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autobuild : MSE's keep coming back
by Lepore, Bryan 17 Sep '10

17 Sep '10

i used "semet=False" the .pdb has MET the .seq has M the output models, however, keep getting MSE's in them, complete with selenium. am i missing something? -bryan

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Re: [phenixbb] Something that came up on the CCP4 list...
by Simon Kolstoe 16 Sep '10

16 Sep '10

Just for the record I've had it make a big difference a number of times as well with both refmac & shelx. I was under the impression that phenix.refine was "cleverly" allowing me to use that trick by just starring the add riding hydrogens in the def file however it seems not - something worth knowing! Simon On 16 Sep 2010, at 20:01, Phil Jeffrey wrote: > I've had it make a big difference in certain circumstances. And in > other circumstances not so much. Definitely worth a try. I do not > use the technique routinely. > > Phil Jeffrey > Princeton > > > > On 9/16/10 11:49 AM, Simon Kolstoe wrote: >> So just to clarify further - if i am having problems with the final >> geometry of a model (eg clashscore as reported by molprobity), is >> it an >> appropriate trick to add hydrogens and then refine in phenix.refine >> using the riding hydrogens option, or does this not really change >> anything? >> >> Simon >> >> On 16 Sep 2010, at 14:26, Pavel Afonine wrote: >> >>> Hi Simon, >>> >>>> Could I just seek some clarification? I was under the impression >>>> that >>>> phenix.refine calculated riding hydrogens by default and took these >>>> into account as a restraint on the geometry? >>> >>> if you want hydrogen atoms to be used in refinement (as "riding >>> model" >>> or explicit) your need to make sure the PDB file that you give to >>> phenix.refine contains H atoms. That is you need to add them using >>> programs like phenix.reduce or phenix.ready_set or using >>> corresponding >>> functionality in the GUI. >>> >>> phenix.refine will not add them internally as part of refinement IF >>> hydrogen atoms are NOT present in input PDB file. >>> >>> Adding hydrogen atoms as 'riding model' does not add any refinable >>> parameters, but the scattering contribution from them is included >>> most >>> of the time. This is why we do not use H atoms silently but require >>> them to be in input PDB file - simply to make sure the reported >>> statistics (such as R-factors) is easily reproducible. >>> >>> All the best! >>> Pavel. >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >

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LABIN labels for Autosol/resolve NCS scores
by Florian Schmitzberger 16 Sep '10

16 Sep '10

Dear All, I would have a number of Phenix related questions: Firstly, I used the anisotropy server ( to anisotropically truncate my mtz file with anomalous signal (SAD data). My question is if the labels (for F+/F- and SIGF+/SIGF- are correctly recognized by Phenix (Autosol). The columns labels are: F_ref for FP; QSIGF_ref for SIGFP; GF(+)pk for F(+); LSIGF(+)pk for SIGF(+), GF(-)pk for F(-); LSIGF(-)pk for SIGF(-). It seems QSIGF and GF(+)pk/LSIGF(+)pk etc. are , but I am uncertain if it recognizes F_ref, because for the LABIN INPUT LABELS it says "NONE" for"F". Phenix does not seem to detect the anistropy ("Not using aniso- corrected data files as the range of aniso b is only 19.52 and 'correct_aniso' is not set); so I suppose I should use the correct_aniso=True keyword. Secondly, what are good values for the evaluation of the NCS mask and NCS averaging Resolve is using in Phenix; NCS overlap values (e.g. in my case 1.1) and NCS_CORR (in my case 0.52) in the "resolve.scores" file. Does an NCS overlap value of greater than 1 make sense? I am working with a (anisotropic) dataset with 4.1/4.5 A resolution, 78 % solvent content, 2-fold NCS; Perhaps a naive question: It is not possible to use B-factor sharpened maps for autobuilding with Phenix Autobuild is it? Thank you for any comments! Regards, Florian ----------------------------------------------------------- Florian Schmitzberger Biological Chemistry and Molecular Pharmacology Harvard Medical School 250 Longwood Avenue, SGM 130 Boston, MA 02115, US Tel: 001 617 432 5602

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f', f'' of Bromide?
by Tri Ngo 16 Sep '10

16 Sep '10

Dear Phenix-BB members, I am trying to solve the MAD data of one bacteria protein. The crystal was soaked with 1M Sodium Bromide. The data were collected at three different wavelength. I intend to use Autosol to solve this structure, but I am not sure which parameter I should put in the field: f' and f''? I think there is a table in the synchrotron but maybe I didn't notice about that. So now what should I do? Thank you very much for your input! Best wishes, -- * TriNgo * Structural Biology Lab School of Medicine - Sungkyunkwan University Phone: 031-299-6150

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Intl Conf on Structural Genomics, Toronto, Canada, May 10-14, 2011
by Thomas C. Terwilliger 16 Sep '10

16 Sep '10

Dear Colleagues, We are pleased to let you know about the upcoming International Conference on Structural Genomics 2011, to be held in Toronto, Canada on May 10-14, 2011. This meeting is the 6th in this series of biennial meetings of the International Structural Genomics Organization. The meeting is designed to serve as a forum to discuss the most recent developments in structural genomics and structural/chemical biology, and their impact on research in biology, medicine and disease. A limited number of student travel fellowships will be available for travel to this meeting. A substantial number of short talks will be selected from poster abstracts. Please see http://www.icsg2011.org for further details. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee

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64-bit Snow Leopard support
by Nathaniel Echols 16 Sep '10

16 Sep '10

Mac users-- The latest nightly version of Phenix (dev-532) is now capable of compiling 64-bit objects on Snow Leopard, which should help those of you working on very large and/or high-resolution structures. You will need to use the source installer for this; it will automatically recognize the machine type as "mac-intel-osx-x86_64" and use the correct sources. There are several things to be aware of before trying this: 1. I had to switch to the development version of wxPython to get the GUI working, and it's both inherently less stable and based on fundamentally different OS libraries, which may cause problems. I've fixed some of the most obvious issues and everything appears to run now, but I expect to find more glitches. (This shouldn't affect command-line users.) 2. We haven't extensively tested 64-bit Phenix on Mac; there may be undiagnosed low-level bugs, even for command-line-only use. This should change soon. 3. For the above reasons, and because source installation is generally difficult to support, we recommend that you continue to use the 32-bit binary installer if you are not experiencing memory problems. (It will figure out what you are trying to do and correct the machine type accordingly.) 4. One side effect of this change is that an installation made on Leopard will not work on Snow Leopard, and vice-versa. I may be able to fix this. Hopefully there will be a binary installer in the near future, if I can ever figure out how to fix NFS on my workstation. -Nat

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Something that came up on the CCP4 list...
by Simon Kolstoe 16 Sep '10

16 Sep '10

In the fascinating current discussion on the ccp4 list Pavel said: >Dear Ed, > >no, if you start with model that has no hydrogens, they will not be generated internally. > >Pavel. > On 9/15/10 2:58 PM, Ed Pozharski wrote: > Sure. But if I start with model that has no hydrogens, they will be > generated but not passed to the output, right. just like refmac. > > On Wed, 2010-09-15 at 14:52 -0700, Pavel Afonine wrote: >> Dear Ed, >> >> On 9/15/10 2:47 PM, Ed Pozharski wrote: >>> On Wed, 2010-09-15 at 16:26 -0400, Phil Jeffrey wrote: >>>> So the riding hydrogen model is imperfect. At least with >>>> phenix.refine >>>> you can measure it, unlike the default behavior of REFMAC. (But >>>> you >>>> can >>>> tell it to write hydrogens out, I believe). >>>> >>> My impression is that default behavior of phenix.refine is the >>> same - I >>> had to change parameters to include hydrogens in the output. >> No, if your input file contains H atoms, the output file will contain >> them too (in phenix.refine). You don't have to change any >> parameters for >> this. >> >> Pavel. Could I just seek some clarification? I was under the impression that phenix.refine calculated riding hydrogens by default and took these into account as a restraint on the geometry? Simon

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nqh-flip option
by Christian Roth 16 Sep '10

16 Sep '10

Dear all, I put manually in the parameterfile from the gui the option nqh_flips=True. After the run starts, a popup comes up claiming about an invalid unsupported option and the refinement stops without producing any file, even not a log-file. Does the nqh option not longer exists or what happend here? I use at the moment phenix 1.6-289. Thanks for your help. Christian

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Re: [phenixbb] autobuild : MSE's keep coming back
by Thomas C. Terwilliger 15 Sep '10

15 Sep '10

Hi Bryan, Hmmm...I can't seem to make it happen with my standard inputs. Can you possibly send me directly (terwilliger(a)lanl.gov) your AutoBuild_run_1_/autobuild.eff file or better yet that plus your input files and I'll try that out here? Thanks a lot, All the best, Tom T >>> are you using a recent version? >> >> v1.6.4 release tag 486 >> >>> is this rebuild_in_place or not? >> >> well, i did not specify rebuild_in_place, however, i poked around and can >> see that autobuild has switched on rebuild_in_place so i call that a >> "yes". >> >> -bryan >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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Re: [phenixbb] autobuild : MSE's keep coming back
by Lepore, Bryan 15 Sep '10

15 Sep '10

> are you using a recent version? v1.6.4 release tag 486 > is this rebuild_in_place or not? well, i did not specify rebuild_in_place, however, i poked around and can see that autobuild has switched on rebuild_in_place so i call that a "yes". -bryan

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