April 2020 - phenixbb - phenix-online.org

covalently linked ligand
by Muhammad Bashir Khan 15 Apr '20

15 Apr '20

Hi All; I have a protein molecule and a ligand structure. I want to make a covalent bond between the ligand and protein molecule, could somebody explain to me how I can do that using phenix. I used the " *phenix.ligand_linking pdb_file_name" commond* It creates apply_link.def and data_link.cif I did refine the structure again giving the above file as well but did not see any covalent bond created between the protein and ligand. Thanks for your help Bashir -- ------------------------------------------------------ Muhammad Bashir Khan, Ph.D. Research Associate Department of Biochemistry Medical Science Bldg. Lab 3-27 University of Alberta Edmonton AB, T6G 2H7 Phone: 780-492-4577- e-mail: mbk(a)ualberta.ca <cbrooks1(a)ualberta.ca>

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helix/sheet outliers
by Casper Larsen 14 Apr '20

14 Apr '20

Hi.. I am doing real space refinement on a protein model build from a cryo-em map. I run the refinement with Amber gradients turned on and with secondary structure restraints (otherwise, more or less default settings). I have some issues with helix and sheet outliers. Every time I run the refinement (after making sure that the bond distance in the helices are within the 3.5 Å) I get a lot of bad annotation remarks, but with outliers just above 3.5 Å (see .log below): ... removed outlier: 3.576A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 3.681A pdb=" N PHE A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.737A pdb=" N MET A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) ... Is this something that I just need to fix in several rounds of refinement or is there an explanation? Amber gradients maybe? In addition, I have some bad sheet annotations such as: ... removed outlier: 6.987A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA B 444 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N THR B 429 " --> pdb=" O ALA B 444 " (cutoff:3.500A) ... When I look at the model, the residues are definitely a part of the sheet - the long distance between the N-O atoms is due to the O being "flipped" (hope it makes sense). Is this because of wrong annotation? Best Casper

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Advanced Light Source open for COVID-19 related research
by Paul Adams 14 Apr '20

14 Apr '20

Dear Colleagues, A quick note to alert researchers to the status of the Advanced Light Source in Berkeley (https://als.lbl.gov): The ALS is now operating in a limited capacity supporting COVID-19 related research. A number of MX beamlines from the ALS-ENABLE program are now taking proposals from the general user community working on COVID-19 via the ALS RAPIDD program (https://als.lbl.gov/rapidd/); choose ALS-ENABLE as the beamline and your proposal will receive prompt review with fast turnaround for beamtime. We are evaluating the possibility of expanding access to include to other techniques such as soft X-ray tomography, and BioSAXS in the near future. Please feel free to contact me with any questions. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

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app which can calculate the number of reflections for a given unit cell, spacegroup, resolution?
by Georg Mlynek 13 Apr '20

13 Apr '20

Dear Scientific community, I am looking for an app which can calculate the number of reflections for a given unit cell, spacegroup, resolution. Preferred would be a graphical output too. The program XRayView http://www.phillipslab.org/downloads comes very close what I imagine but it is not possible to select a spacegroup. It would like to use it for teaching parts of practical part during lockdown. Many thanks, br Georg.

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Two Ph.D. studentships at Newcastle University, UK Prof. Bert van den Berg
by Arnaud Basle 13 Apr '20

13 Apr '20

Dear All, Please see the attached documents for two Ph.D. studentships at Newcastle University, UK. The positions are in Prof. Bert van den Berg's laboratory and informal inquiries should be directed to him (Bert.Van-Den-Berg(a)newcastle.ac.uk). Cheers, Arnaud -- Dr Arnaud Basle X-ray facilities manager Newcastle Structural Biology Laboratory Biosciences Institute Faculty of Medical Sciences Newcastle University Framlington place NE2 4HH Newcastle upon tyne Phone 0191 208 5482

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Postdoctoral position in the Korostelev Lab
by Loveland, Anna 12 Apr '20

12 Apr '20

Postdoctoral position open at the University of Massachusetts Medical School, in the Korostelev Lab: https://www.umassmed.edu/korostelev-lab/. We study translation regulation, using cryo-EM and biochemistry. We are particularly interested in: (1) Translation accuracy; (2) Ribosome's central role in bacterial stress signaling and gene regulation; (3) Neurodegenerative and other diseases, which originate from dysregulation of translation. References to some lab publications are provided below. Our laboratory is housed at the RNA Therapeutics Institute, a vibrant and highly interactive research community: https://www.umassmed.edu/rti/about-the-rti/faculty-members/. Our colleagues are interested in nearly all aspects of RNA biology, from small to large RNAs to RNA chemistry and therapeutics development. We seek a highly motivated person who very recently received a PhD, or will soon receive a PhD. Applications sent prior to the dissertation defense date are welcome. Please submit the following information via email to: ann.powers(a)umassmed.edu 1) your CV (including publication list); 2) in less than 2 pages, an outline of your: (i) previous work - focusing on your most interesting finding(s); (ii) your current/future scientific interests, and whether/which aspects of translation regulation sound interesting to you; 3) email addresses of three references. Selected publications (accessible via the provided links): - Svidritskiy et al. “Extensive ribosome and RF2 rearrangements during translation termination<https://elifesciences.org/articles/46850>”. eLife.2019. - Loveland et al. “Ensemble cryo-EM elucidates the mechanism of translation fidelity<https://www.nature.com/articles/nature22397>”. Nature. 2017. - Demo et al. “Structure of RNA polymerase bound to ribosomal 30S subunit<https://elifesciences.org/articles/28560>”. eLife. 2017. - Abeyrathne et al. “Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896748/>”. eLife. 2016. - Loveland et al. “Ribosome•RelA structures reveal the mechanism of stringent response activation<https://elifesciences.org/articles/17029>”. eLife. 2016. --- Anna Loveland, Ph.D. anna.loveland(a)umassmed.edu 617 610 4321 (cell) Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential, proprietary and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender immediately and destroy or permanently delete all copies of the original message.

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Problem with molecular replacement
by Shramana Chatterjee 09 Apr '20

09 Apr '20

Hi, I am trying to solve a structure using a data solved by SAD as an reference (ensemble in phaser). The structure I am trying to solve has 100% sequence identity with the solved one. The problem that I am facing during Phaser MR is that, in the solved structure there are 6 molecules in the ASU although I am getting maximum 4 molecules in the ASU and also Rfree is around 0.49 just after the phaser. Phaser is showing a good values of LLG (>500) and TFZ (>8). It would be very helpful if I get any suggestion about the above-mentioned problem. Thank you in advance.

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Re: [phenixbb] Problem with molecular replacement
by Shramana Chatterjee 09 Apr '20

09 Apr '20

Thanks Roger. I am trying through looking at packing of crystal lattice.It seems that there are some gaps in the lattice. May be this is identical with the solved one because of identical cell dimension and space group. Although I think I should cross check with lattice as Matthew's analysis suggest a different number of copies. On Thu, Apr 9, 2020 at 8:51 AM Roger Rowlett <rrowlett(a)colgate.edu> wrote: > For MR solutions with more than 4 molecules in the ASU, you can improve > your chances of finding a solution by employing the following > considerations: > > The number of protein units in the ASU predicted by Matthew's analysis my > not be accurate for n>4. Always look at the molecular packing of potential > solutions in the ASU using Coot or Pymol. You may discover you have too > many molecules, and therefore overlaps, or too few molecules, leaving > protein size gaps in the crystal lattice. Lattice packing of partial > solutions may guide your thinking about the correct number of molecules in > the ASU. A good solution should normally have symmetrical and clear solvent > channels, and good contacts between all molecules. > > You may nave a better chance of obtaining a initial solution by searching > with dimers (if structurally appropriate) than monomers. > > Unless your crystal form is identical to the solved version, there is no > guarantee your N will be the same as the solved N molecules in the ASU. Use > the Matthew's analysis and lattice packing as your guide. > > Using this approach I've been able to obtain MR solutions for ASUs with > N=6-8, even with identities as low as 30%. > > Good luck. > > Roger Rowlett > Gordon & Dorothy Kline Professor, Emeritus > Colgate University > > > On Wed, Apr 8, 2020, 11:43 PM Shramana Chatterjee <schatter90(a)gmail.com> > wrote: > >> Hi, >> >> I am trying to solve a structure using a data solved by SAD as an >> reference (ensemble in phaser). The structure I am trying to solve has 100% >> sequence identity with the solved one. The problem that I am facing during >> Phaser MR is that, in the solved structure there are 6 molecules in the ASU >> although I am getting maximum 4 molecules in the ASU and also Rfree is >> around 0.49 just after the phaser. Phaser is showing a good values of LLG >> (>500) and TFZ (>8). >> >> It would be very helpful if I get any suggestion about the >> above-mentioned problem. >> >> Thank you in advance. >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org > >

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refinement of EM models with hydrogens using phenix.real_space_refine
by Coudray, Nicolas 08 Apr '20

08 Apr '20

Hi all, We had a question regarding how the phenix.real_space_refine works when used to refine CryoEM models with hydrogens: are hydrogens treated as riding or are they explicitly refined? Regards, Nicolas

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LINK to chromophore
by 김경현[ 교수 / 생명정보공학과 ] 06 Apr '20

06 Apr '20

Hi, I get linking problems of the CRF chromophore in GFP, where the peptide bonds connecting to each end of the chromophore to the protein do not show planar configuration. The LINK cif seems to only constrain bonds and angles. Any help how to fix the planar peptide bonds at the connecting ends? Many thanks. Regards, Kyung hyun == Prof. Kyung Hyun Kim, Ph.D. Rm 244 R&D Center Green Campus Korea University Anam dong, Sungbuk gu, Seoul 136-701 Department of Biotechnology & Bioinformatics Korea University Sejong Campus, Sejong, Korea Tel : +82 2 3290 3444, +82 10 9014 1416 Homepage : *sbl.korea.ac.kr <http://sbl.korea.ac.kr>*

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