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Computational Crystallography Newsletter - Volume 6, Number 1
by Nigel Moriarty 17 Feb '15

17 Feb '15

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 2015 Articles Improved Probabilistic Estimates of Biocrystal Solvent Content Rapid evaluation of non-bonded overlaps in atomic models Short Communications Plan a SAD experiment, scale SAD data, and analyze your anomalous signal Validation of carbohydrate structures in CCP4 6.5 Disulfide bond restraints Fitting Tip #9: Avoiding excess cis peptides at low resolution or high B FAQ - Tips for coordinated metal refinement 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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Quick request for addition to the line at the end of all these mails
by Morten Grøftehauge 16 Feb '15

16 Feb '15

Dear administrators of this list, Could you please add a line at the very end of these mails with: To unsubscribe click: www.somelink.com As it is it seems that some people have trouble getting off the list after they sign up. Because my spam filter keeps sending phenixbb mails into the spam folder. Which is likely because someone out there keeps flagging them as spam. If there's a link like that then gmail will even offer to attempt to unsubscribe for you. Just a thought. Cheers, Morten

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Please comment on the twinning analysis of my data by Xtriage
by Smith Liu 15 Feb '15

15 Feb '15

Dear All, I have done a Xtriage twinning analysis on my data. I summarize the result as following, Twinning analysis summary: The results of the L-test indicate that the intensity statistics below as expected. No twinning is suspected. Multivariate Z score L-test: 1.625. It further shows, Possible twin operators o merohedral twin operator(s) found, 1 pseudo-merohedral twin operator(s) found. Type Axis R metric(%) delta(le Pa) delta (lebed) Twin law PM 2-fold 4.934 2.547 0.036 l -k h Based on the above information, will you please advise me whether I need to input "l -k h" in the "Twin law" in "Other options" in "Refinement settings" in the Phenix refine graphical interface? I am looking forward to getting your reply. Smith

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On the cycles of the Phenix refinement
by Smith Lee 15 Feb '15

15 Feb '15

Dear All, The default number of cycles for the Phenix refinement graphical interface is 3 (should be macro-cycles). I have done a refinement with 3 default cycles, and I get the acceptable refinement results. Then I kept everything same, except I changed the cycles of refinement from 3 to 5, however the refinement result was ugly which was unacceptable. Someone told me once I have corrected the outliers by Coot, I can have a Phenix refinement with macro-cycles as 1, in order to avoid the Ramachandran corrected ones changing backing to Ramachandran outliers (Will you please further comment whether this strategy to correct Ramachandran outliers is acceptable or not). Thus can we regard the macro-cycles of Phenix refinement as one parameter for the refinement? And why the macro-cycles of the refinement can affect the refinement result? I am looking forward to getting your reply. Smith

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Re: [phenixbb] Fw: Fw: Question related to Phenix refinement
by Pavel Afonine 14 Feb '15

14 Feb '15

> From the attached the image, on the x-axis you can see the 4' rsrg and > 5'rsrg. > > I am looking forward to getting an explanation from you. Dear Smith, hope this will lead you to the answer: chevy:/net/chevy/raid1/afonine/sources % which fifig fifig: aliased to libtbx.find_files -g chevy:/net/chevy/raid1/afonine/sources % fifig rsrg ./cctbx_project/mmtbx/refinement/print_statistics.py: "realsrg" : "rsrg", chevy:/net/chevy/raid1/afonine/sources % All the best, Pavel

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Question related to Phenix refinement
by Smith Lee 14 Feb '15

14 Feb '15

Dear All. In the Phenix refine "run status" window, with the progression of the refinement, it occurs 3' bss, 3' rsrl, 3' xyz, 3' adp (for 3rd round of refinement). I guess xyz means the strategy is for x, y, z coordinates? Then what do bss, rsrl and adp mean? I am looking forward to getting your reply. Smith

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Test
by Paul Adams 14 Feb '15

14 Feb '15

-- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Hydrogen adding and real space refinement
by Smith Lee 12 Feb '15

12 Feb '15

Dear All, I find when I add H in the PDB file, in a refinement by Phenix, there is no real space refinement step (rsrl). If I do not add H in the PDB file, there is the rsrl step in the refinement. Somebody told me it was because there was a bug in the Phenix I downloaded, somebody told me if H added, there would be no real space refinement. I myself cannot clarify it by reading documents. Will you please clarify whether no rsrl step after H addition was because of bug or because of H addition leading to no rsrl step? And why H addition can lead to no rsrl step? I am looking forward to getting your reply. Best regards. Smith

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How should we estimate the "uncertainty" of the occupancy of an atom?
by Masaki UNNO 12 Feb '15

12 Feb '15

Hello We determined the structure of an enzyme-substrate complex. The substrate of the enzyme contains some partially occupied atoms. We were able to calculate the occupancies of these atoms using PHENIX_refine. By the way, I would like to know the uncertainties of the occupancies of these atoms. How can I estimate the uncertainties? For example, the occupancy of an atom was calculated as 0.65; can we write it as 0.65 (+/- 0.05) or 0.65 (+/- 0.1)? I know that it is related to B-factor and depends on the resolution (number of diffraction data per parameters), but I would like to know how to estimate (calculate?) the uncertainty. Could someone tell me about this issue? Best regards ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Masaki UNNO Graduate School of Science and Engineering Ibaraki University, JAPAN 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan Tel&Fax +81-294-38-5041 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Re: [phenixbb] How should we estimate the "uncertainty" of the occupancy of an atom?
by Dale Tronrud 11 Feb '15

11 Feb '15

On 2/11/2015 12:34 PM, Keller, Jacob wrote: >> If your interpretation of your model depends on whether the occupancy of this atom is 0.65 or 0.75 crystallography is the tool you need. > > Did you mean *not* the tool...? > > JPK > You are right. I meant crystallography is NOT your tool. Sorry. Dale Tronrud

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