- phenixbb - phenix-online.org

Turn off side chain optimizations in phenix real space refine?
by Oliver Clarke 11 Jun '21

11 Jun '21

Hi, Is there any way to turn off rotamer fitting/side chain optimization in phenix.real_space_refine? Sometimes it seems to do more harm than good, and repositions sidechains completely out of the density, but I couldn't find how to switch it off. Cheers Oli

2 4

General interest: the history of the European Crystallography Schools
by John R Helliwell 11 Jun '21

11 Jun '21

Dear Colleagues, Th history of the European Crystallography Schools, initiated by Italian colleagues (ECS1 was held in Pavia), is described here at the ECA’s website:- https://ecanews.org/european-crystallography-school/ Several of these previous Schools’ details, but not all as yet, can be found here:- https://ecsx.ecanews.org/ ie replacing the x by the number. The current one ‘Budapest’ being 6. (In each the ECA website is mirrored to the local host organising team.) Greetings, John Emeritus Professor John R Helliwell DSc ECA Past President 2007 to 2010

1 0

European Crystallography School ECS6
by John R Helliwell 10 Jun '21

10 Jun '21

Dear Colleagues, I commend to you the European Crystallography School ECS6. Full details are here:- https://akcongress.com/ecs6/ Best wishes, John Emeritus Professor John R Helliwell DSc

1 0

Restraints for small molecules in macromolecular crystal structures
by Marie Elizabeth Fraser 10 Jun '21

10 Jun '21

Hello, The parameters we use as restraints for small molecules in complex with macromolecules have improved greatly, but we still get complaints when submitting to the Protein Data Bank. We use grade to obtain restraints for these small molecules, but when we submit to the PDB, some of their restraints do not match. I am not clear where the PDB gets these restraints, but we edit our file to match the values sent and finish the refinement. What do others do? As well, PHENIX and COOT aren’t accessing the same library for restraints. Is this due to how I’ve installed ccp4 (for COOT) and PHENIX? The small molecule whose restraints I currently need is ADP metavanadate (AD9), which grade won’t accept because of the vanadium, so I used elbow to calculate restraints. Thank you, Marie

2 1

Associate Researcher Position in the KU Protein Structure Laboratory
by Lovell, Scott W 08 Jun '21

08 Jun '21

The Protein Structure Laboratory (PSL) at the University of Kansas (KU) is seeking a full-time Associate Researcher to assist with various structural biology projects. As a core laboratory, the PSL collaborates with a diverse range of investigators to obtain structures of their proteins of interest using X-ray crystallography and delivers dozens of structures annually. Additionally, the PSL manages the structural biology efforts for extramurally funded research projects particularly aimed at inhibitor development. For a full description of the position and to apply, GO TO: https://employment.ku.edu/associate-researcher/19212br Regards, Scott __________________________________________________ Scott Lovell Ph.D., Director Protein Structure and X-Ray Crystallography Laboratory University of Kansas Del Shankel Structural Biology Center 2034 Becker Drive Lawrence, KS 66047 Office: SBC 1015 email: swlovell(a)ku.edu<mailto:[email protected]> phone: 785-864-3772 fax: 785-864-8141 __________________________________________________

1 0

Postdoctoral Scholarship Opportunity in the Lane group (PBIO) CFEL/DESY, Hamburg, Germany
by TJ Lane 08 Jun '21

08 Jun '21

Uncovering protein dynamics: developing statistical crystallography Postdoctoral Scholarship Cluster of Excellence: Advanced Imaging of Matter Center for Free Electron Laser Science (CFEL), Hamburg, Germany Protein motion is at the heart of life, but remains challenging to witness firsthand. Proteins move to reading and copying DNA, convert sunlight into chemical energy, and transmit signals between cells, yet our ability to image these functions is limited by the technology we have to image protein dynamics. A new opportunity to meet this challenge is emerging, however, as crystallographic methods advance. We can now collect data from thousands to millions of crystals of the same protein, and it is clear no two crystals are identical. Thus, analyzing their distribution may reveal protein structural fluctuations directly. Can we develop a statistical crystallography to turn these large datasets into knowledge about protein dynamics? Can we use statistical analysis of crystal-to-crystal variation to separate signal from noise in time resolved experiments, revealing protein motion induced by mixing with a ligand or excitation with a pump laser? We seek a computational scientist who will answer these questions. As the ideal candidate, you will have the following key attributes: * A doctoral degree in physics, biophysics, chemistry, applied mathematics or a related field * Working knowledge of macromolecular crystallographic methods and software * A track record of scientific computing and programming * The ability to drive your work independently and show initiative And you will be excited to take on the following responsibilities: * Mathematical modeling of protein dynamics and protein crystal diffraction data * Interpretation and analysis of experimental results * Open-source development to make your insights available to the broader scientific community * Presenting your work in written and oral form to the scientific community * Helping to foster an environment conductive to collaboration, learning, growth, and fun Available immediately is a two-year contract with a competitive salary and the opportunity to work and live in the beautiful and vibrant city of Hamburg, Germany. The group is housed at the Center for Free Electron Laser Science on the vibrant DESY campus (Luruper Chaussee 149, 22761 Hamburg, Germany). This position is funded through the Advanced Imaging of Matter Cluster of Excellence (https://www.cui-advanced.uni-hamburg.de/en.html). The successful candidate will become a fellow of the cluster and have access to career support, training opportunities, and an engaging scientific network via the cluster. The candidate will have additional technical and mentorship support from partners Andrea Thorne, Arwen Pearson, and Nicholas Pearce and their groups during the course of the project. We are an equal opportunity employer. Women and minorities are encouraged to apply and handicapped persons will be preferred given equal qualifications. Application deadline: 17 June 2021 Applications should include a cover letter, a tabular curriculum vitae, and copies of degree certificate(s). Please send applications by email to: < thomas.lane(a)desy.de> For more details, write directly to TJ Lane: <thomas.lane(a)desy.de> Cross-Posting on the AIM Cluster of Excellence page (funding source for this project): https://www.uni-hamburg.de/stellenangebote/ausschreibung.html?jobID=4c3ff9d…

1 0

Quick calculation of mean ADP
by Martin Malý 07 Jun '21

07 Jun '21

Dear mailing list members, I would like to calculate the mean ADP of a structure model (PDB) from a Python script using tools in CCTBX/PHENIX. I tried to find out how and dig it from Python source code but I have been unsuccessful yet. Please, how to do it (in Python)? Although It is quite easy to calculate it in on my own directly from PDB for isotropic ADPs, the situation can be a bit complicated for anisotropic ADPs... Thank you. Best regards, Martin Mal ----- Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní odpovědnost Biotechnologického ústavu AV ČR, v. v. i. Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Biotechnology of the Czech Academy of Sciences. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract, nor does it create any pre-contractual liability on the part of Institute of Biotechnology of the Czech Academy of Sciences.

4 4

Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 03 Jun '21

03 Jun '21

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 11 JUN 2021. Please consider writing an article of general interest to the community. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

1 1

Twinned data with Phaser
by Thomas, Leonard M. 25 May '21

25 May '21

Hello, I have been working on a structure for a very long while. We have a number of data sets with the good ones mostly around the 3.1-3.2 A range. I do have a determination of the structure but would like to see if I can get the structure determined with a slightly higher resolution data set at around 2.7 A. Problem is the 2.7 data is twinned. Are there settings in Phaser to handle twinned data or is the twinning only handled during refinement? Thank you for any advice, outside of forgetting about the twinned data. Len Leonard Thomas, Ph.D. Macromolecular Crystallography Laboratory Oklahoma COBRE in Structural Biology Price Family Foundation Institute of Structural Biology University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmthomas(a)ou.edu<mailto:[email protected]> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl

3 3

Problems with sharpening in Autosharpen
by Carlos HENRIQUE FERNANDES 25 May '21

25 May '21

Dear all, I am facing some problems with sharpening in Autosharpen. My current map is about 3.2 Å resolution, which I obtained after CTF-Refinement and Polishing in Relion. When I use Autosharpen in default parameters, it tells me that are applied an overall Bsharp applied of 220.34 and a final Biso of 87.42; but very little sharpening is done; I was unable to observe a typical helices sharpening at this value of resolution. I did some tests setting progressive Bsharp values (240; 260; 280; 300), but I am still unable to visualize a typical helices sharpening. Has anyone had problems like that? Any tips? Thanks in advance, Carlos.

3 3

Exclude atoms from real space refinement
by Florian Nachon 23 May '21

23 May '21

Hello, I want to exclude a residue from XYZ refinement, but I noticed that my atom selection "not (chain A and resid 100)" is ok for reciprocal-space, but not real-space? Someone encounter a similar problem 10 years ago: http://www.phenix-online.org/pipermail/phenixbb/2012-December/019297.html Is it a known bug? Any clues? Thanx in advance — Florian

2 2

Fwd: [SRCC #47733] Fwd: Phenix GUI showing unreadable squares
by Dong-Hua Chen 19 May '21

19 May '21

Hi All, I asked Stanford cluster admin and he is questioning the CentOS version incompatibilities (see the following). Any suggestions? Thanks Dong-Hua ---------- Forwarded message --------- From: Kilian Cavalotti <srcc-support(a)stanford.edu> Date: Thu, May 13, 2021 at 12:20 PM Subject: Re: [SRCC #47733] Fwd: [phenixbb] Phenix GUI showing unreadable squares To: <donghua.chen(a)gmail.com> Hi Dong-Hua, It looks like the software is built for CentOS 6.10, while Sherlock is running CentOS 7.x, so incompatibilities are likely. Is there a way to rebuild it from source. maybe? Cheers, -- *Kilian Cavalotti* Stanford Research Computing Center *Sherlock // *web <https://www.sherlock.stanford.edu> | docs <https://www.sherlock.stanford.edu/docs> | status <https://status.sherlock.stanford.edu> | news <https://news.sherlock.stanford.edu>47733:1231609

2 1

Cryo-EM Facility Manager - Berkeley California
by Paul Adams 18 May '21

18 May '21

Dear Colleagues, I would like to draw your attention to a job opening here in Berkeley California, for a Cryo-EM Facility Manager: https://lbl.referrals.selectminds.com/jobs/cryo-em-facility-manager-3801 This position requires expertise in biological cryo electron microscopy (cryo-EM). The successful candidate will be responsible for maintaining the in-house transmission electron microscopes (TEMs) and accessory equipment in excellent working order as well as training new users, scheduling access, and assisting with the collection of high-quality data. Duties will include providing complex technical support for sophisticated biotech-laboratory equipment including maintenance, calibration, repair and troubleshooting of instrumentation, control systems, experimental apparatuses, computers, and peripheral equipment as well as coordinating and scheduling vendor related maintenance and repairs. This is a full time, 3 year, term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. Diversity, equity, and inclusion are core values at Berkeley Lab. Our excellence can only be fully realized by faculty, students, and staff who share our commitment to these values. Successful candidates for our faculty positions will demonstrate evidence of a commitment to advancing equity and inclusion. Lawrence Berkeley National Laboratory encourages applications from women, minorities, veterans, and other underrepresented groups presently considering scientific research careers. Berkeley Lab (LBNL) addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. Working at Berkeley Lab has many rewards including a competitive compensation program, excellent health and welfare programs, a retirement program that is second to none, and outstanding development opportunities. Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

1 0

Deadline today -- IUCr SARS-CoV-2 special symposia.
by Pearce, N.M. (Nick) 17 May '21

17 May '21

Dear BB, As you might be aware, there are a few microsymposia that have been added to this year’s IUCr conference on developments around SARS-CoV-2. Given the wide interests of this board, I wanted to advertise all four of the sessions, for which the (official) deadline is TODAY: - Structural biology of coronaviruses This session covers new structural and functional insights about the life cycle and virus-host interaction of SARS-CoV-2 and other coronaviruses with a particular view to integrative uses of crystallography in connection with other methods. - New methods to fight the pandemic This session covers new methods in crystallography and structural biology to better understand SARS-CoV-2 and the COVID-19 pandemic, including advances in computational methods, beamline instrumentation and integrative structural biology. - Crystallography against Corona This session covers the efforts of the crystallographic community to find drug candidates for COVID-19 both in-silico and in the lab by using structural models of viral proteins. - Using crystallography for education during the pandemic Using crystallography for education during the pandemic *** Please submit your abstracts today! If this isn’t possible, email us to let us know you intend to submit an abstract in the coming days! *** For each session, 4 relevant abstracts will be selected for 20-minute presentations. You can submit your abstracts through the conference website: https://iucr25.org/scientific/ Looking forward to reading the abstracts, Session co-chairs

1 0

questions about using experimental phases in phenix.refine
by David A Case 15 May '21

15 May '21

I'm trying to use experimental phases derived from an cryoEM density map do carry out reciprocal space refinement in phenix.refine. I used phenix.map_box to get the map coefficients, and then the CCP4 program chltofom (with the -colin-phifom flag) to create the HL coefficients from F/PHI computed from the electron density map. 1. If I ask for the mlhl target, I get quite odd target values, e.g. for a 2.9 Å data set: | normalized target function (mlhl) (work): -5862.311069 | | target function (mlhl) not normalized (work): -6438670043.811632 and attempted refinements more or less destroy my protein and increases both the mlhl target value and the R-factors. Is there an example data set I could access to help me find out what I'm doing wrong? (Using the ml target, as suggested in DeMaio et al, Nature Methods 10:1102, 2013, seems to work well, and has a postive target function, but seems sub-optimal if phase information is available.) 2. Is there a way to do a "simple" least-squares refinement, minimizing sum( w_i * |Fobs_i - Fcalc_i|**2 ) where both Fobs and Fcalc are treated as vectors? Does the ls target perhaps do this if use_experimental_phases=True? Usual apologies if there is some great tutorial on this that I've not found. ...thanks...dave case

3 2

Release of ISOLDE 1.2
by Tristan Croll 13 May '21

13 May '21

Hi all, I'm very happy to announce the release of ISOLDE 1.2, now available for installation into the ChimeraX 1.2 release. To get it, first download and install ChimeraX 1.2 from https://www.rbvi.ucsf.edu/chimerax/download.html, then go to "Tools/More Tools..." in the menu and follow the links to install ISOLDE. Key new features include: * The ability to add residues to the ends of protein chains (see https://twitter.com/CrollTristan/status/1391747032579289089?s=20; support for nucleic acid chain extension still in development) * Lower-fidelity simulation modes for greatly improved performance on lower-end GPUs (see https://twitter.com/CrollTristan/status/1390709520876331009?s=20) * Commands to write input files for phenix.refine and phenix.real_space_refine with recommended settings for refining models from ISOLDE * Command to write a ProSMART-like restraint definition file to softly restrain the model to its current geometry in Refmac * Improvements to stability and performance of bulk solvent/scaling in crystallographic datasets * Short aliases for commonly-used commands to make life easier for power users. Please enjoy! Best regards, Tristan

1 0

Scientific software programmer at UCLA
by Johan Hattne 12 May '21

12 May '21

Dear all; The Gonen lab at UCLA's Department of Biological Chemistry is looking for a research specialist in scientific software programming to develop software for computational biological image analysis. The Gonen lab works toward understanding how membrane proteins help cells maintain homeostasis. To that end, the lab studies channels, transporters, and receptors, structurally and functionally. More information about the lab can be found by visiting https://cryoem.ucla.edu/. Details about the position and application instructions here: https://hhmi.wd1.myworkdayjobs.com/External/job/University-of-California-Lo… // Best wishes; Johan

1 0

Help with den refine
by Alex Singer 11 May '21

11 May '21

Hi: I recently installed the Linux-64 version of phenix1.19.2-4158 and used the command line to run phenix.den_refine. The command was just Phenix.den_refine xxx_refine_25.pdb xxx_refine_25.mtz (xxx is just the name of the project, and is made up, but I did the same thing for two different projects) And then it ran for a while until it started the initial minimization before the den routine, ie coordinate minimization before annealing and then it crashed with the error message TypeError: %d format; a number is required, not Autotype I believe this is a python error, but is there something straight-forward that I can do about this so that den_refine can work? Thanks for your help Dr. Alex U. Singer

1 0

Call for abstracts: IUCR session on SARS-CoV-2 structural biology
by Andrea Thorn 11 May '21

11 May '21

Dear all, Gianluca Santoni and I are co-chairing a session at IUCr meeting 2021 entitled "Structural biology of coronaviruses" on the 16th of August. The subject of the session are structural and functional insights about the life cycle and virus-host interaction of SARS-CoV-2 and other coronaviruses with a particular view to integrative uses of crystallography in connection with other methods. Abstract deadline has been extended to the 15th of may. We will select 4 abstracts for a 20 minutes talk. You can submit your abstracts through the conference website: https://iucr25.org/scientific/ Please feel free to forward this to scientists who may want to contribute an abstract, including junior researchers! We are looking forward to the meeting and the abstracts, best wishes, Gian and Andrea -- Dr. Andrea Thorn | group leader andrea.thorn(a)uni-hamburg.de HARBOR (Institute for Nanostructure and Solid State Physics), Universität Hamburg Luruper Chaussee 149 / Bldg. 610 | 22761 Hamburg | Germany Tel. +49 (0)40 42838 3651 www.thorn-lab.de | www.insidecorona.de

1 0

Re: [phenixbb] real space rotamer restrains
by Pavel Afonine 10 May '21

10 May '21

Dear Leonid, thanks for sharing this and for your patience while waiting for the fix! All the best! Pavel On 5/10/21 06:36, Leonid Sazanov wrote: > Dear Pavel, > > Many thanks for this fix! > > Using local_grid_search now does not produce those rare outliers - > illustrated in the attachment for the benefit of others. > > "Before" is the earlier version refine run and "after" is using > phenix/1.20-dev-4224. > > Best wishes, > > Leonid > > > On 27.04.21 01:46, Pavel Afonine wrote: >> Dear Leonid, >> >> this is fixed now, residues won't leave good density any more. Next >> nightly build (dev-4218): >> >> http://phenix-online.org/download/nightly_builds.cgi?show_all=1 >> >> should have the fix. >> >> Please note, this is not the official released version meaning that >> while it is automatically tested it is not tested as thoroughly as >> regular official releases. With this in mind, it is advisable to keep >> around whatever version you are using currently just in case while >> using the latest nightly! >> >> Let us know should you discover any more problems! >> >> Cheers, >> Pavel >> >> >> On 4/26/21 13:53, Pavel Afonine wrote: >>> Dear Leonid, >>> >>> thanks for sharing files and my apologies for slow replies. >>> >>> I was able to reproduce the issue and I'm on it investigating right >>> now. I agree, this looks bad! >>> >>> More soon as progress happens. >>> >>> All the best! >>> Pavel >>> >>>

1 0

Call for abstracts: IUCR session on SARS-CoV-2 structural biology
by Gianluca SANTONI 10 May '21

10 May '21

Dear all, Andrea Thorn and I are co-chairing a session at IUCr meeting 2021 entitled "Structural biology of coronaviruses" on the 16th of August. The subject of the session are structural and functional insights about the life cycle and virus-host interaction of SARS-CoV-2 and other coronaviruses with a particular view to integrative uses of crystallography in connection with other methods. Abstract deadline has been extended to the 15th of may. We will select 4 abstracts for a 20 minutes talk. You can submit your abstracts through the conference website: https://iucr25.org/scientific/ Please feel free to forward this to scientists who may want to contribute an abstract, including junior researchers! We are looking forward to the meeting and the abstracts, best wishes, Gian and Andrea

1 0

Re: [phenixbb] quick demo of phenix.autosol ?
by James Holton 06 May '21

06 May '21

Thank you all for the excellent suggestions! I think the built-in tutorials are a good place to start. I noticed a couple of things: 1) the autosol GUI "Status" tab always shows the number of sites to be zero, despite having solved the structure. Is that a bug? 2) the autosol GUI requires data filenames to be non-unique after removing the directory names. These days a rather large fraction of data files are called "XDS_ASCII.HKL". Now, for me personally, I don't mind opening a shell and making some links, but the students are sometimes confounded by that. Am I not doing the workflow right here? Again, thank you all for all the effort that goes into making Phenix great! -James Holton MAD Scientist

1 0

Phenix GUI showing unreadable squares
by Dong-Hua Chen 06 May '21

06 May '21

Hi All, I am trying to install Phenix version 1.19.2-4158 on a node of a cluster and the installation was complete. After I tried to run phenix, the pop-up window showed lots of unrecognized small squares instead of letters (see the picture attached). I also tried to install the version 1.18.2 and got the same problem. Any suggestions would be greatly appreciated. Thanks, Dong-Hua

1 0

Postdoc position micro electron diffraction / single particle analysis @Braunschweig/Germany
by Blankenfeldt, Wulf 04 May '21

04 May '21

Dear colleagues, together with Rolf Müller (one of this year's Leibniz Prize winners in Germany) we are currently looking for a postdoc to help us establish micro electron diffraction (and single particle analysis) in natural product research. Details about the position can be found here: https://www.helmholtz-hzi.de/en/career/open-positions/jobs/view/job/details… I'd be grateful if you could inform potential candidates. Regards, Wulf ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Silke Tannapfel Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

1 0

Re: [phenixbb] Model required for combine_focused_maps
by Tom Terwilliger 03 May '21

03 May '21

Hi Fengwei, The model has to be pretty good as it is used to evaluate the maps. I would improve the model first, at least by refinement , then combine the maps, then maybe iterate the whole process with a new model. -Tom T On Mon, May 3, 2021 at 14:19 Zheng, Fengwei <Fengwei.Zheng(a)vai.org> wrote: > Dear Phenix developers: > > Thank you for developing this so powerful and elegant software packages > for our community! > > I am a newbie in cryoEM, and recently I got a consensus map, and split it > into two parts to do the further focused refinement, after that I want to > combine them together, and then to build my model, I learned that this > "combine focused maps" module in Phenix can achieve this, I read through > this online tutorial ( > https://www.phenix-online.org/documentation/reference/combine_focused_maps.…), > for the starting input files, I seem need to provide my initial/consensus > map, two focused maps and a model, but I have a question about this > provided model: > > 1st, need me to provide my final refined model (i.e. I need to finish my > model building firstly according to my two focused maps), or I can use a > homologue model for this combination? > > 2nd, if I use a homologue model that only can be roughly fitted into my > consensus map, will this affect my final combination results? > > Appreciate! > > Best, > Fengwei > > -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

1 0