- phenixbb - phenix-online.org

non-consecutive residue selection in phenix.polder
by Schulz, Eike-Christian 29 Mar '18

29 Mar '18

Dear all, To generate unambiguous ligand density in a number of structures we would like to omit the surrounding active site residues in the polder-map calculation. However, so far we were unable to figure out how non-consecutive residues can be selected for phenix.polder. https://www.phenix-online.org/documentation/reference/atom_selections.html The documentation only explains how to select ranges of residues but not how to select say 5 individual residues. Is there a syntax to achieve this ? Thanks for your advice, Eike

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iNEXT EM and X-ray bundles!
by a.perrakis＠nki.nl 26 Mar '18

26 Mar '18

Dear all, iNEXT, a European program to support access to research infrastructures for Structural Biology, is now welcoming applications for the “EM and X-ray bundles", to help people carry a project all the way from the starting sample to the initial structure determination, by EM or X-rays. To apply for either bundle you need exciting translational research projects, for which you have the macromolecule or complex you want to study in purified soluble form, and you want to engage in structural studies. In a short application form (less than one thousand words overall), you will need to describe the background of the project in your lab and current results, the general scientific background, and the value for translational research (short term but also long term value in any short of biomedical or biotechnological application). No prior experience on either method is required. For the EM bundle, projects will start with an initial characterisation for optimal stability conditions, molecular weight in solution, and negative stain EM (if you send enough sample, we can also try to crystallise it if you wish - just in case!). At this stage you will only need to send the sample to us. Projects that look most promising after that first step, will proceed to optimising the cryo-conditions in one of the iNEXT EM facilities, with your participation. Finally, projects that do best in cryo-optimisation, will proceed to collect data in one of the high-end microscopes available to iNEXT. For the X-ray bundle, projects will start with an initial characterisation for optimal stability conditions, molecular weight in solution, and crystallisation trials. Projects that either yield crystals, or promising precipitates, will proceed to extensive crystallisation trials. For all projects that will yield crystals diffraction data will be collected in one of the fully automated X-ray facilities that collaborate in iNEXT. You will only need to send the sample to us and in most cases physical presence will not be required. It should be emphasised, that no re-application will be needed at any step and iNEXT will cover all experimental expenses, and contribute to travel costs, when needed. There is a single deadline on Friday 20th April 2018. You can Submit a Proposal by clicking here<https://www.structuralbiology.eu/submit-proposal/?t=inext> or go to the iNEXT web site: http://www.inext-eu.org and follow the “Submit Proposal” link. Please note, that given the iNEXT resources availability, this is likely the only call for these “bundle” access. These will serve as pilots for likely requesting future funding from the EU, if such an opportunity becomes available. We note that researchers from all EU and associated countries can apply, but also international labs are eligible, albeit in a more limited capacity. Please forward this email beyond this bulletin list, especially to colleagues that might be less familiar with structural biology. Consider asking this colleague of yous that wanted to do a structural biology project and you never had time or the resources to try hers or his exciting idea! Preliminary results from this bundle access, or a structure, can be the basis for your next grant application! Please also keep in mind that iNEXT remains open to all kinds of Structural Audit, Enhanced Support, and High-End data collection, for projects that involve X-ray Crystallography, SAXS, solution and solid state NMR, EM single particles, EM tomography or CLEM, biophysics for looking at macromolecular interactions, advanced light imaging, and ligand and fragment screening! All these access modalities are listed on our web site! Best regards and looking forward receiving your project, The iNEXT coordination and management team and all iNEXT partners

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Phaser.find_anomalous_substructure error
by Janine Gray 25 Mar '18

25 Mar '18

Hi, I am trying to run phaser.find_anomalous_substructure to identify the anomalous peaks of some phosphorus atoms and get the following error: AttributeError: 'NoneType' object has no attribute 'as_pdb_string' Looking in the log file), it states a file opening error with my PDB file: ****************************************************************************************** *** Phaser Module: AUTOMATED EXPERIMENTAL PHASING 2.8.1 *** ****************************************************************************************** ** Steps: ** Anisotropy correction ** Experimental Phasing ** SAD Phasing CPU Time: 0 days 0 hrs 0 mins 0.02 secs ( 0.02 secs) Finished: Fri Mar 23 15:23:15 2018 ****************************************************************************************** *** Phaser Module: SINGLE-WAVELENGTH ANOMALOUS DISPERSION 2.8.1 *** ****************************************************************************************** Keyword input too long to echo to output (>10000 characters) ------------------------------------------------------------------------------------------ FILE OPENING ERROR: ATOM 1 N MET A 1 5.825 -12.222 -3.663 1.00 89.47 N Has anyone seen this before and/or knows how to fix this? Cheers, Janine

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nucleic acid secondary structure restraint sigmas
by Dyda 24 Mar '18

24 Mar '18

Hi, Does anyone one whether is it possible (and if so how) to change the target sigmas of the H-bonds restraining base pairs? It seems that base pair restraints can do several things: base_pair { enabled = True base1 = chain 'C' and resid 21 base2 = chain 'D' and resid 5 saenger_class = 19 restrain_planarity = False planarity_sigma = 0.176 restrain_hbonds = True restrain_hb_angles = True restrain_parallelity = True parallelity_target = 0 parallelity_sigma = 0.0335 What I'd like to know whether the restrain_hbonds and restrain_hb_angles sigmas can be adjusted. Or is it the case that parallelity_sigma is doing what I'm looking for? Thanks! Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

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11th CCP4/APS Crystallographic School in the US
by Qingping Xu 23 Mar '18

23 Mar '18

Dear Colleagues, We are pleased to announce the *11th annual CCP4 crystallographic school *“From data collection to structure refinement and beyond” will be held on June 18-25, 2018 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at http://www.ccp4.ac.uk/schools/APS-2018/index.php. *Dates*: June 18 through 25, 2018 *Location*: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: *data collection workshop* and *crystallographic computing workshop*. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). *Applicants*: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. *Application*: Application deadline is *Wednesday May 2nd, 2018*. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2018/index.php *Registration fees*: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Garib and Qingping

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Fwd: [ccp4bb] Xtriage anomalous signal measurement- mosflm data processing
by Pavel Afonine 22 Mar '18

22 Mar '18

---------- Forwarded message ---------- From: *Manoj Saxena* <00001d16aa30e8a1-dmarc-request(a)jiscmail.ac.uk> Date: Wednesday, March 21, 2018 Subject: [ccp4bb] Xtriage anomalous signal measurement- mosflm data processing To: CCP4BB(a)jiscmail.ac.uk Hi all, I have a dataset for which I got the .sca file from a collaborator and I am trying to look at the strength of the anomalous signal. Looking at archives in the CCP4bb I found many people suggesting using the Chi**2 values using ScaLAPACK using HKL2000. However, at the moment, I have access only to Xtriage from Phenix which gives a clear graph showing that my data has no significant difference anomalous signal. So my question is how reliable is this analysis by Xtriage and is it possible that during data processing anomalous scattering difference was lost. I would like to reprocess the data using mosflm any suggestions for data processing (to see the anomalous signal) would be appreciated. Thanks Manoj Saxena Postdoc University of Puerto Rico

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Phenix.Refine: Missing High Resolution Data
by Mark A. White 17 Mar '18

17 Mar '18

Hello, I have several data sets which seem to loose completeness in their high-resolution shells when the HKL *.sca file is converted into an MTZ. I am using the recommended Diederichs CC1/2 cut off of 0.5, which is usually an I/s <2. I also have an usually high redundancy in these data sets, not sure if that has any effect. Here is a typical comparison of the Phenix statistics and the HKL values. Note that the resolution bins do not match, and that the Phenix refinement was truncated to 3.0Å. PHENIX HKL2000/Scalepack RESOLUTION RANGE COMPL total CC1/2 CC* Redn ScP-Angstrom 50.1353 - 8.8720 97 97.8 0.989 0.997 10.9 70.00 7.87 8.8720 - 7.0483 99 - 7.0483 - 6.1591 100 99.6 0.990 0.997 12.8 7.87 6.25 6.1591 - 5.5968 100 99.7 0.991 0.998 12.9 6.25 5.46 5.5968 - 5.1961 99 - 5.1961 - 4.8900 99 99.6 0.991 0.998 13.0 5.46 4.96 4.8900 - 4.6453 99 99.5 0.986 0.996 12.9 4.96 4.60 4.6453 - 4.4432 99 99.2 0.990 0.997 13.1 4.60 4.33 4.4432 - 4.2723 99 - 4.2723 - 4.1249 99 99.8 0.988 0.997 13.3 4.33 4.11 4.1249 - 3.9960 99 99.9 0.989 0.997 13.4 4.11 3.94 3.9960 - 3.8818 99 99.9 0.987 0.997 13.5 3.94 3.78 3.8818 - 3.7796 100 - 3.7796 - 3.6875 100 99.8 0.985 0.996 13.4 3.78 3.65 3.6875 - 3.6037 100 100.0 0.975 0.994 13.5 3.65 3.54 3.6037 - 3.5270 100 - 3.5270 - 3.4565 100 100.0 0.964 0.991 13.5 3.54 3.44 3.4565 - 3.3912 100 - 3.3912 - 3.3307 97 99.9 0.966 0.991 12.1 3.44 3.35 3.3307 - 3.2742 87 100.0 0.916 0.978 10.2 3.35 3.27 3.2742 - 3.2214 68 100.0 0.857 0.961 8.5 3.27 3.19 3.2214 - 3.1719 54 - 3.1719 - 3.1252 41 100.0 0.763 0.930 7.4 3.19 3.12 3.1252 - 3.0812 33 99.9 0.616 0.873 6.4 3.12 3.06 3.0812 - 3.0396 24 - 3.0396 - 3.0001 18 98.4 0.547 0.841 5.8 3.06 3.00 95.1 0.307 0.685 5.2 3.00 2.95 89.8 0.302 0.681 4.8 2.95 2.90 98.9 0.982 0.995 10.9 All reflect. -- Yours sincerely, Mark A. White, Ph.D. Associate Professor of Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics Macromolecular X-ray Laboratory, Basic Science Building, Room 6.658A University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 mailto://[email protected] http://xray.utmb.edu QQ: "Don’t persist in folly. Some people commit themselves to their errors. They commit one error and consider it constancy to go on that way." - Baltasar Gracian (1658)

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cis-Pro and trans-Pro refinement
by 张士军 17 Mar '18

17 Mar '18

Dear all I am refining a structure which has cis-Pro and trans-Pro, the tans-Pro is gone when I set the "threshold degrees for cis-peptide " from default 45 to 65, but still has cis-Pro. While no significant change when I set it to 15. My question is how to set in phenix refinement in phenix GUI to clear the Pro residues in cis- or trans- conformations. Best Regards shijun

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Phenix refine ligand with alt conf and occupancy<1
by Leonhard Kick 17 Mar '18

17 Mar '18

Dear all, I'm currently working on a structure with a series of ligands which have occupancies of ~80% (according to phenix.refine). So far so good, a few of these also show alternate conformations which I'd like to let phenix refine as well, but phenix.refine adjusts the occupancy of the whole ligand (conformation A+B) automatically to 1. I see that this is useful in most cases, but not in this one. Is there a possibility to adjust the overall occupancy or another work-around that anyone can suggest? Thank you Best Leo -- ================================================== Leonhard Kick AG Schneider Technische Universität München Dept. Chemistry, Chair of Biochemistry Lichtenbergstr. 4 D-85748 Garching b. München +49 89 289 13359 leonhard.kick(a)tum.de ==================================================

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Real space refinement of complete virus structure
by #TOFAYEL AHMED# 13 Mar '18

13 Mar '18

Dear all, I am trying to refine a complete virus pdb structure (possessing icosahedral symmetry) in a cryo-EM map using phenix.real_space_refine. The run fails complaining "Multi-model PDB (with MODEL-ENDMDL) is not supported". So, I followed a previous post in phenixbb: http://www.phenix-online.org/pipermail/phenixbb/2011-May/017079.html and merged multiple models into one but faced following problems: 1. This merged file is unreadable in UCSF Chimera. 2. The secondary structure definition in the PDB file header is not recognizable anymore in Phenix. In my understanding, both the problems are arising due to PDB format's inability to handle more than 62 chains and 99999 atoms in a file. So, what will be the work-around to perform a real space refinement of the complete virus structure at once? Also, how to maintain secondary structure during such refinement? Any help is highly appreciated. Best regards, Tofayel ............................................ Tofayel Ahmed Graduate Student (PhD) | Lab-02n-01 School of Biological Sciences Nanyang Technological University 60 Nanyang Drive, Singapore 637551 +65 8650.0473 |tofayel001(a)e.ntu.edu.sg<mailto:[email protected]>

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