- phenixbb - phenix-online.org

Submissions for next CCN newsletter
by Nigel Moriarty 07 May '13

07 May '13

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the June 2013 issue is 31 May, 2013 but if you can send me drafts before the 15th of May we can get started on generating proofs. 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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43rd Mid-Atlantic Macromolecular Crystallography Meeting
by Charles Pemble 07 May '13

07 May '13

*43**rd** Mid-Atlantic Macromolecular Crystallography Meeting* *May 30 – June 1, 2013* *Duke University* *Durham, NC* This is a reminder for the 43rd Mid-Atlantic Macromolecular Crystallography Meeting, which will be held at Duke University in Durham, North Carolina. This meeting fosters discussion and interaction among structural biologists from around the Mid-Atlantic region. Registration and details can be found at http://www.mid-atlantic.org. The deadline for registration is May 15th. This year will feature keynote speaker Tom Terwilliger from Los Alamos National Lab, workshops on PHENIX and MolProbity, plus many talks & posters on new and exciting research. Presentations will be selected from submitted abstracts and preference will be given to young researchers. The best presentation and poster by a Graduate Student & Postdoctoral Fellow will be awarded (total of 4). We encourage you to submit your abstracts and sign up for the workshops as these are separate processes from registration. *DEADLINES:* Registration - May 15th Abstract submission for presentation - May 10th Abstract submission for poster - May 27th *IMPORTANT: *A block of rooms have been reserved at the Millennium hotel as well as the Duke dormitories. The deadline for reserving a room at the Millennium is May 9th. With best wishes on behalf of the primary Organizing Committee, Charlie Pemble _____________________________ Charles W. Pemble IV, Ph.D. Duke University Medical Center 308 Research Drive LSRC, A06 Durham, NC 27708 charles.pemble(a)duke.edu We thank our current sponsors for their generous contributions: Rigaku Americas Corporation, Agilent Technologies Inc., GlaxoSmithKline, Art Robbins, Bruker, HKL Research Inc., Molecular Dimensions, Hampton Research, Labcyte, GenScript, Genentech, Emerald BioSystems, TTP LabTech, Oxford Cryosystems, PhD Posters, Duke University School of Medicine, Duke Human Vaccine Institute, and Avanti Polar Lipids Inc.

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Morphing only a part of the model?
by Guenter Fritz 06 May '13

06 May '13

Dear all, I am working on a multisubunit protein complex (ca. 2000 residues). I would like to morph only a part or one subunit into the experimental electron density without morphing the rest of the protein. iIs there a way to select a subunit or a part of the model? Best regards, Guenter

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Find Difference peaks and holes
by John Rose 03 May '13

03 May '13

Hi, I can't seem to find the "Find Difference peaks and holes" utility in the PHENIX 1.8.2-1309 distribution. I found it to be very useful. Can you tell me where it is hiding. Regards, John John Rose Ph.D. Associate Professor B204B, The Fred C. Davison Life Sciences Complex 120 Green Street Department of Biochemistry and Molecular Biology University of Georgia Athens, GA 30602-7229 ========================================= Phone: 706-542-1750 Fax: 706-542-3077

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ReadySet & phenix.refine problem: NAG-Asn with hydrogen atoms
by Zhijie Li 29 Apr '13

29 Apr '13

Hello, I am refining my structure with hydrogen atoms on (phenix 1.8.2-1309). The protein contains two Asn-linked GlcNAc. I noticed two problems with respect to the NAG-Asn linkage in the presence of hydrogen atoms: 1) After running ReadySet (to add hydrogen to the PDB ab initio), the H1 on the NAG is pointing to the amino group of Asn, ie, the NAG seems to be interpreted as in its alpha anomer instead of beta (should be GlcNAc beta1,N-Asn). This is not really a problem as it doesn't seem to affect the refinement. 2) The H21 in Asn is correctly removed by ReadySet, leaving only H22. However, if I send this PDB to phenix.refine, the refinement will fail almost instantly complaining that H22 of the Asn has an unknown nonbonded energy type symbol. But if I simply change the atom name of H22 to H21, the refinement will proceed to completion with no problem, only leaving an H21 at the position where H22 should be. I was not sure what caused this error. So I trimmed my PDBs down to the Asn and NAG only, and fed the small PDB to ReadySet and phenix.refine (with an eff file indicating the NAG-Asn linkage) and got the same behavior: H22 on Asn - error; H21 on Asn - OK. I hope someone can look into this. Thanks in advance. Zhijie

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SIGF in refinement
by Aksyuk, Anastasia (NIH/NIAMS) [F] 29 Apr '13

29 Apr '13

Hi, I was wondering how SigFobs values are used in phenix refinement and how important those are. I am asking in view of P1 space group with low redundancy or even cryo-EM map based Fobs. Maybe you can point me to a useful reference on likelihood targets. I feel lost in those that I have. Thanks, --Anastasia ------------------------------ Anastasia A Aksyuk, PhD Laboratory of Structural Biology, NIAMS Bldg 50, Room 1511, 50 South Drive MSC 8025 N.I.H., Bethesda, MD 20892-8025 tel 301 451-8247 e-mail: anastasia.aksyuk(a)nih.gov

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Re: [phenixbb] clashscore discrepancies
by Alex Theodossis 27 Apr '13

27 Apr '13

Dear phenixbb, I have carried out refinement using the latest version of PHENIX, which gives improved molprobity stats. However, these stats still do not match those porvided by the molprobity server: PHENIX output Molprobity server Existing H-model Electron-cloud H-model All atom clashscore 2.57 4.2 (81st perc) 3.25 (88th percentile) Rotamer outliers 0.7 1.14 1.14 Overall score 1.04 1/24 (89th perc) 1.16 (93rd percentile) Given that PHENIX is now giving me the best results and all scenarios give reasonable results I am less inclined to be concerned. However, I still find these inconsistencies rather puzzling and am curious to learn what is causing them. Thanks in advance.

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phenix.elbow: Best ploy to generate restraints files for similar compounds ?
by Phil Jeffrey 25 Apr '13

25 Apr '13

I've got homologues of small molecule compounds I want to generate restraints for. The changes I'm looking at are converting O to S and moving a substituent around on a phenyl ring. I expect them to have similar conformations overall. Is the best method to: 1. create a new PDB file of the homolog, change atom types and do some primitive modeling, assuming that the --opt method will fix geometry snafus ~or~ 2. use a SMILES string, edit the numbering of the PDB file and regenerate the restraints from that Thanks Phil Jeffrey Princeton

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clashscore discrepancies
by Alex Theodossis 25 Apr '13

25 Apr '13

Dear phenixbb, Have refined a 1.05A structure with riding hydrogen model in phenix v1.8.1-1168 and doing final validation. The molprobity statistics output by phenix include: all atom clashscore = 4.12 Rotamer outliers = 0.71% Overall score = 1.2 Put through the molprobity server I am given the option of analysing with existing hydrogen model, or replacing with the 'electron-cloud parameters' they recommend for X-ray crystal structures. The results end up being very different: existing H model: electron-cloud model: All atom clash score: 4.66 (78th percentile) 3.72 (85th percentile) Poor rotamers: 1.14% 1.14% Overall score: 1.28 (88th percentile) 1.20 (92nd percentile) While all three scenarios give acceptable statistics, I am surprised by the inconsistency in the results given by molprobity, even when using the same hydrogen model. I am also wondering whether I am using a suboptimal riding model in my refinement (generated using phenix ready-set). Can anyone advise on the reason for these inconsistencies (is it just due to differences in the version of molprobity being run in each case). Is there anything I should be doing differently? Thanks in advance. On 18 November 2012 12:36, Alex Theodossis <alex.theodossis(a)monash.edu>wrote: > Hi, > > I'm attempting to install the latest version of phenix on mac 10.5.8, > using the command line installer. > > Installation proceeds well until towards the end, where it hangs on: > > precompiling .py files > > I can leave it for up to an hour without any further progress, but upon > typing: > > ctrl+c > > The installation comes back to life and proceeds to completion. > > Can anyone advise as to what might be causing this and on how reliable > this installation is going to be? > > Thanks in advance. > > >

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Postdoctoral positions in structure and function of membrane proteins at the NIH
by Anirban Banerjee 24 Apr '13

24 Apr '13

Dear all, Will you please bring this to the attention of suitable candidates ? Postdoctoral positions in structure and function of membrane proteins at the NIH The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows to start from September, 2013 or later. The broad interests of the lab are in membrane protein structure and function. We will combine macromolecular crystallography with functional assays with detergent-solubilized and liposome-reconstituted proteins to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab is part of the Cell Biology and Metabolism (CBMP) program and is part of a large and diverse macromolecular crystallography and NMR community in the NIH campus. There is ample opportunity to interact with other scientific groups across a broad range of scientific disciplines. CBMP is part of the National Institute of Child Health and Human Development (NICHD). Our lab also has an affiliation to the National Institute of Neurological Disorders and Stroke (NINDS). The DC Metro area is a wonderful place to live, the weather is pleasant and the NIH is a vibrant international community. Candidates must be motivated and have a strong background in biochemistry and structural biology. Experience with protein expression, purification and crystallization is required. Prior experience in membrane protein biochemistry will be an added advantage. Candidates should hold a Ph.D. degree by the time they join and have no more than one year of postdoctoral experience at the time of applying. To apply, please send an email of interest to anirban.banerjee(a)nih.gov with a CV and a summary of previous research experience and future research interests. Best regards, Anirban

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