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Coot failed to launch in Phenix after CCP4 update
by Shun Liu 06 Jan '15

06 Jan '15

Dear all, After I updated ccp4 to a new version (ccp4-6.5), I found that coot failed to launch in phenix. /Applications/PHENIX-1.9-1692/Contents/phenix-1.9-1692/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/start_coot.sh: line 37: /Applications/ccp4-6.4.0/coot.app/Contents/MacOS/coot: No such file or directory Apparently it requires ccp4-6.4.0, which has been deleted. I tried to modify find_coot_command.py in phenix, but it didn’t work. Can anybody give me some suggestions so that I can figure this problem out? Thanks! Best, Shun

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Coot launch failure
by Shun Liu 06 Jan '15

06 Jan '15

Dear all, After I updated ccp4 to a new version (6.5), I found that coot failed to launch in phenix. Can anybody give me some suggestions to figure this problem out? Thanks! Best, Shun

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a question related to Phaser-MR
by Wind Sui 05 Jan '15

05 Jan '15

Dear All, In the Phenix Phaser-MR (simple interface, will you please tell me what should I input for the "sequence identities"? I am looking forward to getting your reply. Wind

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FEM maps
by Colin Levy 04 Jan '15

04 Jan '15

Dear All, when using FEM maps I notice that some solvent structure has clean (ish) 2Fo-Fc but not FEM density. Is this indicative of the water without FEM density being simply noise or is it more complicated than that? Many thanks, Colin Manchester Protein Structure Facility Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 c.levy(a)manchester.ac.uk<mailto:[email protected]>

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phenix.refine reference?
by Ulrich Baumann 04 Jan '15

04 Jan '15

Dear colleagues, a very happy New Year 2015 to all of you! Is there a specific reference for phenix.refine, please? Or is it ok if we cite Adams et al., Acta Cryst D66, 213-221 (2010) or the 2011 paper on Phenix? What about Xtriage? Thanks you very much for your kind help! Best wishes, Ulrich

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a command on Phenix refine
by Wind Sui 04 Jan '15

04 Jan '15

Dear All, I use the graphic phenix.refine to do a refinement, and Phenix informed me I need to have a command "refinement.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None". Will you please tell me by graphic phenic.refine, how can I input this command? Wind

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a question related to phenix.refine
by Wind Sui 04 Jan '15

04 Jan '15

Dear All, After I finished a refinement by Phenix.refine and I closed the Phenix software, is any method I can get the exact phenix.refine window as the moment the Phenix.refine just finished the refinement? I mean by all the documents saved automatically by the Phenix.refine after it finished a refinement, how can I get the Phenix refine window once more, for the check of Log output, Run status, Results, MolProbity, Real-space correlation, Atomic properties, and sequence check? Wind

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Fw: Reading a shelx file
by Rex Palmer 25 Dec '14

25 Dec '14

Can I read a Shelx file with Phenix and output the new pdb in Phenix format? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com

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Announcement: Membrane Protein Structures 2015 Meeting (MPS 2015)
by Nagarajan Venugopalan 22 Dec '14

22 Dec '14

Posted on behalf of the organizing committee: Registration is now open for Membrane Protein Structures 2015 Meeting (MPS 2015) Location: Argonne National Laboratory, Lemont, IL, USA Dates: April 10 - 12, 2015 Accompanying workshops: Membrane Protein Technologies Location: Argonne National Laboratory, Lemont, IL, USA Date: April 9, 2015 Meeting WEBsite: http://aps.anl.gov/mps2015. _Important dates_: _Registration deadline_: February 15, 2015 (https://www.regonline.com/mps2015) _Accommodation deadline_: March 10, 2015 (http://www.aps.anl.gov/Users/Communications/User_News/2014/MPS_hotel_info.p…) Thanks Naga -- ************************************************************************ Nagarajan Venugopalan, Ph.D. GM/CA@APS, Sector 23, X-ray Science Division Bldg 436, D005 Argonne National Laboratory 9700 S Cass Ave, Argonne IL 60439 Tel: 630-252-0669 Fax: 630-252-0667 email: vnagas(a)anl.gov ************************************************************************

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29th European Crystallographic Meeting
by Igor Sabljić 22 Dec '14

22 Dec '14

Dear Phenixbb users, I am delighted to tell you the registration for the 29th European Crystallographic Meeting is open. Just to remind you ECM29 (August 23-28, 2015) is taking place in beautiful city of Rovinj in Croatia. You can find more information on our web site, and please visit, like and share our Facebook page! I hope I will see you all there! Web: http://ecm29.ecanews.org/ Facebook: https://www.facebook.com/29thEuropeanCrystallographicMeeting?ref=hl Sincerely, Igor [1] IGOR SABLJIĆ _Social networks editor_ Ruđer Bošković Institute Division of Physical Chemistry Bijenička cesta 54, 10000 Zagreb, CROATIA http://ecm29.ecanews.org [1] Facebook [2] home [3] Links: ------ [1] http://ecm29.ecanews.org [2] http://www.facebook.com/29thEuropeanCrystallographicMeeting [3] http://www.irb.hr/eng/Research/Divisions-and-Centers/Division-of-Physical-C…

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