information, I used the command phenix.reflection_statistics and the result is as following. Resolution range: 31.6787 1.91132 Completeness in resolution range: 0.783333 Completeness with d_max=infinity: 0.783193 Anomalous completeness in resolution range: 0.599544 Bijvoet pairs: 15786 Lone Bijvoet mates: 9291 Mean anomalous difference: 0.0671 Space group of the intensities: P 2 2 2 Space group of the metric: P m m m Tolerance used in the determination of the lattice symmetry: 3 degrees Possible twin laws: None Completeness of 4-8-(GlcNAc)5/output4-8.sca:I(+),SIGI(+),I(-),SIGI(-): unused: - 31.6830 [ 0/9 ] 0.000 bin 1: 31.6830 - 1.9113 [28083/29673] 0.946 unused: 1.9113 - [ 0/0 ] There are two completeness values 0.783 and 0.946. So which is the correct one? Look forward to the reply. Yong Zhou _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]>

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error in Phaser
by Alexandra Deaconescu 14 Mar '19

14 Mar '19

Hello, I have been trying to run Phaser using a map ensemble when I encountered the error listed below, which caused Phaser to fail. I have also attached the log file. Any help would be much appreciated. Thank you, Alexandra UNHANDLED ERROR: Program internal error in source file TraceMol.cc (line 229) *** Consistency check (wang_mask.size()) failed. ***

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completeness issue
by yong zhou 12 Mar '19

12 Mar '19

Hi, Recently I deposited a structure to PDB. However, I was told there is a large difference between reported (77.89%) and calculated (88.36%) values for data completeness. In order to confirm the information, I used the command phenix.reflection_statistics and the result is as following. Resolution range: 31.6787 1.91132 Completeness in resolution range: 0.783333 Completeness with d_max=infinity: 0.783193 Anomalous completeness in resolution range: 0.599544 Bijvoet pairs: 15786 Lone Bijvoet mates: 9291 Mean anomalous difference: 0.0671 Space group of the intensities: P 2 2 2 Space group of the metric: P m m m Tolerance used in the determination of the lattice symmetry: 3 degrees Possible twin laws: None Completeness of 4-8-(GlcNAc)5/output4-8.sca:I(+),SIGI(+),I(-),SIGI(-): unused: - 31.6830 [ 0/9 ] 0.000 bin 1: 31.6830 - 1.9113 [28083/29673] 0.946 unused: 1.9113 - [ 0/0 ] There are two completeness values 0.783 and 0.946. So which is the correct one? Look forward to the reply. Yong Zhou

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Re: [phenixbb] Fo-Fo difference map for non-isomorphous datasets
by Jordan Luke Pederick 12 Mar '19

12 Mar '19

Also, I am interested if anyone knows of any publications that have included a real-space difference map? Cheers, Jordan ________________________________ From: Jordan Luke Pederick Sent: Monday, 11 March 2019 1:25:57 PM To: Eric Montemayor; Pavel Afonine; Philip Kiser; Tim Gruene; phenixbb(a)phenix-online.org Subject: Re: [phenixbb] Fo-Fo difference map for non-isomorphous datasets Thank you all for the prompt responses and suggestions. My metal ion of interest is Cesium in this case, so I guess I am more interested in using this approach for visualization rather than peak identification - the strong density of Cs is fairly obvious I have attached a few images of the superimposed (Fo, Phi) maps and resulting difference map using either Superpose maps in phenix or transform_map in coot following Tim's suggestions. I also tried using maprot (CCP4) to apply the rotation/translation operator from the LSQ superpose but the resulting map was not superposed correctly (not sure why). Both results seem kind of reasonable - I have shown one of the difference peaks for what is likely to be a bound Cs. For both approaches the peak was very obvious at a 3 sigma level, and could still be observed to around 10 sigma in both cases. I am still unsure about differences in scaling, so although strong positive peaks can be identified, I wouldn't be confident using the map to interpret smaller differences. In response to Eric - I checked the anomalous signal, which was fairly weak. The resulting anomalous difference map did show positive peaks up to a level of ~10 sigma that matched those observed in the above real-space difference maps, with a 3 sigma level corresponding to 0.0137 e/A^3. The CCanom was also low (1-5% between shells), so I was thinking that another approach might be more suitable for this data? Cheers, Jordan ________________________________ From: Eric Montemayor <montemayor.eric(a)gmail.com> Sent: Sunday, 10 March 2019 4:50:21 AM To: Jordan Luke Pederick Subject: Re: [phenixbb] Fo-Fo difference map for non-isomorphous datasets Why not just look for peaks in the anomalous difference Fourier for just the derivative dataset? If there’s even a weak anomalous signal, you won’t need to mess with non-isomorphism between multiple datasets.... the information you need is already contained alone in the derivative dataset. What is the metal? The above approach won’t work for something like magnesium, but should work for almost any transition metal. Eric On Sat, Mar 9, 2019 at 3:23 AM Jordan Luke Pederick <jordan.pederick(a)adelaide.edu.au<mailto:[email protected]>> wrote: Hi, I am trying to generate a Fo-Fo difference map for two data sets of the same protein at ~2.3 angstrom resolution. One dataset is native and the other was soaked with a metal ion, so the purpose of the map is for identifying and visualizing peaks that may correspond to a bound metal ion. These datasets differ by 6 angstroms (~10%) along the A edge - an isomorphous difference map generated in Phenix GUI wasn't useful As an alternative I was planning to make a real-space Fo-Fo difference map making use of Superpose Maps in Phenix Gui as follows: Superpose maps would be used to superimpose (Fobs.metal, PHI.metal) and (Fobs.native, PHI.native) The superimposed maps will be opened in Coot and a difference map generated using "Extensions -> Maps -> Make a difference map" There were two things I was unsure about: Does this seem like a reasonable alternative? Is scaling of the two datasets required before generating the difference map? Cheers, Jordan _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]>

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