Re: [ccp4bb] R-factors of various kind
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/R-factors would be a start ... HTH, Kay On Fri, 18 Jan 2013 09:37:12 +0530, Teri Arman teriar...@gmail.com wrote: Hi, it would be nice if you highlight different type of R-factors used in the literature. I like to understand various kind of R-Factors, their mathematical formula, and relations among them. Thank you. Teri
Re: [ccp4bb] R-factors of various kind
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Teri, maybe you could point out how much effort you have put into finding out so far. Any publication reporting a structure (at least those in respectable journals) not only mentions several R-values with respect to data and to the model, but also provides the corresponding formula. (Unfortunately despite being obsolete, most publications still cite R_int (aka R_sym) instead of R_meas (aka R_rim)). Best, Tim On 01/18/2013 05:07 AM, Teri Arman wrote: Hi, it would be nice if you highlight different type of R-factors used in the literature. I like to understand various kind of R-Factors, their mathematical formula, and relations among them. Thank you. Teri - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQ+9RmUxlJ7aRr7hoRAhDzAJ4zupy0oyOexzP1EQITDOXK/AZvpgCfVJll KHcC54OMGD6xi2SGUzXeIOM= =YCQz -END PGP SIGNATURE-
Re: [ccp4bb] CCP4 Update 014
Hi Andrey, Eugene and others - it is time to say that this new system is extremely useful, and so easy to use at the same time! Gone are the times when one had to worry about manually updating parts of CCP4. I just wonder why there should ever be a need for a CCP4 6.4.0 release; a rolling update seems just adequate to me - but that's just a user's perspective, and probably this has been discussed somewhere although I'm not aware of it. thanks for making this available, and the hard work to make it so perfect! Kay On Fri, 18 Jan 2013 19:04:37 +, Andrey Lebedev andrey.lebe...@stfc.ac.uk wrote: Dear CCP4 Users A CCP4 update has just been released, consisting of the following changes. All systems: * Ctruncate: Introduced DNA/RNA reference curve; uses flat prior on request, or when have tNCS or twinning * Othercell: Various bug fixes * PISA, QtPISA: Stability fixes and generation of Remark 350 in no-complex situations * PDBCur: Finish gracefully, rather than terminate, when atom selection is empty * PDB_Merge: Various bug fixes * Xia2: Correction to Ctruncate wrapper Linux and Mac only: *) * Aimless: Various bug fixes * Pointless: Correction for XDS input * Scala: Corrected output for CC(1/2) *) Corresponding changes for Windows have been already included in update No 13 Windows only: * Phaser.ensembler: Corrected path to syminfo.lib If you do not currently receive updates, consider re-installing your CCP4 setup using the latest binary packages, which now have CCP4 Update manager (ccp4um) integrated. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk Many thanks for using CCP4. Andrey Lebedev -- Scanned by iCritical.
Re: [ccp4bb] CASP ROLL needs your structures!
Hi, The definition of new fold at the PDB depends on how it is categorised in SCOP version 1.75, which was released in June 2009. Once the SCOP database is updated again, we'll see how many new folds were really represented by PDB entries deposited in the last few years. Randy - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 20 Jan 2013, at 07:05, Ethan Merritt wrote: On Saturday, 19 January 2013, Luecke, Hartmut wrote: In recent CASPs, there has been a shortage of new folds (according to PDB exactly zero new folds deposited since 2009) and membrane protein targets. I have been wondering about that. It is true that the PDB has not listed any new folds since 2009, but that hasn't stopped people from publishing new structures and claiming they are new folds. Is this because there is no single recognized criterion for new in these cases? Or possibly the PDB hasn't updated their statistics since 2009? E.g. from the 1st page of Google Scholar hits for protein structure new fold 2RSXR Arai, S Fukui, N Kobayashi, J Sekiguchi - JBC 2012 Solution Structure of IseA, an Inhibitor Protein of dl-Endopeptidases from Bacillus subtilis, Reveals a Novel Fold 3RX6R Banerjee, S Nath, A Ranjan, S Khamrui, B Pani, R Sen, U Sen - JBC 2012 A search of the Protein Data Bank using the DALI server (19) and PDBeFold (20) did not produce any significant match with the Psu structure designating it to be a new fold 2L8K Ioannis Manolaridis, ..., Eric J. Snijder - J. Virology 2011 Structure and genetic analysis of the arterivirus nonstructural protein 7α Ethan Merritt The lack of such targets makes it problematic to reliably quantify the state of the art in the area of protein structure prediction. To remedy this situation, CASP organizers have recently launched a new project called CASP ROLL (http://predictioncenter.org/casprol), where amino acids sequences of challenging targets are released throughout the year when structure solution is imminent. CASP specifically needs sequences of low-homology membrane targets that are about to be solved or have been solved but not released by PDB or elsewhere yet. It is important that structural information about the targets has not been publicly exposed (including things like coordinates, images, papers, conference abstracts) until after the prediction window for a given target has been closed. Each target will be available for prediction for a period of three to four weeks; in some cases a longer hold (up to 8 weeks) may be requested to allow the same target to be re-used for additional modeling experiments. So if you have anything suitable - please let CASP know. As you saw from the information above, your targets need not be fully refined structures. And if you need to make public a target's structure before the CASP window closes, simply contact CASP. We would rather lose a few targets than not have any at all! A good perspective for solving the structure in a few months is a good enough assurance for CASP. The submission mechanism is really simple. You can submit a target using the CASP Target Submission Form (http://predictioncenter.org/casprol/targets_submission.cgi), by sending email to c...@predictioncenter.org, or by marking your PDB deposition as CASP target in PDB's ADIT system (this way PDB will automatically put your target on hold for CASP for 8 weeks). Submission details can be found at http://predictioncenter.org/casprol/targets_submission.cgi Thanks and hoping for lots of targets. Hudel, UC Irvine This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Re: [ccp4bb] CCP4 Update 014
I can only echo Kay's comments. The CCP4 update system is just great. Together with a few others I was one of the initial beta testers of the update system. Beta-testing could not have not been easier. The thing just worked! Congratulations on an brilliant and extremely useful piece of software. Roberto On 20 Jan 2013, at 11:32, Kay Diederichs kay.diederi...@uni-konstanz.de wrote: Hi Andrey, Eugene and others - it is time to say that this new system is extremely useful, and so easy to use at the same time! Gone are the times when one had to worry about manually updating parts of CCP4. I just wonder why there should ever be a need for a CCP4 6.4.0 release; a rolling update seems just adequate to me - but that's just a user's perspective, and probably this has been discussed somewhere although I'm not aware of it. thanks for making this available, and the hard work to make it so perfect! Kay On Fri, 18 Jan 2013 19:04:37 +, Andrey Lebedev andrey.lebe...@stfc.ac.uk wrote: Dear CCP4 Users A CCP4 update has just been released, consisting of the following changes. All systems: * Ctruncate: Introduced DNA/RNA reference curve; uses flat prior on request, or when have tNCS or twinning * Othercell: Various bug fixes * PISA, QtPISA: Stability fixes and generation of Remark 350 in no-complex situations * PDBCur: Finish gracefully, rather than terminate, when atom selection is empty * PDB_Merge: Various bug fixes * Xia2: Correction to Ctruncate wrapper Linux and Mac only: *) * Aimless: Various bug fixes * Pointless: Correction for XDS input * Scala: Corrected output for CC(1/2) *) Corresponding changes for Windows have been already included in update No 13 Windows only: * Phaser.ensembler: Corrected path to syminfo.lib If you do not currently receive updates, consider re-installing your CCP4 setup using the latest binary packages, which now have CCP4 Update manager (ccp4um) integrated. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk Many thanks for using CCP4. Andrey Lebedev -- Scanned by iCritical. Roberto A. Steiner Group Leader Randall Division of Cell and Molecular Biophysics King's College London roberto.stei...@kcl.ac.uk Room 3.10A New Hunt's House Guy's Campus SE1 1UL London Phone 0044 20 78488216 Fax0044 20 78486435
Re: [ccp4bb] CCP4 Update 014
Dear Kay, Many thanks for nice words! We appreciate feedback from all our users. Indeed, we expect that the update system will result in a lower frequency of releases. Yet, full-scale releases will be needed. A good analogy here are the update vs upgrade procedures in operating systems. An upgrade is needed whenever we face the need for structural changes in the Suite, which cannot be easily accommodated by a mere update due to a considerable number of various dependencies to be followed. At present, we still need full releases because: 1) currently we are doing a considerable work under the hood of the CCP4 Suite, which is not reflected in what a general user would see. Some elements of that include better organised source repositories, synced with updates, completely new build mechanism, which would allow one to update installations compiled from sources, new test system and some others. From time to time, this results in structural changes in the backyard of CCP4 suite, which cannot be accommodated by update mechanism 2) sometimes we have new contributions which change really a lot. For example, when new GUI comes to release, it will change about everything 3) sometimes, new versions of various components result in changes far beyond their own scope. Usually (but not always), this relates to new versions of phaser, cctbx, refmac and some other programs 4) incremental updates make the Suite asynchronous on component versions. For example, recent phaser update resulted in duplication of cctbx, which was necessary in order to keep other cctbx-related components running. With time, this results in higher complexity and lower manageability of the suite. I am sure that this list is far from complete, hence one more reason 5) unpredictable things happen, when updater cannot manage something. I hope that these reflections give some insight into maters and you will be less disappointed by having to upgrade to 6.3.1 fairly soon :) Best regards, Eugene On 20 Jan 2013, at 11:32, Kay Diederichs wrote: Hi Andrey, Eugene and others - it is time to say that this new system is extremely useful, and so easy to use at the same time! Gone are the times when one had to worry about manually updating parts of CCP4. I just wonder why there should ever be a need for a CCP4 6.4.0 release; a rolling update seems just adequate to me - but that's just a user's perspective, and probably this has been discussed somewhere although I'm not aware of it. thanks for making this available, and the hard work to make it so perfect! Kay On Fri, 18 Jan 2013 19:04:37 +, Andrey Lebedev andrey.lebe...@stfc.ac.uk wrote: Dear CCP4 Users A CCP4 update has just been released, consisting of the following changes. All systems: * Ctruncate: Introduced DNA/RNA reference curve; uses flat prior on request, or when have tNCS or twinning * Othercell: Various bug fixes * PISA, QtPISA: Stability fixes and generation of Remark 350 in no-complex situations * PDBCur: Finish gracefully, rather than terminate, when atom selection is empty * PDB_Merge: Various bug fixes * Xia2: Correction to Ctruncate wrapper Linux and Mac only: *) * Aimless: Various bug fixes * Pointless: Correction for XDS input * Scala: Corrected output for CC(1/2) *) Corresponding changes for Windows have been already included in update No 13 Windows only: * Phaser.ensembler: Corrected path to syminfo.lib If you do not currently receive updates, consider re-installing your CCP4 setup using the latest binary packages, which now have CCP4 Update manager (ccp4um) integrated. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk Many thanks for using CCP4. Andrey Lebedev -- Scanned by iCritical. -- Scanned by iCritical.
Re: [ccp4bb] Golden Jubilee of Ramachandran Plot
Dear Colleagues, This paper on the early days of crystallographic computing will be of relevance:- http://garfield.library.upenn.edu/classics1980/A1980JR2291.pdf Greetings, John Prof John R Helliwell DSc On 20 Jan 2013, at 06:38, Edward A. Berry ber...@upstate.edu wrote: Edward A. Berry wrote: http://www.computerhistory.org/revolution/timeline And this paper describes their use of a digital computer as if it were rather routine: Sternberg, J., Stillo, H. Schwendeman, R. (1960). Spectrophotometric Analysis of Multicomponent Systems Using the Least Squares Method in Matrix Form. Analytical Chemistry 32, 84-90. Well, not exactly routine by today's standards. I was going by memory- actual description is: The matrix inversions were . . . carried out on the MISTIC Computer at Michigan State University. The assistance of Susann Brimmer in carrying out the calculations on the MISTIC computer is gratefully acknowledged.
