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sugar puckering refinement with phenix refine
by Almudena Ponce Salvatierra 14 Apr '15

14 Apr '15

Dear all, does anyone know how phenix.refine deals with the sugar puckering of an RNA or a DNA strand? Does it refine it? Or does it leave it as it was built? Thank you very much in advance. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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Link NGA and THR
by Cory Brooks 14 Apr '15

14 Apr '15

Hello! I am refining a structure with O-link glycosylation (GalNAc linked to Thr). Phenix seems to remove the link during refinement. Can anyone suggest a solution that will maintain the bond during refinement? Regards, Cory Cory Brooks,Ph.D.

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elbow-readyset
by Tarek DawoD 14 Apr '15

14 Apr '15

Dear All if i have pdb file for CdCl2, how could i generate cif file (to use later in phenix.refine) from that using readyset or elbow or any other tool.i could not find 3 letter could for CdCl2. COMPND UNNAMED AUTHOR GENERATED BY OPEN BABEL 2.3.1 HETATM 1 CD LIG 1 0.994 8.428 20.546 1.00 0.00 Cd HETATM 2 CL1 LIG 1 -0.441 6.507 20.373 1.00 0.00 Cl HETATM 3 CL2 LIG 1 3.190 7.731 21.231 1.00 0.00 Cl END Thank you for Help.regardsTK_DawoD

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Submit your abstract for the ACA Annual meeting in Philadelphia July 25-29, 2015
by Terwilliger, Thomas Charles 14 Apr '15

14 Apr '15

Hi Phenix users! You are invited to the ACA meeting in Philadelphia! Abstracts are still being accepted (see the invitation below). All the best, Tom T Tom Terwilliger Vice President, ACA Abstracts still being accepted ACA 2015 Meeting - July 25-29 Philadelphia, PA Is this email not displaying correctly? View it in your browser<http://us2.campaign-archive2.com/?u=3e43dd9d1724b97d2bc286881&id=0f524b9d2c…>. [https://gallery.mailchimp.com/3e43dd9d1724b97d2bc286881/images/2a8238a9-d30…] [http://www.amercrystalassn.org/2015-mtg-homepage]<http://amercrystalassn.us2.list-manage.com/track/click?u=3e43dd9d1724b97d2b…> ABSTRACT SUBMISSION DEADLINE IS EXTENDED ACA Annual Meeting • Philadelphia, PA • July 25 - 29, 2015 Submit abstract now to be considered for an oral presentation. Once all the lectures are scheduled, abstracts will continue to be accepted for poster presentations. [https://gallery.mailchimp.com/3e43dd9d1724b97d2bc286881/images/21952137-733…] Exhibit Show<http://amercrystalassn.us2.list-manage.com/track/click?u=3e43dd9d1724b97d2b…> First-time exhibitors receive 25% discount Discount rates for Not-for profits Corporate Members receive an additional discount Coffee breaks & poster sessions held in the exhibit hall to offer multiple opportunities to reach your target audience Your website linked on the meeting page Free listing in ACA RefleXions and Program & Show Guides Special sponsorships for Exhibitors only [https://gallery.mailchimp.com/3e43dd9d1724b97d2bc286881/images/d9f63f39-b8b…] Call for Papers:<http://amercrystalassn.us2.list-manage.com/track/click?u=3e43dd9d1724b97d2b…> 40% of talks selected from contributed abstracts No abstract submission fee Lower registration fees for members Sessions for students & young scientists on career directions, reviewer practices & more Full scientific program:www.AmerCrystalAssn.org<http://amercrystalassn.us2.list-manage1.com/track/click?u=3e43dd9d1724b97d2…> [https://gallery.mailchimp.com/3e43dd9d1724b97d2bc286881/images/961e8c70-86c…] Registration<http://amercrystalassn.us2.list-manage.com/track/click?u=3e43dd9d1724b97d2b…>: Join or pay membership dues and save on Registration fees Corporate Members receive advertising and exhibiting discounts Early bird rates until May 31 Online registration now open<http://amercrystalassn.us2.list-manage2.com/track/click?u=3e43dd9d1724b97d2…> follow on Twitter<Twitter%20Account%20not%20yet%20Authorized> | friend on Facebook | forward to a friend<http://us2.forward-to-friend.com/forward?u=3e43dd9d1724b97d2bc286881&id=0f5…> Copyright © 2014, AmericanCrystallographicAssn. All rights reserved. Our mailing address is: aca(a)hwi.buffalo.edu<mailto:[email protected]> ACA, PO Box 96, Buffalo, NY 14205 [Email Marketing Powered by MailChimp]<http://www.mailchimp.com/monkey-rewards/?utm_source=freemium_newsletter&utm…> unsubscribe from this list<http://amercrystalassn.us2.list-manage.com/unsubscribe?u=3e43dd9d1724b97d2b…> | update subscription preferences<http://amercrystalassn.us2.list-manage.com/profile?u=3e43dd9d1724b97d2bc286…>

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pdbtools: how to set the occupancy for an atom selection?
by Alejandro Virrueta 13 Apr '15

13 Apr '15

Hello, I was wondering if someone could show me a way to set the occupancy of a specific set of atoms to 0 using phenix.pdbtools. I noticed here <http://www.phenix-online.org/download/documentation/cci_apps/pdbtools.html#…> that there is no option under modify => occupancies to do an 'atom_selection'. Any help would be appreciated. Cheers, Alex

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Deposition question
by mohamed noor 13 Apr '15

13 Apr '15

Dear all I solved my structure using SAD from heme to 2 A and then did molecular replacement with a dataset diffracting to 1.2 A. Do I deposit only the mtz and pdb file from the last refinement run and report the corresponding statistics in 'Table 1'? Should I specify the experimental f' and f'' values? Thanks.

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expermiental sigma or SIGFP of the mtz file
by Smith Lee 13 Apr '15

13 Apr '15

Dear All, Will you please let me know what is the expermiental sigma or SIGFP of the mtz file? If a mtz file lacks the expermiental sigma or SIGFP, what does it mean? I am looking forward to getting your reply. Smith

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Reference model restraints in real space refinement?
by Oliver Clarke 13 Apr '15

13 Apr '15

Hi all, Is it possible to use reference model restraints at the moment during real space refinement (in phenix.real_space_refine)? I can’t see it in the documentation. On a related note, would it be possible at some point to allow users to set d_max in the phenix.map_to_structure_factors utility? At the moment it seems like the user can set d_min but not d_max - sometimes it is convenient to restrict the low res to 20 or 50Å, rather than the whole box size of an EM-map, which is the default. Best, Oliver.

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Phenix command to align the PDB sequence and input sequence
by Smith Liu 11 Apr '15

11 Apr '15

Dear All, Will you please tell me the Phenix command to align the PDB sequence and input sequence? I am looking forward to getting your reply. Smith

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Error refining with ramachandran restraints
by Oliver Clarke 11 Apr '15

11 Apr '15

Hi all, When I attempt to run a refinement using phenix.refine from the command line, using the parameter “ramachandran_restraints=true”, in the latest nightly build of phenix (dev-2006), I get the following error: ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. Traceback (most recent call last): File "/Applications/phenix-dev-2006/build/../modules/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/Applications/phenix-dev-2006/modules/phenix/phenix/refinement/command_line.py", line 96, in run master_params=customized_master_params) File "/Applications/phenix-dev-2006/modules/phenix/phenix/refinement/driver.py", line 272, in __init__ secondary_structure_manager=self.sec_str, AttributeError: refine instance has no attribute 'sec_str' This happens for two different structures, so I don’t think it is a structure-specific thing, and I don’t recall this happening in older builds of phenix. The refinement runs fine if I don’t specify ramachandran restraints. Is there something obvious I am doing wrong? Best, Oliver.

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