Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Petr, there may be a couple of reasons, e.g. - - your data are not really 1.1A, but you simply integrated a lot of noise - - you entered some odd command or another option which allows refmac5 such a deviation - - your model is incomplete - - surely several more. When a well tested program does something unexpected, it is usually the user and not the program which misbehaves... The optimisation of the weighting scheme is based on the geometry of the model and not one the gap between R and Rfree. Cheers, Tim On 12/08/2011 08:43 PM, Petr Leiman wrote: Dear Tim, I agree with you completely. The question then becomes why does the automatic weighting scheme in refmac allow R and R-free to run away from each other by 8% in a 1.1 A resolution structure? Petr On Dec 8, 2011, at 6:50 PM, Tim Gruene wrote: Dear Christopher, if your R/Rfree from Refmac5 really are 10% vs. 18%, you might simply be looking at an electron density map with strong model bias, i.e. the map shows the features of the model and not of the data. Although at 1.1A resolution this seems quite unlikely, but that's what might explain this great gap between R and Rfree. Tim On 12/08/2011 06:36 PM, Christopher Browning wrote: Dear All, Question: Has anybody ever refined the same structure using PHENIX and then tried REFMAC to see what happens? I did and I stumbled on something funny. I'm refining a structure at 1.1A resolution which was solved with Iodine phasing using PHENIX AutoSolve. Got a great map and the structure was built almost completely. I had to build a few residues myself, and using the published sequence, I started filling in the residues, but as I came nearer the N-terminus, it looked like the density did not match residues from the sequence. I kept the residues as in the sequence, but as you can see from the PHENIX refined picture (below is the link) it still looks like the amino acid sequence in the crystal does not match the published protein sequence. Out of interest I refined the same file in REFMAC, and now the electron density is correct, and the sequence of the amino acids in the crystal matches the published sequence (see link for picture below). Not only that. my R/Rfree improved (16.5/19 for PHENIX, 10/18 for REFMAC). I've also refined the occupancies of the iodide, however the the output FO-FC map from PHENIX complains and the REFMAC map is fine. How can this be and what causes this? Link for the pictures: Both maps are at identical Sigma levels in both pictures. PHENIX: http://dl.dropbox.com/u/51868657/PHENIX_refined.png REFMAC: http://dl.dropbox.com/u/51868657/REFMAC_refined.png Cheers, Chris Browning - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO4cyCUxlJ7aRr7hoRAqDTAJkBsSEIp2bH7hZlB23LJadHL2VhVQCg0r38 LGVjgK1z29vPc5V4lUh74vw= =wP9n -END PGP SIGNATURE-
Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled
Hi Everybody, First off, thanks for the replies. They definitely fixed my problem. It was indeed as Garib Murshudov said. The flags got swapped, and therefore the percentage of Rfree reflections were 95%. So, if Rfree is created from CCP4.use Rfree flags with a value of 0 and a value of 1 if the Rfree was created with PHENIX. Both maps now look the same, and it indeed looks like the protein in the crystal is different from the sequence. Cheers, Chris -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04 40
Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled
Hi Christopher, just a remark: for phenix.refine it does not matter where the flags come from and what is the test/work value since it automatically scores the values in the flags array and guesses the right one. Still one can imagine corner case, so it's good to be careful -:) Pavel On Fri, Dec 9, 2011 at 2:08 AM, Christopher Browning christopher.brown...@epfl.ch wrote: Hi Everybody, First off, thanks for the replies. They definitely fixed my problem. It was indeed as Garib Murshudov said. The flags got swapped, and therefore the percentage of Rfree reflections were 95%. So, if Rfree is created from CCP4.use Rfree flags with a value of 0 and a value of 1 if the Rfree was created with PHENIX. Both maps now look the same, and it indeed looks like the protein in the crystal is different from the sequence. Cheers, Chris -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04 40
Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled
On Fri, 2011-12-09 at 05:45 -0800, Pavel Afonine wrote: just a remark: for phenix.refine it does not matter where the flags come from and what is the test/work value since it automatically scores the values in the flags array and guesses the right one. Still one can imagine corner case, so it's good to be careful -:) Since it does not matter to phenix.refine and it will remain backward compatible, how about changing the default behavior so that when the test set is missing, it is created with test_value=0? Unless the test_value=1 expectation is hard-coded somewhere else, this seems like an easy fix, and will prevent the problems Chris was having. I always thought that test_value=1 is essentially inherited from the CNS default. But when you think about it, the way it's done in refmac/freeflag makes much more sense because of: a) tiny improvement in code readability, since bool(0)=False (a very python-esque argument); b) if one wishes to use a different test set, 1/fraction of them are already generated. Cheers, Ed. -- After much deep and profound brain things inside my head, I have decided to thank you for bringing peace to our home. Julian, King of Lemurs
Re: [ccp4bb] How to assess geometry in a model?
Along you can consider also using MolProbity online. Best, Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabetat medecine.uhp-nancy.fr Cell.: +33 (0)6.11.35.69.09 On 09/12/2011 06:52, Robbie Joosten wrote: Hi Matt, WHAT_CHECK writes out a file called check.db that contains per-residue scores for several quality metrics. It is fairly easy to parse. Cheers, Robbie Date: Thu, 8 Dec 2011 23:08:45 -0500 From: mattw...@gmail.com Subject: [ccp4bb] How to assess geometry in a model? To: CCP4BB@JISCMAIL.AC.UK Hi Folks I'm looking for a way to score each atom (or residue) in a model based on it's geometry. I know these scores exists because various software packages speak of outliers, even including a sigma value in some cases. So I'm looking for a simple way to get a complete list (not just outliers). Does anyone know of a package that can be made to output these scores? Thanks, Matt
Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled
Hi Ed, changes like this generate more confusion then good, I guess. Current phenix.refine behavior does not create any problem for phenix.refine users, so I don't feel a strong reason for changing anything. It's not just a flipping the flag value somewhere, but it's updating the documentation, replying a whole lot of emails offline subjected why is this, etc etc.. On the other hand, I would rather suggest making the other programs automatically recognize the right flag in most cases - it is a trivial coding exercise that any developer can do within an hour, and does not require changing habits. Pavel On Fri, Dec 9, 2011 at 6:34 AM, Ed Pozharski epozh...@umaryland.edu wrote: On Fri, 2011-12-09 at 05:45 -0800, Pavel Afonine wrote: just a remark: for phenix.refine it does not matter where the flags come from and what is the test/work value since it automatically scores the values in the flags array and guesses the right one. Still one can imagine corner case, so it's good to be careful -:) Since it does not matter to phenix.refine and it will remain backward compatible, how about changing the default behavior so that when the test set is missing, it is created with test_value=0? Unless the test_value=1 expectation is hard-coded somewhere else, this seems like an easy fix, and will prevent the problems Chris was having. I always thought that test_value=1 is essentially inherited from the CNS default. But when you think about it, the way it's done in refmac/freeflag makes much more sense because of: a) tiny improvement in code readability, since bool(0)=False (a very python-esque argument); b) if one wishes to use a different test set, 1/fraction of them are already generated. Cheers, Ed. -- After much deep and profound brain things inside my head, I have decided to thank you for bringing peace to our home. Julian, King of Lemurs
[ccp4bb] Neutron Scattering Applications in Structural Biology - Course Announcement
First Announcement: Third Course on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 4 - June 8, 201 2 Application deadline: March 19 , 2012 The Course in Neutron Scattering Applications in Structural Biology aims at educating and enabling a new generation of researcher to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in an intensive course focusing on neutron techniques used in structural biology. The course is designed for graduate students with knowledge of protein function and structure, new or with limited experience of neutron scattering. Course Objectives: 1. Educate graduate students in neutron scattering techniques, instrumentation and data collection, analysis and interpretation by offering courses taught by neutron scattering scientist. 2. Expose participants to cutting-edge research in structural biology by presenting seminars from national and international scientists to detail how neutron scattering integrate in their research program. 3. Build interactions between graduate participants and their university groups and ORNL neutron scattering experts to develop new research projects. Detailed information can be found on the course web page: http://neutrons.ornl.gov/conf/gcnb2012. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (1/2 to 1 page), should be sent electronically to meille...@ornl.govmailto:meille...@ornl.gov before March 19 , 2012 . Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome. However the course organization will not be able to offer travel or accommodation support. The number of participants will be limited to 15. Attendance to the course is free of charge for all selected participants. Best Regards, Flora Flora Meilleur Assistant Professor Molecular Structural Biochemistry N C State University Neutron Scattering Sciences Division Oak Ridge National Laboratory Phone: 865-241-2897
