December 2013 - phenixbb - phenix-online.org

phenix.find_ncs_from_density density_search.dump_ncs_density doesn't output mtz
by Francis Reyes 11 Dec '13

11 Dec '13

I'd like to see the region of my maps that obey the NCS operators and I was hoping for separate mtz's for each region given I had set density_search.dump_ncs_density = True. However, I'm not getting any output mtzs. Any ideas? Thanks, F --------------------------------------------- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

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phenix.refine nproc
by de Waal, Parker 10 Dec '13

10 Dec '13

Hello Everyone, I recently compiled phenix 1.8.4-1496 on a CentOS 6.4 server and am having trouble using phenix.refine in parallel using the nproc flag which always runs as a single thread. Please find my input parameters here: https://gist.github.com/anonymous/13b9d4d39ed4d0c9622a I'm wondering if maybe OpenMP isn't configured properly on our server? Or maybe the correct version is not installed when I compliled phenix. If anyone has any input or experience with a problem such as this I would be extremely grateful. Cheers, Parker

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Spatial filtering
by Machius, Mischa Christian 06 Dec '13

06 Dec '13

Potentially silly question: is spatial filtering used for increasing contrast in electron density maps? Is it used for any other kind of data manipulation in macromolecular crystallography, e.g., diffraction data processing, density modification, etc. I'm a bit fuzzy on that subject, and so I said 'potentially silly', because it could be that such approaches are totally common but have different names (such as local averaging/scaling and so on). Many thanks in advance. Cheers, MM

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Submissions for next CCN newsletter
by Nigel Moriarty 06 Dec '13

06 Dec '13

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the January 2014 issue is 15 December 2013 but if you can send me an email we can make exceptions so you can use the holiday break to work on your drafts. 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 64R0246B, Physical Biosciences Division 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

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DEN refinement
by Scott Thomas Walsh 05 Dec '13

05 Dec '13

Dear Phenix Users, Is it possible to use NCS restraints in DEN refinement like we can do in regular phenix.refine refinement? Thank you for your help. Cheers, Scott ************************************************ Scott T. R. Walsh, PhD Assistant Professor University of Maryland IBBR/CBMG 3127E CARB-2 9600 Gudelsky Drive Rockville, MD 20850 USA phone: (240) 314-6478 fax: (240) 314-6225 email: swalsh12(a)umd.edu<mailto:[email protected]>

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new Linux installers
by Nathaniel Echols 05 Dec '13

05 Dec '13

Hi Linux/Phenix users-- We are now building installers on several "new" platforms, including Ubuntu 10.04 and several versions of CentOS (which isn't much different from Fedora, except that it's supported by the virtual machine software we're using). Since we don't actually run these OSes outside of the VMs, we're going to crowd-source the testing a little more than usual. Our goal is to retire our ancient Fedora 3 systems - these are old and slow and take up too much space, but it's also the most compatible with other distributions. I'm hoping that the CentOS 5 builds will be a suitable replacement, or perhaps CentOS 4 (but we can only build the 32-bit installer on that OS). In addition to Ubuntu, I'm particularly interested in hearing whether any of these builds runs smoothly on SuSE and Debian. The virtual machine software supposedly supports these OSes too but I haven't yet managed to install SuSE on it after several attempts. The latest builds are here: https://www.phenix-online.org/download/phenix/nightly/?version=dev-1558&sho… We're missing the 64-bit CentOS 5 build right now, but I hope to get that working in the next few days. thanks, Nat

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Re: [phenixbb] reduce hangs
by Andreas Förster 05 Dec '13

05 Dec '13

Dear all, I'm not sure how much of my conversation with Jeff Headd and the comments from others that I received made it onto the mailing list. The problem with reduce being stuck in an infinite loop and refinement never completing has now a workaround, if no solution: Mark van Raaij pointed out that running refinement repeatedly while varying the number of cores would eventually avoid the infinite loop. I didn't observe that, but while running refinement with a handful of Xeons got stuck, running the same job with the same executable on the same OS with a bucketful of Opterons instead succeeded. As I said, there's no solution but a number of ways to get unstuck if you find yourself in the same situation like Mark and me. Best. Andreas -------- Original Message -------- Subject: Re: [phenixbb] reduce hangs Date: Wed, 4 Dec 2013 09:46:20 -0500 From: Jeff Headd <jjheadd(a)lbl.gov> To: Andreas Förster <docandreas(a)gmail.com> If the different machine is a slightly different architecture it's possible that it may run, even under the same OS version. My guess is that it's down to slight floating point differences in the coordinates throughout the course of refinement, but it's so hard to pinpoint. If you have access to other machines it is probably worth trying. <snip> Jeff

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Coot not allowing real space refinement when connected to phenix
by Jobichen Chacko 05 Dec '13

05 Dec '13

Dear All, I recently upgraded to latest version of coot (version0.7.2). When I try to do the Real space refine zone option, coot is giving the following complaint (Refinement setup failure. Failed to find restraints for PROLYSILE). But it works fine when I open coot separately from a terminal and read the pdb and mtz file. I downloaded this coot along with the ccp4 package and it also works fine when I open from ccp4 interface. Any suggestions will be much appreciated. Jobi

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hi.
by Hexi Zhang 04 Dec '13

04 Dec '13

http://satis.egitmeni.org/dxibo/axzjmylquusc.html Hexi Zhang

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reduce hangs
by Andreas Förster 03 Dec '13

03 Dec '13

Dear all, I'm refining a structure with 11 molecules in the asymmetric unit. Recently I took out NCS (data are to 2.2A and differences between molecules of interest). Refinement now stalls halfway through with two reduce jobs running at 100% CPU. The current job has been sitting like this for four days. The last entry in the log file are a few XYZ individual lines. Refinement includes XYZ, TLS, individual B, weight optimization. I launched 8 cycles. Phenix hangs after 4_bss. I've observed this twice in a row. Any suggestions to overcome this, short of going back to using NCS? This is with Phenix dev-1538 on RHEL 6.3. Thanks. Andreas -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London

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