- phenixbb - phenix-online.org

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 05 May '21

05 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

Error at fix_insertions_deletions
by Carlos HENRIQUE FERNANDES 03 May '21

03 May '21

Hello all! I'am facing a problem running the phenix.fix_insertions_deletions. I'am using in the command line: phenix.fix_insertions_deletions sharpened_map.ccp4 resolution=3.5 protein.pdb seq.dat I've been encountering this error: File "/usr/local/phenix-1.19.2-4158/build/../modules/phenix/phenix/command_line/fix_insertions_deletions.py", line 7, in <module> run_program(program_class=fix_insertions_deletions.Program) File "/usr/local/phenix-1.19.2-4158/modules/cctbx_project/iotbx/cli_parser.py", line 72, in run_program task.run() File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/programs/fix_insertions_deletions.py", line 515, in run self.fix_insertions_deletions.run() File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 1331, in run self.run_macro_cycles() File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 1464, in run_macro_cycles self.run_cycles(mc=mc) File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 1485, in run_cycles self.overall_rebuild_worst_residues(icycle,mc=mc) File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 1528, in overall_rebuild_worst_residues mc=mc) File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 1027, in rebuild_worst_residues map_coeffs=map_coeffs) File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 589, in rebuild_one_loop end_rebuild=end_rebuild,) UnboundLocalError: local variable 'new_model' referenced before assignment Has anyone encountered this error before? Thanks in advance, Carlos Fernandes

1 0

quick demo of phenix.autosol ?
by James Holton 02 May '21

02 May '21

Hello all, I'm involved in an X-ray course at Stanford this coming week and one of the things we want to do is demonstrate things like phenix.autosol. However, typical run times with borderline data and default settings can be more than a few minutes. Can anyone recommend a test data set / settings where phenix.autosol finishes very quickly? I was going to try and whip something up that is small, moderate resolution, screaming phasing signal, etc. However, since I'm sure many on this mailing list have done this hundreds of times you no doubt have a favorite example off the top of your head? thanks again! -James Holton MAD Scientist

1 0