- phenixbb - phenix-online.org

Units in intensity?
by Murpholino Peligro 09 Mar '19

09 Mar '19

If I do `phenix.xtriage XDS_ASCII.HKL` I get a log file. In the "Statistics for data merging" of this log file I have: Resolution: 26.02 - 1.40 Observations: 44675 Unique reflections: 16306 Redundancy: 2.7 Completeness: 70.37% Mean intensity: 1656.8 Mean I/sigma(I): 19.8 SigI < 0 (rejected): 644 observations R-merge: 0.027 R-meas: 0.032 R-pim: 0.017 My question is... what units does Mean intensity has? Thanks Ps I am not sure if this has to do with the detector used which was a CCD (type) ADSC QUANTUM 210 (model).

3 5

difference in Wilson B calculated in Xtriange or Polygon
by Eze Chivi 09 Mar '19

09 Mar '19

Hi, The value of Wilson B calculated in Phenix differs for the same data when I use Polygon or Xtriange, why? In Xtriange-->Absolute scale and Wilson analysis: ML estimate of overall B value: 48.88 A**2 In Polygon: 52.05 Thank you Ezequiel

1 0

contour values for Polder and FEM
by V F 08 Mar '19

08 Mar '19

Hi all, What is the recommended values for contouring for Polder and FEM? In pymol, I have a isomesh polder_COA_mesh, polder_207_1, 3, select_COA, carve=2 isomesh FEM_COA, fem_coa_190, 1, select_COA, carve=2 Are these sensible values? Many thanks, Vero PS: Both identify ligand very well!

2 1

AUC2019 – registrations are open.
by Renwick Dobson 07 Mar '19

07 Mar '19

Dear Structural Biology community, AUC2019<https://auc2019.uleth.ca/>, the 24th AUC Workshop and Symposium, will be held at the University of Canterbury, Christchurch (New Zealand) from 24-29 August 2019. The format of the event is a 2-3 day workshop<https://auc2019.uleth.ca/workshops.php> offering parallel, hands-on training in experimental design and the latest AUC data analysis software from the world experts in this area followed by a 2 day research symposium on AUC and complementary approaches: methodological development, combination with orthogonal techniques (SAXS, SANS, SPR, MST, SEC-MALLS etc), application in biosciences and material sciences. Registrations are now open and details can be found at this website: https://auc2019.uleth.ca/ As the scientific program<https://auc2019.uleth.ca/symposium.php> for AUC2019 emerges, events will be uploaded to the website. We strongly encourage you to submit abstracts for talks and posters<https://auc2019.uleth.ca/abstracts.php>. The meeting is also timed such that delegates can also attend the Queenstown Molecular Biology Conference<https://www.queenstownresearchweek.org/> (which is in Queenstown), although note that this is a separate conference. Lastly, The European Biophysics Journal has kindly agreed to run a special issue to celebrate the research presented at AUC2019. Therefore, we invite those who wish to extend their talks to a journal publication to consider contributing original research articles to this issue. Please indicate your interest for inclusion in this volume below. Deadline for registration of a contribution is August 30 2019. We look forward to welcoming you to Christchurch, New Zealand next Spring(-ish)! Ren Dobson, Chair AUC2019 On behalf of the AUC2019 Scientific Organising Committee ---- Prof. Ren Dobson Co-Director, Biomolecular Interaction Centre (BIC) http://www.bic.canterbury.ac.nz/ School of Biological Sciences | Te Kura Pūtaiao Koiora University of Canterbury | Te Whare Wānanga o Waitaha Private Bag 4800 Christchurch | Ōtautahi New Zealand | Aotearoa E: renwick.dobson(a)canterbury.ac.nz<mailto:[email protected]> T: ++64 (03) 369-5145 x 95145 F: ++64 (03) 364-2590 W: http://dobsonlab.org/

1 0

Postdoctoral position in structural biology of influenza virus transcription Cusack group, EMBL Grenoble
by Stephen Cusack 05 Mar '19

05 Mar '19

Postdoctoral position in structural biology of influenza virus transcription Cusack group, EMBL Grenoble We are looking for a highly motivated and ambitious individual to progress our understanding of the mechanism of transcription by influenza virus RNA-dependent RNA polymerase. The work is in the frame of the ANR-funded FluTranscript project that brings together the complementary expertise of the groups of Stephen Cusack (EMBL Grenoble, project coordinator) and Nadia Naffakh (Institut Pasteur) in structural biology and molecular virology, respectively. The project follows on from a recent joint publication (Structural basis of an essential interaction between influenza polymerase and Pol II CTD. Lukarska et al, Nature 2017) and aims to reconstitute and determine the structure of functional transcription complexes. A secondary goal is to use the acquired structural information to develop new approaches to anti-influenza drug development. The Cusack group uses X-ray crystallography and cryo electron-microscopy to study the structural biology of protein-RNA complexes involved in RNA virus replication, innate immunity and cellular RNA metabolism. Group website: https://www.embl.fr/research/unit/cusack/index.html The successful candidate should have a PhD in Molecular Biology or related field and a strong background and interest in biochemistry and structural biology. We are looking for a creative and ambitious person with good communication skills and keen to work on a challenging project. Experience in insect cell expression systems, reconstitution of protein-RNA complexes, X-ray crystallography or cryo-electron microscopy would be particularly beneficial. EMBL is one of the world’s leading research organizations in the life sciences. The Headquarters Laboratory is located in Heidelberg, with additional sites in Barcelona, Grenoble, Hamburg, Hinxton, and Rome. EMBL Grenoble has excellent access to state-of-the-art structural biology technologies with the in house EM facility being equipped with a T12 microscope and 200kV Glacios/Falcon III . Additionally, we have access to the Titan Krios at the adjacent ESRF as well as those in EMBL Heidelberg. Other facilities on the Grenoble Campus include the ESRF synchrotron X-ray beamlines, neutron scattering at the ILL, high-field NMR at the IBS as well as high-throughput crystallization platform, mammalian and insect cell facilities, biophysical platform and confocal microscopy. You can find out more about this vacancy at: https://www.embl.fr/jobs/searchjobs/index.php?ref=GR00133 or by contacting Stephen Cusack: cusack(a)embl.fr Please apply online through www.embl.org/ Stephen Cusack -- ********************************************************************** Dr. Stephen Cusack, FRS Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL) Group leader in structural biology of protein-RNA complexes and viral proteins ********************************************************************** Email: cusack(a)embl.fr Website: http://www.embl.fr Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7123 Fax: (33) 4 76 20 7199 Postal address: EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue des Martyrs, 38000 Grenoble, France **********************************************************************

1 0

Are TLS parameters applied when TLS refinement is OFF?
by Mark Saper 05 Mar '19

05 Mar '19

I have a structure where at one stage TLS parameters were determined and then refined. It caused the R-free to increase so I stopped refining the TLS parameters. Are the TLS parameters still applied to the structure on subsequent refinement runs even when the TLS refinement is off? Is it appropriate to refine anisotropic B’s for a high resolution (1.35 Å) structure AND apply TLS parameters? Thanks, Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III saper(a)umich.edu +1 (734) 764-3353 mobile: (734) 276-6505

2 3

MAD merged dataset deposition
by Eugene Osipov 03 Mar '19

03 Mar '19

Hello, everyone, I have solved the structure of heme containing protein using anomalous signal from Fe atom (~1.739 anstroms) and further refined it using native dataset (0.9 angstroms). Structure was solved in AutoSol. The question is "What is the best way to deposit mtz with both datasets?" Should I merge and scale them simultaneously or can I deposit output file from AutoSol overall_best_refine_data.mtz, which contains F,FP, Rfree and HL coefficients? P.S.: please, respond in PM, I have only digest subscription on phenixBB. Thank you in advance! -- Evgenii Osipov Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, KU Leuven O&N2

2 1

Rotamer restraints in phenix.real_space_refine
by Ashley Pike 01 Mar '19

01 Mar '19

Hi - Am I right in thinking that rotamer restraints behaves differently in latest official release (1.14-3260) compared to last but one official release (1.13-2998)? Issuing rotamer_restraints=True from command line or GUI used to give 0% rotamer outliers in the molprobity analysis at end of log in 1.13-2998 but now in 1.14 gives non-zero for same input model. It is as if they are not being applied. In the old log file it used to clearly print - **Update rotamer restraints*** after every macrocycle, in the 1.14 logs this is omitted. Many thanks, Ashley

3 4

molprobity in phenix 1.14
by Roberto Marabini 26 Feb '19

26 Feb '19

Hi, In the past (phenix 1.13) I have been able to execute molprobity with the command line: ============== phenix.python /usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py /home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/5ni1.cif map_file_name=/home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/molprobity.mrc d_min=2.200000 pickle=True pdb_interpretation.clash_guard.nonbonded_distance_threshold=None nproc=4 pdb_interpretation.clash_guard.nonbonded_distance_threshold=None ================== Unfortunately, for version 1.14 I get the error: ========================== Traceback (most recent call last): File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py", line 310, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py", line 193, in run map_params=params) File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/validation/molprobity/__init__.py", line 216, in __init__ molprobity_map_params=map_params.input.maps) File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/validation/experimental.py", line 198, in __init__ from mmtbx.command_line.map_model_cc import get_fsc ImportError: No module named map_model_cc ============== That is, there is an error in the line "from mmtbx.command_line.map_model_cc import get_fsc" By the way, if I just run the command: ============== phenix.python /usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py /home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/5ni1.cif ================== the program is executed without any problem. What should I do in order to execute molprobity.py with the option map_file_name. best wishes Roberto

2 1

real space refine generates non-compliant PDB files
by Edwin Pozharski 23 Feb '19

23 Feb '19

Not sure whether anyone would care now that we got our marching orders to abandon PDB format and move to mmCIF, but the output of phenix.real_space_refine includes a number of lines that are not legit PDB records, i.e. this section ... REMARK 3 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.004 0.049 74053 ANGLE : 0.747 12.299 100513 CHIRALITY : 0.052 0.232 11312 PLANARITY : 0.006 0.069 13125 DIHEDRAL : 11.589 179.958 44947 MIN NONBONDED DISTANCE : 2.276 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 5.04 RAMACHANDRAN PLOT: OUTLIERS : 0.30 % ALLOWED : 8.63 % FAVORED : 91.06 % ROTAMER OUTLIERS : 8.76 % CBETA DEVIATIONS : 0 PEPTIDE PLANE: CIS-PROLINE : 3.7037037037 CIS-GENERAL : 0.0 TWISTED PROLINE : 1.85185185185 TWISTED GENERAL : 0.316455696203 REMARK 3 ... This does result in errors when this output PDB file is used as input to other software that is more stringent with format compliance. Cheers, Ed.

2 1