- phenixbb - phenix-online.org

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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install problem on Ubuntu 12.10
by Guan Hong Hsiang 24 Apr '13

24 Apr '13

Dear all: When I wanted to install phenix on my computer with ubuntu 12.10 (./install), the error message showed that "/usr/local/phenix-installer-1.8.2-1309/bin/install-from-binary:130:export:6 core : bad variable name. I am a newbie of phenix. Could anyone give me some suggestion? Thank you Hong-Hsiang

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phenix.refine - blocking sorry error
by Maxime Cuypers 24 Apr '13

24 Apr '13

hello, i just installed the latest buid of phenix : 1356 i now get the following error in phenix.refine - this was ok with previous version ' Sorry: Your refinement strategy includes anisotropic ADPs for hydrogen atoms refined individually; hydrogens should be left as isotropic even for individual refinement. ' which is the new specific command to add to the .params file that will force anisotropic refinement of deuteriums please? PS: this is needed for my neutron structure refinement. thanks for your help -- Dr. Maxime Cuypers Institut Laue Langevin (ILL), Deuteration lab Rue Jules Horowitz, 6, BP 156 38042 Grenoble cedex 9 France

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Clashes while searching second copy using phaser.AUTOMR
by Rojan Shrestha 22 Apr '13

22 Apr '13

Hello, I have same problem as in the following link which is the previous thread in this bb. If you solved the problem who posted, please let me know the solution how it can be tackled. http://www.phenix-online.org/pipermail/phenixbb/2009-April/013136.html I am trying to find 6 copies in ASU. The space group of diffraction set is P3121. I have obtained one copy with high TFZ scores (18.5) without clashes. However, while searching for second copy, Phaser gave so many clashes with no solution. As I read in above thread, it could be due to parallel pseudo-translation symmetry. Can somebody suggest me to overcome this type of problem? Regards, Rojan

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ICSG 2013 Abstract Deadline extended to May 15, 2013: International Conference on Structural Genomics - Structural Life Science
by Terwilliger, Thomas C 22 Apr '13

22 Apr '13

Dear Colleagues, We hope that you are planning to attend the International Conference on Structural Genomics 2013, which will be held in Sapporo, Hokkaido, Japan, July 29th – August 1st, 2013. ICSG2013-SLS is intended to provide an overview for the most recent developments in Structural Genomics and its impact on research in biology, medicine and disease, and to foster international collaboration among researchers. Five oral presentations will be chosen from the posters, and four poster prizes will be awarded (one HKL Research Best Technology Poster Prize and three Journal of Structural and Functional Genomics Poster Prizes)! Please submit your abstracts by May 15, 2013! You can see all the details of the conference at: http://www.c-linkage.co.jp/ICSG2013 The scientific topics covered in ICSG2013-SLS include the wider life science research fields with particular attention to drug discovery (small molecules and biopharmaceuticals), biotechnology and industrial issues while keeping strength in the high-throughput technologies and integration of hybrid methods. These technologies are now leading to the new field of “Structural Life Science”. In order to widen the opportunity to junior researchers to study more, we have organized several satellite workshops before ICSG2013- SLS (during the day on July 29, 2013). The topics will include “Small molecule screening”, “Automation of X-ray Structure Determination”, “Cell-free Protein Production”, “Automated NMR methods”, "Eukaryotic expression", “Interaction analyses" and "Bioinformatics”. We hope you also find the satellite workshops are informative and productive. The conference will be held in Keio Plaza Hotel Sapporo, in walking distance of Hokkaido University's main campus and Sapporo station. The summer in Sapporo is a great time to stay and enjoy the cool summer night of Japan. ICSG2-13-SLS is partially supported by the Grant-in-Aid for Scientific Research on Innovative Areas; “Structural Cell Biology”, “Intrinsically Disordered Protein” and “Transient Macromolecular Complexes”, from Ministry of Education, Culture, Sports, Science and Technology (MEXT) . We are looking forward to welcoming you to Sapporo this summer! Sincerely yours, Katsumi Maenaka, Ph.D. Chair, International Conference on Structural Genomics 2013 -Structural Life Science- (ICSG2013-SLS) Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Japan Soichi Wakatsuki Chair of Program Committee, ICSG2013-SLS Photon Science, SLAC National Accelerator Laboratory Department of Structural Biology School of Medicine Stanford University The International Structural Genomics Organization Executive Committee Shigeyuki Yokoyama Dino Moras Joel Sussman Jennifer Martin Aled Edwards Tom Terwilliger

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Refinement of perfect twined data of P31/P32
by miyatake 22 Apr '13

22 Apr '13

Hello, Phenix users, Now I'm triying to refine almost perfect twining data (mixing of P31 and P32). It has a twining operation of (h, k, l) = (-h, -k, l), detected by the xtriage program. The data qualigy seems to be good, deflacting to 1.6A resolution with Rmerge ~ 5%. When I refined the MR structures with phenix.refine, however, the model geometries have been worse as over the 20% residues fall into disallowed Ramachandran region, and Rfree stacked around 30%. I tried many options such as real space refinement, SA, bad rotamer fixation, NCS restrain,,.., but they seem to be not so effective as usual twininig cases.. One molecule consists of 202 residues, and three molecules are inolved in AU. Of course, I used the twin option (-h, -k, l) during the refinement. Manual collection of the models could not improve the model anymore. Would anyone please advise me how should I refine the twinned data? Sincerely, Hideyuki, M.

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Turn off non-bonded interactions to measure distance in case of unknown interaction
by Edward A. Berry 22 Apr '13

22 Apr '13

I have a phenix-specific question and a general chemistry question. In a ligand-bound structure, S in an aromatic ring (substituted thiophene) may be H-bonding NH1 of arginine guanidino group. The general question is whether thiophene S can act as H-bond acceptor (assuming one lone pair is in the aromatic pi system for a total of 6 e, the other lone pair is available as H-bond acceptor?). The phenix-specific question involves whether non-bonded interactions will push the atoms apart during refinement, and how to turn off the nonbonded interaction between these two atoms to allow the xray data to determine the position. Under geometry_restraints.edits I define a bond, but give a very large sigma of 1A. Will this effectively remove non-bonded interactions between these two atoms?

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dummy atom v.s. model with zero occupancy.
by Jinzhong Lin 21 Apr '13

21 Apr '13

Dear PHENIX users, In phenix, in order to improve bulk solvent model when the model is not complete, you can add dummy atom and set "refinement.mask.ignore_zero_occupancy_atoms=False". My question is that can I just put a model ( I know the approximate position for the model) there instead of dummy atoms and set all atoms in the model zero occupancy and keep the same setting. Will I get the same result? I suspect that model will still be used to calculate the Fc even though the occupancy is zero, so the map will be severely model biased. Lithlin

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Re: [phenixbb] how to fix a side chain not to be refined?
by Rongjin 19 Apr '13

19 Apr '13

Hi Nat, You are right. By turning off the "fix rotamers" the Arg does not move any more. Best Rongjin ------------------ Original ------------------ From: "Nathaniel Echols"<nechols(a)lbl.gov>; Date: Apr 20, 2013 To: "PHENIX user mailing list"<phenixbb(a)phenix-online.org>; Subject: Re: [phenixbb] how to fix a side chain not to be refined? On Fri, Apr 19, 2013 at 2:14 PM, Rongjin <guanrj(a)foxmail.com> wrote: > I have an Arg with flexible side chain, close to an iodide ion. Every time > I refine it, the side chain of Arg will push the iodide ion away, even I > selected The syntax below looks correct to me, although you should probably do the same thing for the ADP selection, but it's a little disturbing that it's doing this. Do you have rotamer correction turned on? That may be the problem, if it is trying to fit to the difference density (I don't think it's very aware of nearby atoms). -Nat > the Arg not to be refined: > > refine { > strategy = *individual_sites individual_sites_real_space rigid_body \ > *individual_adp group_adp tls *occupancies group_anomalous > sites { > individual = "not (chain A and resid 40)" > } > } > > > The residue 40 in Chain A is that Arg close to the Iodide. Is this selection > correct? > How to fix the side chain of Arg in refinement? > > I attached two pictures, one before and one after refinement, the local area > of the Arg > and the iodide. The iodide is bound to an Asn residue of one symmetric > molecule. > > Thank you > Rongjin Guan > > > > _______________________________________________ > 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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how to fix a side chain not to be refined?
by Rongjin 19 Apr '13

19 Apr '13

Hello I have an Arg with flexible side chain, close to an iodide ion. Every time I refine it, the side chain of Arg will push the iodide ion away, even I selected the Arg not to be refined: refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous sites { individual = "not (chain A and resid 40)" } } The residue 40 in Chain A is that Arg close to the Iodide. Is this selection correct? How to fix the side chain of Arg in refinement? I attached two pictures, one before and one after refinement, the local area of the Arg and the iodide. The iodide is bound to an Asn residue of one symmetric molecule. Thank you Rongjin Guan

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Unusually low B factors
by Brennan Bonnet 17 Apr '13

17 Apr '13

Hi all, I have produced xenon derivatives for SAD phasing of several standard proteins by placing them under xenon gas pressure and then immediately flash freezing in liquid nitrogen. Everything has worked out nicely as far as successful phasing, nice models, and low R factors. Now I've noticed that the B values have decreased from initial processing values. Several rounds of manual changes and phenix.refine have caused B values to decrease each round of refinement to values of around 10 (I guess 20 is a more common value). Does anyone know why this is happening or what the explanation might be? I'm not sure what other information to include so please contact to discuss further. Thanks! ~Brennan

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Exclude atoms from refinements
by Simon Kolstoe 16 Apr '13

16 Apr '13

Hi, I want to exclude some atoms from refinement altogether in phenix.refine. Googling this I came up with the following link: http://phenix-online.org/pipermail/phenixbb/2011-December/018020.html however was wondering how you implement this sort of thing in the GUI? Thanks, Simon --------------------------------------------------------------- Dr. Simon Kolstoe Honorary Senior Research Associate Laboratory for Protein Crystallography Wolfson Drug Discovery Unit University College London Rowland Hill Street, London, NW3 2PF http://www.ucl.ac.uk/~rmhasek ---------------------------------------------------------------

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Pause phenix runs
by Mark J van Raaij 12 Apr '13

12 Apr '13

Just wondering if being able to pause a phenix run would be something useful. Currently, it appears one can only abort. Currently doing refinement of a large structure, and doing several simultaneous runs with different options is slowing down the computer too much. Individual runs take about 72 hrs, so o/n is not an option (o/weekend will be...) (or is it possible and I have missed it?) if the FPLC can do it, why not phenix? Seriously, I don't know how easy or difficult it would be to implement, or if paused runs would still take up too many resources, but it seems like something that might be useful - i.e. set several long runs running, and temporarily interrupt them for other jobs on the same computer (like watching youtube movies, as some people seem to think I do all day...) Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij

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Problem with MR-Rosetta
by Marta Sanz Gaitero 12 Apr '13

12 Apr '13

Hi to everyone, I've have a little problem running MR-Rosetta in Phenix. Some weeks ago, I tried to solve some data which didn't have very much identity with any PDB model using MR-Rosseta. The program started running but after a few hours it stopped suddenly. To check if the problem was that it was not possible to solve my data because they were very complicated or if something was going wrong with MR-Rosetta, I decided to run it using model data. I runned it using the mtz of a protein we had already solved in the lab, its sequence, and its own PDB file, generated after solving it. After 10 minutes, the program stops when it's starting the rebuild step. I think the program shouldn't have any problem to solve this data, since the model used for molecular replacement is exactly the same protein in the mtz, so I wonder if i'm doing something wrong. If someone could gave me any idea which helped me to solve the problem i would be very grateful. I attatch a snapshot of the error. Thank you in advance, Regards, Marta

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Re: [phenixbb] base stacking
by Ed. Pozharski 10 Apr '13

10 Apr '13

I wonder whether something simple like restraining a model to that of an ideal dna (a la den refinement) would do the trick with existing tools. -------- Original message -------- From: Nathaniel Echols <nechols(a)lbl.gov> Date: 04/10/2013 7:27 PM (GMT-05:00) To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Subject: Re: [phenixbb] base stacking On Wed, Apr 10, 2013 at 4:09 PM, jp d <yoyoq(a)yahoo.com> wrote: is there a way to do base stacking in phenix ? If you mean restraints on base stacking, no, we don't have anything like this right now. The only implementation of this anywhere, as far as I know, is the one from your (Noller) lab, but (aside from the lack of an explicit license) the fact that it's derived from CNS makes me very reluctant to even look at the code. However, if anyone has the derivation for the restraint energy function, we'd be happy to consider adding this to Phenix - we need to make a lot of changes to how we handle base-pairing anyway. -Nat

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Official release vs nightly builds
by Folmer Fredslund 10 Apr '13

10 Apr '13

Hi phenixbb/developers, Recently, some people have experienced problems with B-factor refinement in the official releases of PHENIX. It seems to me that, generally speaking, the first suggestion is to use the nightly builds of phenix. So, my question is: How does the official releases work? Is it a snapshot of the development version, or are you doing some kind of stabilization during the development of the official releases? Are you updating the official releases after release (to fix bugs) or are the bugs only fixed in the nightly builds. With the current official releases, would I be better off using the nightly builds for refinement? (I have also seen some weird behavior with B-factor refinement). Best regards and thank you for developing phenix, Folmer -- Folmer Fredslund Post doc MAX IV Laboratory Lund Sweden

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Postdoc Position - Berkeley
by Paul Adams 10 Apr '13

10 Apr '13

Lawrence Berkeley Laboratory Postdoctoral Researcher Job ID: 75785 Division: Physical Biosciences Date Opened: 4/9/2013 Summary: A postdoctoral position is available to work on developing new methods for macromolecular structure determination and refinement with the PHENIX software system. To learn more about Phenix visit: http://www.phenix-online.org Duties: Development and implementation of computational algorithms for structure determination using crystallography. Including methods for the assessment of crystallographic data quality, improved methods for minimization of target functions, algorithms for the automated parameterization of structure refinement, new target functions for the refinement of structures, and enhanced structure deposition tools. Qualifications: Ph.D. in computational crystallography or a related field. Demonstrated experience with computational methods development. Publications in macromolecular crystallography or closely related field. Familiarity with software development tools such as C++, C and scripting languages such as Python. Strong programming and mathematical skills. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Note that this is a multi-year position that is renewed annually on the basis on performance and continued funding. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 13 Nobel Prize recipients over the past 75 years, and 57 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. To apply visit https://lbl.taleo.net/careersection/2/jobsearch.ftl?lang=en and search for the job number 75785 or visit: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=75785 -- 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 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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!!!
by Hexi Zhang 06 Apr '13

06 Apr '13

http://www.pispy.com/mmog/bupedamkfovmstocspifxj.bjyhn

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Atoms with iso. B <=0
by Stephen Weeks 05 Apr '13

05 Apr '13

Dear phenixBBers I have a curious case of refinement of a 2.6 Angs structure, where some of the atoms have a calculated b-factor of 0.00. It seems to be somewhat random where this occurs and includes atoms within the backbone e.g. the nitrogen in the following residue: ATOM 2014 N THR A 264 -2.685 42.357 -35.833 1.00 0.00 N ATOM 2015 CA THR A 264 -3.952 41.776 -35.425 1.00 1.50 C ATOM 2016 CB THR A 264 -4.684 41.052 -36.593 1.00 1.70 C ATOM 2017 OG1 THR A 264 -4.077 39.772 -36.846 1.00 2.24 O ATOM 2018 CG2 THR A 264 -4.669 41.867 -37.855 1.00 1.72 C ATOM 2019 C THR A 264 -3.687 40.729 -34.368 1.00 2.42 C ATOM 2020 O THR A 264 -2.571 40.210 -34.263 1.00 2.63 O The structure contains 4 NCS related monomers but with a quick glance I don't see any obvious correlation between each one as to which atoms are 0.00. I did use phenix.pdbtools to randomise the B-factors (no atoms had a value 0.00 afterwards) but upon repeating the refinement the same problem occurs. Does anyone have a suggestion how to fix this ? Cheers Stephen

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43rd Mid-Atlantic Macromolecular Crystallography Meeting
by Charles Pemble 05 Apr '13

05 Apr '13

*43**rd** Mid-Atlantic Macromolecular Crystallography Meeting* *May 30 – June 1, 2013* *Duke University* *Durham, NC* The 43rd Mid-Atlantic Macromolecular Crystallography Meeting (MAMCM) 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 is now open 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. We encourage you to submit your abstracts and sign up for the workshops as these are separate processes from registration. *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

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table 1 no CC values, selenomethionine occupancy refinement
by Georg Mlynek 04 Apr '13

04 Apr '13

Dear All, I have 3 minor questions/problem and would be grateful for some help. 1a. Providing the XDS_ASCII.HKL to phenix tableI works perfect, however there are no values written for CC1/2. The same file in phenix.merging_statistics I get the CC1/2. Am I missing something? 1b. The only value phenix tablel one takes from INTEGRATE.LP (i guess CORRECT.LP will work too) is the wavelength - true? 2. I see some negative density around the seleniums in my selenomethionine labeled protein. I guess this is due to radiation damage. Is the accepted standard to do occupancy refinement for just the sidechain, or just parts of the sidechain, the whole residue or just leave it like it is. For the side chain refinement.refine.occupancies { constrained_group { selection = resname MSE ( name CB or name CG or name SE or name CE or name HB2 or name HB3 or name HG2 or name HG3 or name HE1 or name HE2 or name HE3 } } should work or? I am using version dev-1334 on ubuntu. Best regards Georg.

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C-alpha r.m.s.d. calculation before and after structural alignment
by Bret Wallace 04 Apr '13

04 Apr '13

Dear All, I have solved a complex structure of two proteins, and a reviewer has asked to compare the altered interface binding of one particular binding partner (protein2) in this complex to various other similar deposited PDBs through r.m.s.d. calculations and rotation/translation matrices. After aligning ~4 structures from the PDB (specifically aligning 1 chain to the other binding partner, protein1) to my structure, I want to calculated the rmsd before and after re-aligning the deposited structures (containing protein2) to my complexed protein2. I have used the superpose utility in phenix to align the C-alphas, however, I am getting very large rmsd values after alignment (~3.3). This is rather strange as the aligned proteins are essentially the exact same, both in sequence and secondary structure. Using various different programs such as SSM, Coot, and others give me an rmsd value of ~1, which is far more reasonable, but they do not output a "start" rmsd value. Any suggestions on what the cause of this large rmsd value? Or possibly another program that could provide start and final rmsd values along with rotation/translation matrices for alignment? Thanks, Bret

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links in phenix summary
by Christian Roth 03 Apr '13

03 Apr '13

Dear all, thanks to the phenix team which helped me a lot to resolve all issues regarding the correct link definitions. I have summarised a few things which one might consider if nonstandard links are necessary. Try phenix ready set to get your links out of the pdb. Do not forget to change the possible LINKR to LINK! Inspect the links and decide if they are useful! Peptide links are automatically incorporated if residues are close (inspect geo file) Non standard peptide links could be created using using an now available alpha release script: elbow.ligand_linking model.pdb Inspect the generated cif file and correct angles and incorporate dihedrals and so on if necessary. Sugar links which exists in the mon_lib.cif should be incorporated using the apply_cif link option like refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain B and resname GLC and resseq 1 residue_selection_2 = chain B and resname GLC and resseq 2 } According to the link definition the C1 oxygen of the following sugar with the higher number must be removed. The automatic incorporation of sugar links will be probably soon available in phenix. Nigel is already working on this. If one want use hydrogens in the refinement, they have to be added previously with ready_set and afterwards the OH4 sugar hydrogen has to be removed before the refinement. For links with symmetry related atoms the symmetry operator must be included in a custom bond definition efinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain A and resname HEM and resid 154 and name FE atom_selection_2 = chain A and resname MTO and resid 155 and name O symmetry_operation = -x,y,-z distance_ideal = 2.2 sigma = 0.01 } } The operator can be obtained using iotbx.show_distances your.pdb > all_distances Search for keyword "sym" or from Coot clicking on the symm option. Coot print out the operator and the translation term separately. Both has to be merged in the final operator used in phenix! Christian

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