Search results for "look through"

Re: [phenixbb] anomalous difference map

by Jason

On Sat, Mar 26, 2011 at 11:57 AM, Nathaniel Echols <nechols(a)lbl.gov> wrote: > On Sat, Mar 26, 2011 at 9:45 AM, Jason <phenix.upitt(a)gmail.com> wrote: > > I was hoping to identify the ligand binding position by resolving the > > anomalous map first. Shouldn't this be the procedure to locate ligand? > > It depends on the ligand, I guess. If it's large enough and actually > bound, it should be detectable in the Fo-Fc map - this would be a good > sanity check to make sure that the anomalous map generation is working > properly. > Unfortunately my ligand is fairly small, about 12 atoms.The Fo-Fc map won't be that helpful. > > I know CCP4 can also generate anomalous difference map. But I myself have > > never done it (I googled online and found it not that straight forward). > Can > > anybody go through it for me please, or there are other handy programs > that > > can make anomalous difference map? > > You don't need to use CCP4 to make the map, just to process the data - > i.e. use MOSFLM/SCALA (xia2 will automate this), or you could also try > HKL2000, then use that as input for Phenix. But I doubt this is going > to give you a different answer. > XDS is the only program that is able to process my data (small oscillation angle and huge data file). On the other hand I am pretty sure xds is doing what it's supposed to do. I was more thinking of another program to generate anomalous map. Since it's phenixbb, probably it's not the right place :) > > Also: run Xtriage and look at the plot of anomalous signal vs. resolution. > > -Nat > ====================== Jason Structural Biology Department University of Pittsburgh ======================

14 years, 10 months

Re: [phenixbb] Problems placing second component in Phaser

by Terwilliger, Thomas C

Hi Morten, I added last week the option of a fixed model in mr_rosetta. So (if it works at least) you should be able to feed in one chain as a fixed model and then look for the other one. I suspect this may have some problems however if the two chains are the same (which I think may be the case here). Mr_rosetta might get confused about them because it uses their sequences to keep track of what is what... All the best, Tom T On Feb 18, 2013, at 7:30 AM, Morten Groftehauge wrote: Hi Gabor, Sounds good but I was hoping for something I could tell phenix.mr_rosetta that would allow it to find a good second solution. Phenix insists on rerunning place model even if you tell it that the model is already placed. So instead of continuing with the placement that worked I end up with one chain based on my original model another one scattered all over the place... I'll try with AMPLE and see what happens there. Cheers, Morten On 18 February 2013 13:01, Gabor Bunkoczi <gb360(a)cam.ac.uk<mailto:[email protected]>> wrote: Hi Morten, this is weird. One way around is to manually superpose the mr_rosetta model onto the original in the full solution, and just do a refinement with Phaser (you can (kind of) do this automatically by running MRage with both models). Another idea is to decrease the rotation peak cutoff when finding the second molecule (PEAKS ROT CUTOFF keyword). BW, Gabor On Feb 18 2013, Morten Groftehauge wrote: Hi guys, So I have a solution that covers some of target and I ran it through phenix.mr_rosetta and I am actually kinda happy with the output from there. However, while I can place both (NCS=2) with the original model I only seem to be able to place one of the rosetta models, even with 'packing function' set to 'all' or 'allow'. Original model - Refinement after placing component 1: LLG 175 Refinement after placing component 2: LLG 620 Rosetta model (packing 'all') - Refinement after placing component 1: LLG 295 Refinement after placing component 2: LLG 390 Rosetta model (packing standard) - Refinement after placing component 1: LLG 295 Refinement after placing component 2: LLG 350 More notably there is little to no increase in TFZ with the placement of the second component... There are more residues in the Rosetta model and I would expect more clashes but this looks weird. Cheers, Morten _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb -- Morten K Grøftehauge, PhD Pohl Group Durham University _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb

12 years, 11 months

Re: [phenixbb] Gap between R and Rfree

by Kendall Nettles

Did you check your data for anisotropy at the UCLA server? This solved a similar problem for me Kendall On Feb 25, 2010, at 12:43 PM, "Young-Jin Cho" <yjcho(a)brandeis.edu> wrote: > > Thanks for your suggestions, Phill. > When I did Ramachandran analysis, it shows 96.60% in preferred > region and 2.62% in allowed regions, and 0.79% is in outlier. > Geometry looks Ok. I also did optimize_wxc and optimize_wxu, and tls > option. it didn't help much. > Now I am trying to scale down. > > Thanks again. > > Young-Jin > > > 0. Use Molprobity or the Validation tools in Coot to look at your > structure and see what errors you can fix. > 1. What is your geometry like ? Try reducing wxc_scale (try > wxc_scale=0.5) and see what happens. > 2. What is the variation of B-factors across bonds ? Try reducing > wxu_scale - perhaps wxu_scale=0.5 or less. > 2a. phenix.refine is autocratic about wxu_scale if you're using TLS > so > setting it yourself does not help. > 3. Since R-free of 0.298 is a little high for a 2.5 Angstrom > structure, > you should carefully check your model. Perhaps you have a high > proportion of disordered structure, which can cause this. If you feel > that your model is correct, you could explore using TLS on your model. > Potential TLS groups can be found using the TLSMD server at: > http://skuld.bmsc.washington.edu/~tlsmd/ although the results should > always be filtered through a common-sense definition of domain/group > boundaries (e.g. don't break in the middle of helices unless there's a > good reason to). > > Phil Jeffrey > Princeton > > > Young-Jin Cho wrote: >> Hi everyone, >> I recently got a diffraction data and am trying to refine it. The >> question is whatever I did the gap between R and Rfree stay far >> away: .2140/.2982 around 2.5 A resolution. (water added and >> isotropic(individual_adp) and so on). >> Although I am redoing with many different approaches, if anyone can >> give me any comments or suggestions, it would be helpful. >> >> Thanks in advance, >> >> Young-Jin > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > > -- > Postdoctoral Fellow, Kern Lab > Biochemistry Department/HHMI > Brandeis University > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

15 years, 11 months

Re: [phenixbb] DNA covalent bond angles deviate from PDB standard dictionary

by Paul Adams

Hi Scott, the RCSB report seems to indicate an ideal (dictionary) value of 108.3, very close to the monomer library value of 108.4. So the refined values are a couple of degrees away from ideal. Given that this angle is between the base and the ribose it might be worth looking at the pucker of the ribose ring. Alternatively, if you have good resolution it might be that these are reasonable values - note that the ESD for this angle defined in the monomer library is 3.0, while the validation analysis performed at the RCSB seems to use 0.3. Cheers, Paul On Jan 5, 2011, at 12:00 PM, Scott Classen wrote: > Hello, > > I'm running into validation problems with DNA when validating on PDB website. > > the validation report indicates that the refined value is significantly different that the PDBs standard dictionary. > > Deviation Residue Chain Sequence AT1 - AT2 - AT3 Bond Dictionary Standard > Name ID Number Angle Value Deviation > ------------------------------------------------------------------------------------------- > 2.2 DG D 6 N9 - C1' - O4' 110.5 108.3 0.3 > 2.6 DC D 7 N1 - C1' - O4' 110.9 108.3 0.3 > 2.3 DC D 8 N1 - C1' - O4' 110.6 108.3 0.3 > 3.0 DT D 9 N1 - C1' - O4' 111.3 108.3 0.3 > > I've looked through a few of these in the .geo file and it appears that phenix.refine is using different values. > > for example, > > angle pdb=" O4' DG D 6 " > pdb=" C1' DG D 6 " > pdb=" N9 DG D 6 " > ideal model delta sigma weight residual > 108.40 110.18 -1.78 3.00e+00 1.11e-01 3.52e-01 > > > ideal is specified as 108.4º so clearly my refinement has converged, but it has NOT converged on the RCSBs accepted value of 110.5º > > What to do? Who is "right" phenix or RCSB? > > Thanks, > Scott > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology 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: Kathleen Moody [ KLMoody(a)lbl.gov ][ 1-510-495-2506 ] --

15 years, 1 month

Re: [cctbxbb] Post-PHENIX changes

by Graeme.Winter＠Diamond.ac.uk

Hi Folks, For info: we took the liberty of removing the “Hold for phenix release” label from those which were held for this. Since the release is out they were no longer held for this reason, so this seems like good housekeeping. Best wishes Graeme On 18 Sep 2018, at 09:00, Winter, Graeme (DLSLtd,RAL,LSCI) <graeme.winter(a)diamond.ac.uk<mailto:[email protected]>> wrote: Morning All, I see from http://phenix-online.org/ That PHENIX 1.14 has been released Now, I see at https://github.com/cctbx/cctbx_project/pulls we have a few fairly hefty pull requests parked as “hold for phenix release” - I would certainly not suggest merging all these in one go however probably we should give some thought to stepping through some of them, deciding which ones we should look at first and starting to merge things? I for one would like Nick’s allocator code to come back into play (so we can make use of it for DIALS) Thoughts / opinions? For info: PHENIX folks did you tag the version which was released in PHENIX 1.14 to allow a release branch for .1 etc. releases? Many thanks Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

7 years, 4 months

Re: [phenixbb] Help with custom bond restraints syntax

by Pavel Afonine

Alternatively, you can do simply this: refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = chain F and resid 1 and name FE1 atom_selection_2 = chain A and resid 69 and name SG distance_ideal = 2.35 sigma = 0.1 slack = None } } Pavel. On 9/29/09 8:54 AM, Andrew T. Torelli wrote: > Hi all, > > I'm having what I believe is a simple problem defining custom bond > restraints between a side chain in my protein model and a ligand > (non-covalent bond). Here is a minimal form of my custom bond > definition file that suffers from the error: > > refinement.geometry_restraints.edits { > Atom1 = chain F and resid 1 and name FE1 > Atom2 = chain A and resid 69 and name SG > bond { > action = *add > atom_selection_1 = Atom1 > atom_selection_2 = Atom2 > distance_ideal = 2.35 > sigma = 0.1 > slack = None > } > } > > I'm using phenix 1.4-153 and I get the following error: > ERROR: Unused parameter definitions: > refinement.geometry_restraints.edits.Atom1 (file > "/HOME/andrew/PHENIX_paramfiles/test.edits", line 5) > refinement.geometry_restraints.edits.Atom2 (file > "/HOME/andrew/PHENIX_paramfiles/test.edits", line 6) > > I've checked through the online manual and I believe my syntax is > correct, but I'm not sure why my custom bond restraint is being > ignored. > > A second question is: once I get the custom bond/angle restraints > correctly implemented, is there a better or more convenient place to > look and confirm that the restraints have been imposed other than the > .geo file phenix.refine outputs? > > Thank you very much for your help, > -Andy > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

16 years, 4 months

Re: [phenixbb] changing the project directory

by Nathaniel Echols

On Wed, Mar 16, 2011 at 12:15 PM, Charisse Crenshaw <ccrenshaw(a)salk.edu> wrote: > I have recently started a project whose folder was located on my > desktop. I would like to move that folder off of my desktop as I've > heard that having a messy desktop slows down one's computer. I moved > the project directory somewhere else, and this resulted in Phenix not > being able to find the project (understandably). So I moved it back > to its original location and Phenix could then open the project. So, > in an X11 shell, I copied the project folder to the new desired > location, then changed the output directory in the Phenix main window > to that new path. But when I clicked on the project again, the output > directory that is indicated changes back to the original path. Now I > am looking through the preferences etc for a way to change the path of > the project directory within Phenix and I cannot. Can anyone tell me > if this is possible and if so, how do I do it? It's possible, but not (yet) straightforward. These steps should do it: 1. Make a copy of the entire project folder in the new location (I guess you've already done this) 2. Open the main GUI and delete the old project. This will not wipe out any data in the old location, but it will delete all of the project tracking files that Phenix creates. 3. Select "Import project" from the File menu, and select the new copy - this should restore the project, but with all directory paths altered. For now, the parameter files used for past jobs will contain the original paths, so restoring old jobs will not bring up the full parameters. I hope to fix this at some point. Obviously I need to add a "relocate project" function too. I suspect the warning about a messy desktop came from a Windows user - I've never heard about other OSes having this problem. -Nat

14 years, 10 months

[phenixbb] Postdoctoral position in structural biology of influenza virus transcription Cusack group, EMBL Grenoble

by Stephen Cusack

Postdoctoral position in structural biology of influenza virus transcription Cusack group, EMBL Grenoble We are looking for a highly motivated and ambitious individual to progress our understanding of the mechanism of transcription by influenza virus RNA-dependent RNA polymerase. The work is in the frame of the ANR-funded FluTranscript project that brings together the complementary expertise of the groups of Stephen Cusack (EMBL Grenoble, project coordinator) and Nadia Naffakh (Institut Pasteur) in structural biology and molecular virology, respectively. The project follows on from a recent joint publication (Structural basis of an essential interaction between influenza polymerase and Pol II CTD. Lukarska et al, Nature 2017) and aims to reconstitute and determine the structure of functional transcription complexes. A secondary goal is to use the acquired structural information to develop new approaches to anti-influenza drug development. The Cusack group uses X-ray crystallography and cryo electron-microscopy to study the structural biology of protein-RNA complexes involved in RNA virus replication, innate immunity and cellular RNA metabolism. Group website: https://www.embl.fr/research/unit/cusack/index.html The successful candidate should have a PhD in Molecular Biology or related field and a strong background and interest in biochemistry and structural biology. We are looking for a creative and ambitious person with good communication skills and keen to work on a challenging project. Experience in insect cell expression systems, reconstitution of protein-RNA complexes, X-ray crystallography or cryo-electron microscopy would be particularly beneficial. EMBL is one of the world’s leading research organizations in the life sciences. The Headquarters Laboratory is located in Heidelberg, with additional sites in Barcelona, Grenoble, Hamburg, Hinxton, and Rome. EMBL Grenoble has excellent access to state-of-the-art structural biology technologies with the in house EM facility being equipped with a T12 microscope and 200kV Glacios/Falcon III . Additionally, we have access to the Titan Krios at the adjacent ESRF as well as those in EMBL Heidelberg. Other facilities on the Grenoble Campus include the ESRF synchrotron X-ray beamlines, neutron scattering at the ILL, high-field NMR at the IBS as well as high-throughput crystallization platform, mammalian and insect cell facilities, biophysical platform and confocal microscopy. You can find out more about this vacancy at: https://www.embl.fr/jobs/searchjobs/index.php?ref=GR00133 or by contacting Stephen Cusack: cusack(a)embl.fr Please apply online through www.embl.org/ Stephen Cusack -- ********************************************************************** Dr. Stephen Cusack, FRS Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL) Group leader in structural biology of protein-RNA complexes and viral proteins ********************************************************************** Email: cusack(a)embl.fr Website: http://www.embl.fr Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7123 Fax: (33) 4 76 20 7199 Postal address: EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue des Martyrs, 38000 Grenoble, France **********************************************************************

6 years, 11 months

Re: [phenixbb] phenix error

by SD Y

Dear Nat, You are right. I added two metal ions Zn and Mg and after that I started getting this error. I did run phenix.metal_coordination to get elbow.edits and add this to refinement to to get same error. I am not running with water update option. I ran the pdb through readyset and added metal restraints, processed pdb file and ligand restraints to the refinement to get same error. The Zinc and Mg are not coordinated well. I have added because nothing fits in the density. I am not sure lack coordination is creating the problem. I will send ATOM records to Pavel. Thanks a lot for looking in to this one. SDY From: nechols(a)lbl.gov Date: Tue, 4 Mar 2014 07:50:31 -0800 Subject: Re: [phenixbb] phenix error To: ccp4_sc(a)hotmail.com CC: phenixbb(a)phenix-online.org You probably have metal coordination restraints that are no longer valid - each time you run phenix.refine with the solvent update enabled, the numbering of waters will change and the old restraints become invalid. áThe utilities menu in the phenix.refine GUI has an option to clear these out entirely; you can then run ReadySet again to generate new restraints. -Nat On Mon, Mar 3, 2014 at 10:31 PM, SD Y <ccp4_sc(a)hotmail.com> wrote: Hi, Could you please tell me why am I getting this error " No atom selected: "name O and chain W and resname HOH and resseq 69".á Log file ends as follows: ============================= Scattering factors ============================= á á á á á á á á ----------X-ray scattering dictionary---------- á á á á á á á á Number of scattering types: 7á Type áNumber á ásf(0) á Gaussiansá áZn2+ á á 1 á á 27.88 á á á 1á áS á á á 10 á á 15.96 á á á 2á áP á á á á2 á á 14.95 á á á 2 á áMg2+ á á 3 á á á9.96 á á á 1á áO á á á635 á á á7.97 á á á 2á áN á á á523 á á á6.97 á á á 2á áC á á 1983 á á á5.97 á á á 2á sf(0) = scattering factor at diffraction angle 0. ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ======================== Summary of geometry restraints ======================= á Number of disulfides: simple=0, symmetry=0á Custom bonds:Sorry------------------------------ Thanks a lotSDY _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

11 years, 11 months

Re: [cctbxbb] Branches

by Ralf Grosse-Kunstleve

Hi Luc, At this point I'd say (b) looks most useful. Ralf On Sun, Apr 22, 2012 at 4:44 AM, Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: > it would be easy to put a crontab on the CCI machine phenix-online, that >> would periodically update from sourceforge and then push to GitHub. >> >> > Or maybe we could setup a mail account that receives the commit messages > which then triggers the git sync? > Ralf > > > We first need to clarify what we want the GitHub repo to be for. Two > choices here as I see it: > (a) a repo that would fit in the git culture: git afficionados would fork > it, do their own development and then send pull notification to us, never > using "git svn"; > (b) a repo whose sole purpose would be to spare the long time necessary to > run "git svn clone" in the first place: users of that repo would share > their development with us solely through "git svn dcommit". > > I had obviously (b) in mind, hence my not being concerned with a slight > lag between sourceforge and GitHub. If option (a) is our goal, then not > only the lag shall be minimised but the "master" branch of the GitHub > repository should be "dcommited" periodically to sourceforge. And of > course, we need a clear policy to deal with those pull requests. That > option (b) would be an alternative to give commit rights to sourceforge to > "casual" cctbx developers. Thanks to git, it would be easy to checkout and > then evaluate their proposed pull, then giving the green light at the press > of a button. As usual with git, it's another world entirely… > > Luc > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > >

13 years, 9 months

Search results for query "look through"