- phenixbb - phenix-online.org

solvent masks
by Kajander, Tommi A 10 Feb '17

10 Feb '17

Hi All, Was there a convenient way to make a solvent mask for a region with a model - its been a while - and use that to generate maps (i have a domain that is only partially visible, could not be found be molecular replacement), its there though. Could be that its not well ordered, but I was wondering if the bulk solvent masking is just wiping it out. (basicly something like half a domain, e.g. half of individual beta-strands, are missing.) resolution is bit limited (at best 3 Å) so automated building and refinement doesnt work terribly well. I could just place a model there and make a mask somewhere and include in map calculation? Thanks for suggestions, tommi

1 0

phenix.composite_omit_map
by Dyda 09 Feb '17

09 Feb '17

Dear Phenix BB, I have a moderate resolution structure that I refined using secondary structure restraints (both for nucleic acid and for protein) I'd like to use phenix.composite_omit_map to calculate such a map. Is it possible (and if so how) to make phenix.composite_omit_map to use the same restraints during annealing of the not omitted parts? 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

2 1

Re: [phenixbb] Running Phenix Gui on Debian 8
by Chow, Martin 08 Feb '17

08 Feb '17

I am having troubling running Phenix 1.11.1.2575 gui under Debian 8 (Jessie), and have same results with different computers that are running the same system. I have no problem with previous versions like 1.9 and 1.10. However, with 1.11, Phenix guy won’t run. It complains about Gtk+ or Glib etc and quits. I know these are related to gui tool kits. I have tried Centro5, Centro6, and even compiled it, they all give similar or same complaints. I believe command-line works, but never try. However, simple commands like —version or —-help etc work. I just tried it on Red Hat, 1.11 works without issues. Clearly, it is a problem with the Linux Distro. Thank you. Martin Chow, Ph.D. Biochemistry University of Kentucky ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of phenixbb-request(a)phenix-online.org [phenixbb-request(a)phenix-online.org] Sent: Tuesday, February 07, 2017 3:20 PM To: phenixbb(a)phenix-online.org Subject: phenixbb Digest, Vol 135, Issue 4 Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/phenixbb or, via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org You can reach the person managing the list at phenixbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Computational Crystallography Newsletter, Volume 8, Number 1 (Nigel Moriarty) 2. Re: Phenix installation on manjaro (Murpholino Peligro) 3. Re: Phenix installation on manjaro (Billy Poon) 4. Re: Phenix installation on manjaro (Murpholino Peligro) 5. Re: Phenix installation on manjaro (Murpholino Peligro) 6. pdbtools atom_selection behavior (wtempel) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Feb 2017 13:21:05 -0800 From: Nigel Moriarty <nwmoriarty(a)lbl.gov> To: PHENIX user mailing list <phenixbb(a)phenix-online.org>, ccp4bb <CCP4BB(a)jiscmail.ac.uk>, developers(a)phenix-online.org, industry(a)phenix-online.org Subject: [phenixbb] Computational Crystallography Newsletter, Volume 8, Number 1 Message-ID: <CANkP=2eK6S4MWS=UJ=wZLXfC5qR9vQpgZEyi91gVv47EvdWQjA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. January 2017 <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf> Articles - Deploying *cctbx.xfel* in Cloud Computing and High Performance Computing Environments <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=10> Short Communications - multi_core_run(), yet another simple tool for embarrassingly parallel jobs <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=6> - Phenix tool to compute a difference map for cryo-EM <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=8> Fitting tips #13 ? O-pairs: The love-hate relationship of carboxyl oxygens <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=2> 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

1 0

pdbtools atom_selection behavior
by wtempel 07 Feb '17

07 Feb '17

Hello all, suppose I would like to remove one alternate conformation B from residue 1 in chain A and set the occupancy of remaining atoms in that residue to 1. phenix.pdbtools alts_minim.pdb occupancies.set=1 \ occupancies.atom_selection=”chain A and resid 1” \ keep=”not (chain A and altid B and resid 1)” \ output.file_name=alts.out.pdb There are better methods to achieve that, but I eventually would like to expand this command to do other “things” to my coordinates. Well, so far I have failed to have the atom_selection to work the way *I* expect. stdout reveals that the program fails to apply a common scope to the command switches, and proceeds to reset occupancies of all atoms. Can this be done on the command line? A minimal (not) working example is attached, and your feedback appreciated. Best regards. Wolfram Tempel

2 1

Phenix installation on manjaro
by Murpholino Peligro 07 Feb '17

07 Feb '17

Dear all. has anyone been lucky with the installation of phenix in manjaro or any other archlinux-based distribution? Thanks Ps. Error looks like http://pastebin.com/WzwrbK8W

2 5

Computational Crystallography Newsletter, Volume 8, Number 1
by Nigel Moriarty 06 Feb '17

06 Feb '17

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. January 2017 <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf> Articles - Deploying *cctbx.xfel* in Cloud Computing and High Performance Computing Environments <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=10> Short Communications - multi_core_run(), yet another simple tool for embarrassingly parallel jobs <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=6> - Phenix tool to compute a difference map for cryo-EM <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=8> Fitting tips #13 – O-pairs: The love-hate relationship of carboxyl oxygens <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=2> 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

1 0

Scale and merge multiple data sets
by Sam Tang 05 Feb '17

05 Feb '17

Dear colleagues Hello again. I would like to scale and merge two different native datasets for a same protein complex (which semed to die off gradually in the beam) using the scale_and_merge tool. The error message was received "Multiple intensity arrays - please specify one: data_labels=I,SIGI data_labels=IPR,SIGPR" However I looked into the log file and I have actually included "data_labels = "IPR,SIGIPR,merged" . Perhaps I have missed something else in the setting? Regards Sam Sam Tang Biochemistry Programme, School of Life Sciences, CUHK

4 5

protein atom selection
by wtempel 03 Feb '17

03 Feb '17

Hello all, in my hands and to my surprise, PHENIX atom selections such as "protein" or "peptide" would include a co-factor like SAM. Did others notice that also? Is this behavior what most users would want or even expect? Best regards. Wolfram Tempel

4 5

Refine a structure with a disconnected region
by Yasser Almeida Hernández 02 Feb '17

02 Feb '17

Hi all, I am refining a structure at 1.9A, which contains a 7 residues C-terminal region. The resolution of the map in that region is low but is clear enough to define some side chains and the backbone. I build this region manually in Coot. This region is disconnected from the core of the protein, since the connecting loop cannot be seen in the density map. After running phenix.refine (GUI) and playing with the options several times, the final model of this region is always out of the map, even when the R values are improved. How can I refine the structure, keeping that part of the protein in its place, fitted to the map? Thanks in advance Best Yasser

2 1

10th CCP4/APS Crystallographic School in the USA
by Sanishvili, Ruslan 01 Feb '17

01 Feb '17

Dear Colleagues, We are pleased to announce the 10th annual CCP4 crystallographic school “>From data collection to structure refinement and beyond”, held at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2017/index.php Dates: June 19 through 26, 2017 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop: 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 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 April 19. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2017/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, lodging and breakfast. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

1 0