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Re: [phenixbb] Real space refine of long side chains
by Leonid Sazanov 27 Nov '19

27 Nov '19

Hi, We have addressed exactly this problem by writing a script, in which B-factors are refined first and only then real-space refinement happens. This allows disordered side-chains to acquire high B-factors and so they are not pulled into backbone anymore. This cycle is repeated twice to achieve convergence. Parameters for B-factor refinement (ADP restrains) were optimized to account for consistent lack of density for acidic side chains in cryoEM. It is described in: https://www.ncbi.nlm.nih.gov/pubmed/31492636 If needed, I can send a script. Best Leonid -- Prof. Leonid Sazanov FRS IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at Date: Mon, 25 Nov 2019 19:11:16 +0000 From: Luca Pellegrini <lp212(a)cam.ac.uk> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Subject: [phenixbb] Real space refine of long side chains Message-ID: <37F0D7B2-3C9E-4FE1-B0BF-6B23F0D8925B(a)cam.ac.uk> Content-Type: text/plain; charset=us-ascii I have noticed that real-space refinement in cryoEM maps has a tendency to pull long disordered side chains (Lys, Glu etc) back towards main chain density, resulting in unrealistic hairpin-like bent conformations. Is there a way to counter or moderate this behaviour? It would save me from having to manually straighten them all out again afterwards... Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom lp212(a)cam.ac.uk tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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Group ADP refinement restraints
by Taylor Stevens 26 Nov '19

26 Nov '19

Hello, I am currently refining a low-ish resolution structure (through the phenix.refine GUI) with phenix version 1.14 and had some questions about the use of restraints in group ADP refinement. In the phenix.refine documentation (https://www.phenix-online.org/documentation/reference/refinement.html#refin… <https://www.phenix-online.org/documentation/reference/refinement.html#refin…>) it is stated that “Group isotropic ADP or TLS refinement do not use any restraints”, however, this does not seem to be the case. If I look in the log file I can see the following lines of text which I believe indicate that the restraints are being applied: |-group b-factor refinement (macro cycle = 0; iterations = 0)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = None | |——————————————————————————————————————| |-group b-factor refinement (macro cycle = 1; iterations = 22)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871| |——————————————————————————————————————| |-group b-factor refinement (macro cycle = 2; iterations = 22)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871| |——————————————————————————————————————| |-group b-factor refinement (macro cycle = 3; iterations = 22)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871| |——————————————————————————————————————| If I manually set the wu parameter to 0 under “Refinement target weights" nothing changes, however, if I navigate to "All parameters > ADP settings > Group B-Factors" in the GUI there is a “Use restraints” box that is checked by default. If I uncheck this box, there are no longer any restraints being applied according to the log file, and in the case of the structure I am refining, there is a substantial drop in the rfree/rwork. Is this an issue with the program or documentation? Or am I misunderstanding how the program is supposed to work? Is it generally a good idea to use group ADP refinement without restraints? Thanks, Taylor

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Real space refine of long side chains
by Luca Pellegrini 25 Nov '19

25 Nov '19

I have noticed that real-space refinement in cryoEM maps has a tendency to pull long disordered side chains (Lys, Glu etc) back towards main chain density, resulting in unrealistic hairpin-like bent conformations. Is there a way to counter or moderate this behaviour? It would save me from having to manually straighten them all out again afterwards... Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom lp212(a)cam.ac.uk tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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Software developer role at Diamond Light Source
by Hall, Dave (DLSLtd,RAL,LSCI) 25 Nov '19

25 Nov '19

Dear all We currently have a role for a software developer to work with the MX group at Diamond Light Source (www.diamond.ac.uk/mx<http://www.diamond.ac.uk/mx>). The successful candidate will work with scientific staff and software developers to enable experiments across the diverse suite of MX beamlines. For details of the role and how to apply see here https://vacancies.diamond.ac.uk/vacancy/data-acquisition-scientist-for-stru… Best regards Dave Hall MX Group Diamond Light Source -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Postdoc position in methods development at LBNL
by Dorothee Liebschner 22 Nov '19

22 Nov '19

Announcing a postdoc position on behalf of Dr. Kanupriya Pande: ======================================================================== Post-doc position in methods development in the Molecular Biophysics and Integrated Bioimaging division at LBL. The overall objectives of the project are to develop theory and computation to extract conformational heterogeneity and disorder from diffraction and imaging data. The position is available immediately with an initial appointment for 2 years with the possibility of renewal based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. Qualified candidates must have a PhD in Biophysics, Physics, Mathematics, Chemistry, or related fields. Job description and how to apply: https://lbl.referrals.selectminds.com/jobs/computational-biologist-postdoc-… ======================================================================== -- Project Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Re: [phenixbb] weight optimization in refinement
by Alexei Gorelik 22 Nov '19

22 Nov '19

Thanks! What I meant is, phenix.refine seems to run a number of optimization threads (usually 10-14) independent of the number of cores specified (for example, 4 or 8). If i specify 8 cores, is there a way to force it to run 8 weight optimizations? On Nov 22, 2019 1:24 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: Hi Alexei, Is there a setting to control the number of parallel weight optimization threads in phenix.refine? nproc parameter controls number of CPUs to be used in weight optimization. Also, is there a way to force phenix.refine to perform global real-space refinement (rsrg)? No. There is some built-in logic, phenix.refine does it when these conditions are met and it can un-do the result if it is not an improvement. Is there particular need to do this in your context? Pavel

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problems running refinement of shaken model against half map
by L. Hielkema 22 Nov '19

22 Nov '19

Hi all, For the validation of my model to my map in phenix 1.17.1 I tried to refine my shaken model (0.5Å) against my half map in phenix real space refine. However, whatever I try I get a weird behaviour in the FSC(Model-map), see the image below. It seems not to be able to reach 0 in the correlation, but keeps getting stuck at 0.1. I tried various things to solve this, but unfortunately nothing helps: - Using the other half map - Cut of the heterogeneous part of my model and map and refine this - Used refined data without using a mask for the last iterations - Used different resolutions to refine against - Tried data from someone else in the lab (same microscope, same imaging conditions), to check if I am doing something wrong (this gave good results) When doing the same refinement in Refmac5 in ccpem 1.4 it does seem to work, however I would not like to switch programs, because this will mess up my final model. Best, Lisa

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weight optimization in refinement
by Alexei Gorelik 22 Nov '19

22 Nov '19

Hi, Is there a setting to control the number of parallel weight optimization threads in phenix.refine? Also, is there a way to force phenix.refine to perform global real-space refinement (rsrg)? Most of the time, when the "real-space" option is selected, it only carries out rotamer fitting (rsrl). I do know there's a separate real-space refinement program in Phenix. Thanks!

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Secondary structure restraints
by Luca Pellegrini 20 Nov '19

20 Nov '19

I have a protein-DNA complex and would like to apply SS restraints. What is the best way to apply the SS restraints to the protein only, using the GUI? I have tried the following: Select ‘Use secondary structure restraints’ in the ‘Refinement Settings’ tab ‘Select Atoms’ In the Selection Editor window, 'Find Secondary Structures' Removed manually all nucleic acid restraints in ‘Base Pairs’ and Stacking Pairs’ tabs Save and close. However, phenix refinement keeps switching SS restraints for nucleic acids to True. Kind regards, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom lp212(a)cam.ac.uk tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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Molybdenum cofactor refinement
by Cristiano Mota 20 Nov '19

20 Nov '19

Hi all, I'm using phenix.refine to refine a structure of a Molybo-protein at 1.9Å. The MGD cofactors (molybdopterin guanine dinucleotide) are being refined with a weird distorted geometry causing some clashes. The Fo-Fc maps show that something is going wrong in the aromatic rings interatomic distances. I'm using the readyset to pick up MGD and metal restraints. Am I using the right protocol? Best regards, Cristiano Mota -- *Cristiano de Sousa Mota* Postdoctoral Researcher, Macromolecular Crystallography Group UCIBIO / FCT - Universidade Nova de Lisboa 2829-516 Caparica, Portugal (00351 212948300, ext 10962) http://xtal.dq.fct.unl.pt/

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