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scattering_table in phenix.real_space_refine
by Keitaro Yamashita 26 Mar '19

26 Mar '19

Dear PHENIX developers, For the refinement of CryoEM structure, I changed scattering_table to electron from default (n_gaussian in phenix-1.13), but the resultant coordinates and ADPs were exactly same while map-model CCs were improved. Looking into the code, I noticed scattering_table is not passed to the ADP refinement code (mmtbx.refinement.real_space.adp.real_space_group_adp_refinery_via_reciprocal_space) and xray_structure is newly constructed from a pdb_hierarchy object; therefore a default table in scattering_type_registry() (which is n_gaussian) is always used. Is this an intended behavior? I modified the code to use the scattering table of electron in ADP refinement, and CCs were improved (CC_mask 0.7566 to 0.7813; both evaluated with scattering_table=electron). Best regards, Keitaro

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Refinement
by StrBio 24 Mar '19

24 Mar '19

ALL. I have data at 2.4 A in P21 sp gr, helical protein. Refined to Rwork 29 Rfree 34 with nice density map and all nice statistics oither Rfactor (by Phenix). Refmac quit same. Should I deposit it or look better data? Any suggestion?

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Phenix Rosetta hybrid refinement PHENIX_ROSETTA_PATH error
by Ahmad Khalifa 23 Mar '19

23 Mar '19

But I have the path set! (base) [labusr@luxor ~]$ echo $PHENIX_ROSETTA_PATH /home/labusr/rosetta:/home/labusr/rosetta/main I attached the log. Please advise.

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Distance constraint to atom in symmetry copy in phenix.refine
by Julian Esselborn 23 Mar '19

23 Mar '19

Dear community, we have a somewhat complicated problem to which I don't seem to find a solution. We have a structure, which has a number of 3-fold and 2-fold symmetry axes in the final assembly structure. The 3-fold axes are hold together by metal atoms on the axis. However, we have three cases of these axes: 1. Symmetry axis falls onto the crystallographic symmetry axis. We can deal with this; setting metal to 0.33 occupancy and setting metal-protein distance constraints. This is a proper symmetry axis. 2. Symmetry axis doesn't fall onto a crystallographic symmetry axis, but all three monomers coming together are within the same symmetry copy of the ASU. Even easier, metal stays at occ=1 and we just set constraints to chain A, chain B, chain C. 3. The really challenging case, where the axis doesn't fall onto the symmetry axis, but the three monomers coming together are in different symmetry copies of the ASU. Cases (2) and (3) are pseudo-symmetric in the crystallographic sense. Usually a bit of intelligent moving around of the monomers to their crystallographic symmetry positions should push all monomers of case (3) into neighboring positions within the same ASU ending up as case (2); problem solved. BUT: In our structure we have too many 3fold axes, such that there will always be one of them ending up as case (3). E.g. the three monomers are chains A, B, C, but they do not end up neighboring in the ASU. Rather the axis is formed by A, B' and C'' (with ' denoting different symmetry copies of the ASU). We could assign the metal to chain A with occ=1 and no metal in B and C. However, we would need to set a distance constraint from the metal to it's ligands in protein monomer B and protein monomer C. But it is only the ligand in B' and C'', which are actually close to the metal in A. The ligands in B and C are at the other end of the ASU. Is there a way to set a distance constraint such that it measures the distance to a crystallographic symmetry copy? A different idea was to just assign an alternative position alt A, alt B and alt C to the metal, with A being close to the ligand in monomer A, B close to monomer B and C close to monomer C. That way we could make constraints. But we would need to cross fingers that the three metal atoms actually end up in the same spot once applying the crystallographic symmetry (and remember, that 3-fold axis is not constructed by applying a 3fold rotational symmetry around that axis; rather an actual crystallographic symmetry somwhere else brings them together; means the ligands with their metal atoms can actually move independently). I'm a bit at a loss how to deal with this and would appreciate input. Thanks a lot in advance! all the best Julian ---- Julian Esselborn Postdoctoral Researcher Tezcan group University of California, San Diego

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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 21 Mar '19

21 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 20 Mar '19

20 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 19 Mar '19

19 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 18 Mar '19

18 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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