- phenixbb - phenix-online.org

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.

3 2

phenix.elbow: Best ploy to generate restraints files for similar compounds ?
by Phil Jeffrey 26 Apr '13

26 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

2 1

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. > > >

3 2

Postdoctoral positions in structure and function of membrane proteins at the NIH
by Anirban Banerjee 25 Apr '13

25 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

1 0

install problem on Ubuntu 12.10
by Guan Hong Hsiang 25 Apr '13

25 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

2 4

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

2 1

Clashes while searching second copy using phaser.AUTOMR
by Rojan Shrestha 23 Apr '13

23 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

1 0

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

1 0

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.

3 2

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?

4 8

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

3 6

Re: [phenixbb] how to fix a side chain not to be refined?
by Rongjin 20 Apr '13

20 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 .

2 1

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

3 2

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

3 5

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 ---------------------------------------------------------------

3 4

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

5 4

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

2 1

Re: [phenixbb] base stacking
by Ed. Pozharski 11 Apr '13

11 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

2 1

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

6 11

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 ] --

1 0

!!!
by Hexi Zhang 07 Apr '13

07 Apr '13

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

1 0

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

3 3

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

1 0

table 1 no CC values, selenomethionine occupancy refinement
by Georg Mlynek 05 Apr '13

05 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.

5 5

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

2 1

links in phenix summary
by Christian Roth 04 Apr '13

04 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

3 2

Fw:Dialing Pretty
by Dialing Pretty 03 Apr '13

03 Apr '13

http://www.riofoliashow.com/bhblnsv/jx.vohys?dwr Dialing Pretty gzdrrasz

1 0

MR-Rosetta server?
by Mark J van Raaij 02 Apr '13

02 Apr '13

Dear All, for a recent dataset, I would like to try MR-Rosetta, as normal MR didn't work (not surprising perhaps, as the closest model is from NMR and with only about 20% sequence identity). Even though I don't think there is much chance of success, I would like to try MR-Rosetta anyway, although without having to install Rosetta if possible. Is there a server that would take care of the whole process? I.e. take the input mtz and the hopefully homologous structure supplied by me, and run Rosetta followed by MR in Phenix? In its defect, is there an online server that does the Rosetta part of MR-Rosetta, that would give a Rosetta-improved output model for putting into MR by Phenix, which I already have installed? Some side-ways related questions: - is it feasible to install Rosetta under MacOSX for a not very computer-literate user? - Phenix seems to slow down my MacPro a lot, even if I use just one of the 8 processors - is 4 Gb of RAM too little? Sorry for the rather rambling mail... Greetings, Mark 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

3 2

.::Hexi Zhang::.
by Hexi Zhang 02 Apr '13

02 Apr '13

http://www.shoes4me.com/jpnnv/qkawwtmiigdaxdliiayzmr.opdpdklrvlts

1 0

which monlib in refinement?
by Konrad Bergen 02 Apr '13

02 Apr '13

Hello phenixbb, i was recently refining a DCT and was a bit puzzled when i got outliers in torsion angles (readout from the final .geo file). The DCT was built in coot (using the ccp4 monomer library) and seems to fit these restraints. A closer look gave me a discrepancy in the torsion angles between the ccp4 (ver 6.3.0) and the corresponding phenix (dev1325) file /usr/local/ccp4-6.3.0/ccp4-6.3.0/lib/data/monomers/d/DCT.cif _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period DCT var_1 O3G PG O3B PB -60.011 20.000 1 DCT var_2 PG O3B PB O3A -179.960 20.000 1 DCT var_3 O3B PB O3A PA -179.992 20.000 1 DCT var_4 PB O3A PA "O5'" 179.964 20.000 1 DCT var_5 O3A PA "O5'" "C5'" 179.986 20.000 1 DCT var_6 PA "O5'" "C5'" "C4'" -179.998 20.000 1 DCT var_7 "O5'" "C5'" "C4'" "O4'" 65.696 20.000 3 DCT var_8 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3 DCT var_9 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3 DCT var_10 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1 DCT var_11 "C4'" "O4'" "C1'" N1 -150.000 20.000 1 DCT var_12 "O4'" "C1'" "C2'" "C3'" 0.000 20.000 3 DCT var_13 "O4'" "C1'" N1 C6 -121.764 20.000 1 DCT CONST_1 "C1'" N1 C2 N3 180.000 0.000 0 DCT CONST_2 "C1'" N1 C6 C5 180.000 0.000 0 DCT CONST_3 N1 C6 C5 C4 0.000 0.000 0 DCT CONST_4 C6 C5 C4 N3 0.000 0.000 0 DCT CONST_5 C5 C4 N4 HN41 179.773 0.000 0 DCT CONST_6 C5 C4 N3 C2 0.000 0.000 0 DCT CONST_7 C4 N3 C2 O2 180.000 0.000 0 /usr/local/phenix.test/latest/chem_data/mon_lib/d/DCT.cif _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period DCT var_3 O1G PG O3B PB 2.570 20.000 1 DCT var_4 PG O3B PB O3A 83.412 20.000 1 DCT var_6 O3B PB O3A PA -132.456 20.000 1 DCT var_7 PB O3A PA O5* -51.566 20.000 1 DCT var_9 O3A PA O5* C5* -166.199 20.000 1 DCT var_10 PA O5* C5* C4* 135.553 20.000 1 DCT var_11 O5* C5* C4* C3* 12.096 20.000 3 DCT var_12 C5* C4* O4* C1* 143.686 20.000 1 DCT var_13 C5* C4* C3* C2* -117.819 20.000 3 DCT var_14 C4* C3* C2* C1* -21.471 20.000 3 DCT var_15 C3* C2* C1* N1 150.776 20.000 3 DCT var_16 C3* C2* C1* O4* 32.781 20.000 3 DCT var_17 C2* C1* N1 C2 121.270 20.000 1 DCT var_18 C2* C1* N1 C6 -65.572 20.000 1 DCT CONST_1 C1* N1 C2 N3 180.000 0.000 0 DCT CONST_2 N1 C2 N3 C4 0.000 0.000 0 DCT CONST_3 C2 N3 C4 C5 0.000 0.000 0 DCT var_19 N3 C4 N4 HN41 0.000 20.000 1 DCT CONST_4 N3 C4 C5 C6 0.000 0.000 0 DCT CONST_5 C4 C5 C6 N1 0.000 0.000 0 I am just wondering which values/library to use or if i got something completely wrong. Best regards Konrad

2 1

2nd announcement: 2013 workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 02 Apr '13

02 Apr '13

4th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN (USA). June 24 – June 28, 2013 Application deadline: April 22, 2013 No registration fee. Travel and accommodation grants available for participants from U.S. institutions. Detailed information available at: http://neutrons.ornl.gov/conf/gcnb2013/ Best Regards, Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

1 0

Fitting ligand using coot
by bsubedi＠btk.fi 31 Mar '13

31 Mar '13

Hi all, I tried to fit the ligand using the coot -> calculate-> other modeling tools-> Find ligands. I have imported cif to coot and also opened the pdb file of my ligand. However, coot do not identify the ligand and asks to adjust r.m.s.d. I can see the density for my ligand. Could anyone suggest me what could be the problem or if I am missing anything here. Best regards. Bishwa

6 13

Re: [phenixbb] question about FFT map coefficients
by Michael Thompson 29 Mar '13

29 Mar '13

Hi Nat, The FFT didn't work out, but I'm not sure if it's due to negative Fs. When I set up the FFT map coefficients utility with my mtz file, after picking my input I get a warning that "The reflections file does not appear to contain any suitable map coefficients." Then if I try to run it anyway I get the error message "There are no map coefficients in this MTZ file." An mtz dump confirms that I have columns FP and SIGFP. Additional info: these Fs were generated using a python script that I wrote, and there are not meaningful values for SIGFP. My script simply wrote out 0.000 to the SIGFP column for each reflection essentially as a place holder. I thought that maybe 0 was not a valid entry for SIGFP so I changed it to 0.001 so there would be some value there, but I get all the same errors. Could this be the problem? Any suggestions? Thanks for the help. Sorry to bug you. Mike ----- Original Message ----- From: "Nathaniel Echols" <nechols(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Thursday, March 28, 2013 3:42:31 PM GMT -08:00 US/Canada Pacific Subject: Re: [phenixbb] question about FFT map coefficients On Thu, Mar 28, 2013 at 3:28 PM, Michael Thompson <miket(a)chem.ucla.edu> wrote: > I have an mtz file with map coefficients that are essentially Fo-Fo for two data sets. I would like to generate a map using these coefficients, but because the subtraction of Fs has already been done, there are some values of FP that are negative. Is "FFT map coefficients" able to handle negative values for FP? My guess would be that the answer is yes, because internally the amplitudes and phases for map calculation are combined to form a single array of complex numbers, and this effectively converts the amplitudes to be all-positive. Also, if this were not the case, the isomorphous or anomalous difference maps would never work. But I haven't actually tried what you're wanting to do with real data - if the result isn't what you expect, let us know. -Nat _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

2 1

question about FFT map coefficients
by Michael Thompson 28 Mar '13

28 Mar '13

Hello All, A quick question about the "FFT map coefficients" utility in the GUI: I have an mtz file with map coefficients that are essentially Fo-Fo for two data sets. I would like to generate a map using these coefficients, but because the subtraction of Fs has already been done, there are some values of FP that are negative. Is "FFT map coefficients" able to handle negative values for FP? If not, I can always change the sign of negative Fs and add 180 to the corresponding model phases, but I was hoping I could avoid this. Thanks in advance for the help! Mike P.S. I do know there is an Fo-Fo map option in phenix, but the origin of my map coefficients is more complicated than simply Fo-Fo, so I cannot use this option. -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

3 2

suggested usage of qsub?
by Scott Classen 28 Mar '13

28 Mar '13

Hi all, We have a HPC cluster configured with TORQUE/MAUI. I see in the Phenix GUI that there is some sort of ability to queue jobs to run via qsub. I can't find any documentation on how to set this up. If I'm working at my office computer and I want to submit to a remote server cluster for refinement, is this possible? Or is it assumed that qsub is available on the local machine? Thanks, Scott

3 2

fwd: Deadline for the CCP4 Summer School application is approaching
by Nathaniel Echols 26 Mar '13

26 Mar '13

> ---------- Forwarded message ---------- > From: "Ruslan Sanishvili (Nukri)" <nukri(a)aps.anl.gov> > To: phenixbb(a)phenix-online.org > Date: Tue, 26 Mar 2013 11:52:44 -0500 (CDT) > Subject: Deadline for the CCP4 Summer School application is approaching > Dear Colleagues, > > The deadline for applications for the 6th annual CCP4 Summer School “From data collection to structure refinement and beyond” is only ten days away. Please submit your applications before April 5, 2013. The school will take place from June 18 to June 26, 2013 at the Advanced Photon Source (APS) near Chicago. > > There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (the program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2013/index.php > > The school will include data collection, processing, structure solution, model building, refinement, validation, automation of many steps etc. Participants are encouraged to bring their own crystals, raw data or processed data for hands-on problem solving under the guidance of software developers and other experts. > We hope to see you in June > > Garib, Ronan and Nukri > > > > Ruslan Sanishvili (Nukri) > Macromolecular Crystallographer > GM/CA@APS > X-ray Science Division, ANL > 9700 S. Cass Ave. > Argonne, IL 60439 > > Tel: (630)252-0665 > Fax: (630)252-0667 > rsanishvili(a)anl.gov > >

1 0

low-res. real-space refinement
by "Weiergräber, Oliver H." 26 Mar '13

26 Mar '13

Hello, when refining a protein structure against a low-resolution dataset (5 A), I wanted to also attempt real-space refinement. However, in the log file I find: |-real space refinement (target=simple)---------------------------------------| rejected... | | | --------------------------------------------------------------------------- | Changing the target to, e.g., diff_map does not change anything; the message will still refer to the "simple" target. I guess this is due to an internal resolution limit, but that's only speculation since it seems to be undocumented. Indeed, there is probably not much to be gained by real-space refinement at this resolution (at least not in terms of side-chain conformations), but I wanted to give it a try anyway. Any comments on this issue? Regards, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

2 1

Drag drop files
by Colin Levy 25 Mar '13

25 Mar '13

Hi all, I am running 1.8.2-1309 under OSX 10.7.5 but I lost the ability to drag and drop files between various phenix windows. Anyone else experiencing this or is it something specific to my setup? Thanks, Colin Manchester Protein Structure Facility MIB 1.025 Tel 0161 306 5185 c.levy(a)manchester.ac.uk<mailto:[email protected]>

2 1

Refinement of B-factors at low resolution
by Florian Brückner 25 Mar '13

25 Mar '13

Dear all I am refining a structure at 3.2 A with phenix.refine using automatic optimization of target weights, solved by molecular replacement with a 2.1A structure of the same crystal form. Rwork=26%, Rfree=28%. I use individual atomic B-factor refinement. The obtained distribution of B-factors after refinement looks reasonable and quite similar to the distribution in the higher resolution model, which I suppose would be expected, since it is the same crystal form. However, the average B-factor does not change substantially, i.e. if I start with the B-factors from the high resolution model (average B-factor around 32 A**2) after 6 macrocycles the average B-factor is still around 32 A**2. If I set all B-factors to the Wilson B-factor determined by phenix.refine (66 A**2), after 6 macrocycles the distribution of B-factors looks again very similar to the high resolution MR model, but the average B-factor is still around 65 A**2. What should I make of this? Is this an expected behavior at this resolution, i.e. the fact that the absolute values of B-factors cannot be determined during refinement, although a reasonable distribution can be obtained as judged by plotting average B-factors vs. residue#? Since the average B-factor does not change much during refinement, which average B-factor should I start refinement with to end up with reasonable absolute values? I have manually determined the Wilson B-factor from the linear part of the Wilson plot (4.5-3.2 A) to be 97 A**2. This seems high to me. Would that be expected for the given resolution, given that the 2.1A structure of the same crystal form has 32 A**2? I should add, that there is not a substantial effect of the average refined B-factor on Rfree. Thanks for any comments or suggestions. Best regards Florian ------------------------------------------------------------- Dr. Florian Brückner Laboratory of Biomolecular Research (LBR) OFLG/102 Paul Scherrer Institut CH-5232 Villigen PSI Switzerland Tel.: +41-(0)56-310-2332 Email: florian.brueckner(a)psi.ch

8 14

molecular replacemnt problem
by Appu kumar 24 Mar '13

24 Mar '13

Dear members, I am doing a molecular replacement of a transcription factor whose ligand binding structure(24000 Da) is available in PDB but not for the DNA binding(13000 Da). When i am searching for the two copies from ligand binding domain as a template model, i am getting very good solution but i am not getting any density for the DNA binding domain to build up in density. The space gorup is P 1 21 1 (4) and unit cell parameters are Unit Cell: 57.43 69.36 105.99 90.00 90.00 90.00. Please guide me how to get the complete model structure. Table below show the matthews statistics For estimated molecular weight 37000. Nmol/asym Matthews Coeff %solvent P(2.20) P(tot) _____________________________________________________________ 1 5.71 78.46 0.00 0.01 2 2.85 56.91 0.62 0.70 3 1.90 35.37 0.37 0.29 4 1.43 13.82 0.00 0.00 _____________________________________________________________ The phaser molecular replacement gives the following table. istogram of relative frequencies of VM values ---------------------------------------------- Frequency of most common VM value normalized to 1 VM values plotted in increments of 1/VM (0.02) <--- relative frequency ---> 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 | | | | | | | | | | | 10.00 - 8.33 - 7.14 - 6.25 - 5.56 - 5.00 - 4.55 - 4.17 - 3.85 -- 3.57 --- 3.33 ------ 3.12 ---------- 2.94 **************** (COMPOSITION*1) 2.78 ----------------------- 2.63 -------------------------------- 2.50 ----------------------------------------- 2.38 ------------------------------------------------ 2.27 -------------------------------------------------- 2.17 ----------------------------------------------- 2.08 -------------------------------------- 2.00 -------------------------- 1.92 --------------- 1.85 ------- 1.79 --- 1.72 - 1.67 - 1.61 - 1.56 - 1.52 - 1.47 * (COMPOSITION*2) 1.43 - 1.39 - 1.35 - 1.32 - 1.28 - 1.25 - TABLE : Cell Content Analysis: SCATTER :N*Composition vs Probability:0|3x0|1:1,2: $$ N*Composition Probability $$ loggraph $$ 1 0.306066 2 0.00141804 $$ Most probable VM for resolution = 2.27817 Most probable MW of protein in asu for resolution = 92664.2 I have initially indexed the data in C2221 but Rfree was not decreasing so i reindexed the data in data in P121 space group keeping the Rfree flag of C2221. While analysing the symmetry mates , i found large space but no density. structure of Ligand binding domain is almost identical with 90% identity in sequence. I am stuck with this problem and don't know how to process further. I run the phenix.xtriage to evaluate the twining but it suggest no twining. When i reindex from C2221 to P21, the completeness of data reduced from 95 % to 35% whereas the map is very good and Rwork and Rfree are 26/31 for 2.2 resolution. I do not understand why the completeness of data reduced so much on reindexing. please Can anyone explain this phenomenon. Please give me your valuable suggestion. I will appreciate your effort. Thank you

1 0

one or more errant TER cards
by jp d 20 Mar '13

20 Mar '13

hi, i am trying to refine using a reference model and keep getting this error *** Adding Reference Model Restraints *** Sorry: chain ' ' in start.pdb contains one or more errant TER cards. Please remove and try again i've tried various things including removing all the TER lines my models (reference and working) has many chains identified by segid's any suggestions ? thanks jpd

2 2

install on ubuntu 12.04?
by Alastair Fyfe 19 Mar '13

19 Mar '13

Hi, I've installed previous phenix builds on ubuntu without problem, but with both 1.8.1-1168 and dev-1269 installers on 12.04, the command "./install --prefix=/home/afyfe" ends with "Error configuring: see /home/afyfe/phenix-installer-dev-1269/build-binary/intel-linux-2.6/svr/log/binary.log for details" and the tail of the binary.log file suggests: -- Creating files in build directory: "/home/afyfe/phenix-dev-1269/build/intel-linux-2.6" dispatcher_include_template.sh dispatcher_head.sh Please re-configure from scratch your cctbx_build:cd cctbx_build; /your/path/to/python ../cctbx_project/libtbx/configure.py [options] [modules] --- I don't see a cctbx_build directory under either the installer or destination directories. Any clues/suggestions? many thanks, Alastair

2 2

International Conference on Structural Genomics - Structural Life Science, Sapporo, Japan, July 29-Aug 1, 2013
by Terwilliger, Thomas C 18 Mar '13

18 Mar '13

Dear Colleagues: On behalf of the organizing committee of the International Conference on Structural Genomics 2013 – Structural Life Science – (ICSG2013-SLS), we cordially welcome you to the conference, to 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. You can see all the details of the conference at: http://www.c-linkage.co.jp/ICSG2013 . Registration for the conference is now open. 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”. 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) . In order to widen the opportunity to young and enthusiastic fellows to study more, we have organized several satellite workshops before ICSG2013- SLS. 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. We are looking forward to welcoming you to Sapporo in the summer of 2013. 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

1 0

MR_rosetta and disulphides
by Morten Groftehauge 17 Mar '13

17 Mar '13

Hi guys, Phenix version 1323 Rosetta version 3.4 I try to run phenix.mr_rosetta rosetta_command="-MR::disulf 129:411 228:281 279-615" mr_rosetta_228.eff but I get the following error in rebuild.log ERROR: Option matching -MR:disulf not found in command line top-level context I lifted the rosetta_command directly from the Version Documentation. Any clues as to why this doesn't work? Sincerely, -- Morten K Grøftehauge, PhD Pohl Group Durham University

2 2

Tutorial of low resolution data?
by 李翔 17 Mar '13

17 Mar '13

Hi everyone, I will work on some low resolution data but have very little experience. (Data are about 4 A to 8 A) Does anyone know where I could find a tutorial for low resolution data please? It is best to work with Phenix, other software is fine. MIR or SAD or MR method will be appreciated and it is very helpful if the tutorial can talk about some details of the data processing. Cheers, Frank

2 1

Phenix DEN-twin-refinement
by Ethayathulla A.S 14 Mar '13

14 Mar '13

hi all I want to do DEN twin-refinement using phenix. For my data phenix.DEN works better than CNS DEN. I want to DEN with twinning. Is there script for adding twinning operator for DEN refinement in phenix phenix.den_refine model.pdb data.mtz den.reference_file=reference.pdb Thank you Abdul --

2 1

Re: [phenixbb] problems installing latest phenix on mac osx lion
by Alejandro Buschiazzo 14 Mar '13

14 Mar '13

Thanks Nat! read your message a bit later (I think I need to change from the digest format, so I receive each message as it comes), looking at http://phenix-online.org/pipermail/phenixbb/2013-March/thread.html Actually, your suggestion worked all right. (and by sourcing the phenix_env.sh as you point out, it's actually the same as the command line -installer of course) Don't know why the errors appeared before, but in any case, now it's running fine. Thank you for your help Alejandro > Not sure what's going on here - I will check it out today. There's > one more option however that should be the safest: did you try the > graphical installer yet? The destination can't be changed, but you > can still use the command line if you want by doing this: > > source /Applications/PHENIX-1.8.2-1309/Contents/phenix-1.8.2-1309/phenix_env.sh > > (or the csh equivalent) > > But I will see if there's an explanation for these errors. > > -Nat On Tue, Mar 12, 2013 at 4:26 AM, Alejandro Buschiazzo <alebus at pasteur.edu.uy <http://phenix-online.org/mailman/listinfo/phenixbb>> wrote: >/ I 'm trying to install phenix 1.8.2-1309 on a Macbook Pro (os x 10.7.5). />/ />/ First tried the binary installer proposed (which is indicated for os x />/ 10.6.7) />/ It didn't work, ending with "fix_mac_python: caught error - exiting." />/ />/ I spotted in the bb that this could've happened because the downloaded />/ installer was somehow corrupted, tried downloading it again, but same />/ result. />/ />/ Tried then the source installer: everything OK - except for wxPython, giving />/ this error />/ />/ WXPYTHON: />/ Using wxOSX_Cocoa build of wxPython 2.9 alpha version />/ />/ building wxPython-src-2.9.4.1 />/ ERROR: installation of wxosx_cocoa failed />/ />/ ERROR: installation of wxpython failed />/ />/ ...now I can work with command lines, but the GUI won't work of course. />/ />/ Your help is appreciated />/ />/ Alejandro />/ />/ />/ -- />/ Alejandro Buschiazzo, PhD />/ Research Scientist />/ Unit of Protein Crystallography />/ Institut Pasteur de Montevideo />/ Mataojo 2020 />/ Montevideo 11400 />/ URUGUAY />/ Phone: +598 25220910 int. 120 />/ Fax: +598 25224185 />/ http://www.pasteur.edu.uy/pxf/ -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

1 0

Fwd: 4th Edition of the ISBC2013
by Nathaniel Echols 14 Mar '13

14 Mar '13

---------- Forwarded message ---------- From: Jose A. Gavira <gavirius(a)gmail.com> Date: Thu, Mar 14, 2013 at 11:20 AM Subject: 4th Edition of the ISBC2013 Dear Colleague, The Laboratory of Crystallographic Studies is pleased to announce the 4th International School on Biological Crystallization (ISBC2013), to be held in Granada (Spain) during May 26-31, 2013. ISBC2013 is intended for postgraduate/postdoctoral students and research scientists from industrial and academic backgrounds. The International School will provide five days of lectures, posters and practical demonstrations focused on the fundamentals of crystallization from solution and their applications to the field of crystallization of biological materials, including biological macromolecules, biominerals and biomimetic materials. One day will be fully devoted to case studies on the crystallization of membrane proteins, viruses and large macromolecular complexes. For more information, please visit http://www.isbcgranada.org/<http://www.linkedin.com/redirect?url=http%3A%2F%2Fwww%2Eisbcgranada%2Eorg%2…> . Best regards, ISBC2103 Organizing Committee --- Gavi http://isbcgranada.org/

1 0

problems installing latest phenix on mac osx lion
by Alejandro Buschiazzo 12 Mar '13

12 Mar '13

Hello, I 'm trying to install phenix 1.8.2-1309 on a Macbook Pro (os x 10.7.5). First tried the binary installer proposed (which is indicated for os x 10.6.7) It didn't work, ending with "fix_mac_python: caught error - exiting." I spotted in the bb that this could've happened because the downloaded installer was somehow corrupted, tried downloading it again, but same result. Tried then the source installer: everything OK - except for wxPython, giving this error > WXPYTHON: > Using wxOSX_Cocoa build of wxPython 2.9 alpha version > > building wxPython-src-2.9.4.1 > ERROR: installation of wxosx_cocoa failed > > ERROR: installation of wxpython failed ...now I can work with command lines, but the GUI won't work of course. Your help is appreciated Alejandro -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

2 1

GUI display items
by Luca Pellegrini 10 Mar '13

10 Mar '13

Hello, Is there a way to change/select the column items displayed in the PHENIX home window, under the 'Job history' tab? At the moment, mine shows: ID/Program/Date/Job title or directory/R-free. I would like to add things like the Overall score from MolProbity etc. I looked under Preferences but couldn't find anything. Thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

4 4