Re: [ccp4bb] how to decide an ideal Weight matrix value in REFMAC
(1). Can I say the X-ray weighting is optimal when it yields the smallest Rfree, meanwhile RMS-Z(bonds) is smaller than 0.85 - 0.146*resolution (angles also maybe)? The weighting is optimal when the free likelihood is maximised with respect to the weights, or equivalently when the negative log of the free likelihood (-LLfree: the number printed by Refmac) is minimised. The practical problem is that this requires a lot of refinement runs with different weights to locate the optimum. Ideally also the B weighting factor needs to be optimised by the same method, but this makes it a 2-parameter optimisation so you would need even more runs of Refmac to locate the optimum. The B weighting factor is resolution-dependent so a single value is really not suitable at all resolutions. I was suggesting using the PDB-REDO based resolution-dependent RMS-Z(bonds) target value as a quick-and-dirty alternative which won't be too far out. (2). Why RMS-Z(bonds) should be lower than that for low resolution data and higher for high resolution? Or why high-resolution can allows more outliers? Bernhard's thought experiment is a good one, I would just say that if you only have low resolution data you can't hope to estimate small deviations from the target values accurately: there's a good chance that half of them will be just random deviations in the wrong direction and only produce overfitting and an increase in Rfree; hence you won't achieve the optimal LLfree. If you have high resolution data then of course you are justified in claiming that the deviations from the target values that you observe are meaningful - that's what 'resolution' means. You're second question about only being able to detect outliers with high resolution data answers your first question! This is analogous to the 'D' factor in D*Fcalc for the map coefficients: the effect of random error is to reduce the expectation. Incidentally, changing the subject briefly to a previous thread: note that Refmac writes out D*Fcalc in the 'FC' column, not Fcalc, so if people deposit this column in the PDB then it cannot be used to reproduce the R factor, which requires Fcalc. Cheers -- Ian
[ccp4bb] CCP4MG Version 2.4.2
Dear All, Version 2.4.2 of the CCP4 Molecular Graphics Program (CCP4MG) has just been placed on the downloads page: http://www.ysbl.york.ac.uk/~ccp4mg/download2/ This release features: * A sequence viewer (Tools-Sequence viewer..), including: o Multiple sequence alignment o Highlight sections of structure by clicking on sequence. o Local blastp search (if blast installed) and remote blast search (EBI). Download of similar structures following search. o Load alignment from external file in many formats. * Speed-ups drawing ribbons * Generally better handling of large structures and structures with multiple NMR models. * Download electron density from EDS (Uppsala). * Electron density is transformed with model following superposition. * Bug fixes (superpose selection problems, crashes) * User can tell the program explicitly to use Zalman stereo * More help for user in editing Picture Wizard generated scenes: o The preferences dialog now informs if any display object has a custom drawing style. o The user can remove a custom drawing style and revert to global preferences. * Debugging (sometimes) possible on Windows. Dumps are created under most crash circumstances. This should help in tracing problem loading PDB files on some Windows machines. * Size of rendered images can be specified in inches and dpi. * Ambient occlusion method in render. * Structure coordinates can be transformed with a matrix which applies to real coordinates or the current view. Please report problems to ccp...@ysbl.york.ac.uk. Best Wishes, CCP4MG
Re: [ccp4bb] heterologous seeding
An old one: Eichele G, Ford GC, Jansonius JN. Crystallization of pig mitochondrial aspartate aminotransferase by seeding with crystals of the chicken mitochondrial isoenzyme. J Mol Biol. 1979 Dec 5;135(2):513-6. PubMed PMID: 537086. Daniel Le 21/09/2010 22:24, Christopher Rife a écrit : Hi, I seem to recall a paper from a few years back that used heterologous proteins for macro/micro seeding, and of course now I can't find it. Seems likely that lysozyme would be involved... I've found plenty on using non-protein compounds as seeds, but nothing for protein. Does anyone know if such a reference is out there? Thanks! Chris
Re: [ccp4bb] 300 projects = maximum in CCP4i?
Dear Charles, 1). I am using CCP4 v. 6.02, the Tcl/Tk middleware is 8.4.14/8.4.14. There is no error message, there simply is no space at the right side of the computer screen to see the 13th column (of 25 entries). 2). Your suggestion to increase the MENU_LENGTH parameter in configure.def has worked nicely, I increased it from 25 to 45, so there is again ample space for more projects. Many thanks! -Joerg PS: Jared Sampson suggested an alternative solution, namely to remove projects from the ccp4 interface without actually deleting the project databases (CCP4_DATABASE) themselves. Dr. Joerg Kallen Novartis Pharma AG PH222426, CPC/SBP:LAB KALLEN CHBS, WSJ-088.9.08B Novartis Pharma AG Forum 1 Novartis Campus CH-4056 Basel Switzerland Phone: +41 61 3245579 Fax: +41 61 3242686 Email : joerg.kal...@novartis.com Charles Ballard charles.ball...@stfc.ac.uk 09/20/2010 11:39 AM To joerg.kal...@novartis.com cc Subject Re: [ccp4bb] 300 projects = maximum in CCP4i? Hi Can you tell me what versions of the ccp4 suite and tcl/tk you are using? Also, the exact error message (if any) The only hardwired figure I can see is the 25 for the columnbreak in the tk menu which is set in your ~/.CCP4/etc/configure.def , the MENU_LENGTH parameter. If your screen is deep enough you might increase this to see if it has an effect, however, this would only be a temporary fix until a new limit is reached. Charles Ballard CCP4 On 20 Sep 2010, at 09:23, Joerg Kallen wrote: Dear all, I wanted to generate the 301'st project in the CCP4i interface Directories+Projects. The problem is that when I click on the button for the Project of this session, there is apparently no space for the 13th column (of 25 entries). I do not want to delete any old projects, so is there a workaround (I am using CCP4i 1.4.4.2)? Many thanks, Joerg Dr. Joerg Kallen Novartis Pharma AG PH222426, CPC/SBP:LAB KALLEN CHBS, WSJ-088.9.08B Novartis Pharma AG Forum 1 Novartis Campus CH-4056 Basel Switzerland Phone: +41 61 3245579 Fax: +41 61 3242686 Email : joerg.kal...@novartis.com _ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately by e-mail and delete the material from any computer. Thank you. -- Scanned by iCritical. _ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately by e-mail and delete the material from any computer. Thank you.
Re: [ccp4bb] how to decide an ideal Weight matrix value in REFMAC
Bernhard's thought experiment is a good one, I picked it up from Ianprobably posted earlier BR
[ccp4bb] Position opening at RCSB PDB/Rutgers University- BIOCHEMICAL INFORMATION ANNOTATION SPECIALIST
The RCSB Protein Data Bank (http://www.pdb.org) is a publicly accessible information portal for researchers and students interested in structural biology. At its center is the PDB archive – the sole international repository for the 3-dimensional structure data of biological macromolecules. These structures hold significant promise for the pharmaceutical and biotechnology industries in the search for new drugs and in efforts to understand the mysteries of human disease. The primary mission of the RCSB PDB is to provide accurate, well-annotated data in the most timely and efficient way possible to facilitate new discoveries and scientific advances. The RCSB processes, stores, and disseminates these important data, and develops the software tools needed to assist users in depositing and accessing structural information. The RCSB Protein Data Bank at Rutgers University in Piscataway, NJ has one opening for a Biochemical Information Annotation Specialist to curate and standardize macromolecular structures for distribution in the PDB archive. The annotation specialists validate, annotate, and release structural entries in PDB archive. The annotation specialists also communicate daily with members of the deposition community. The position is an academic position with state benefit. The salary is compatible with faculty level. A background in macromolecular crystallography or small molecule crystallography is a strong advantage. Biological chemistry (PhD, MS) is required. Experience with linux computer systems, biological databases is preferred. The successful candidate should be self-motivated, pay close attention to detail, possess strong written and oral communication skills, and meet deadlines. This position offer the opportunity to participate in an exciting project with significant impact on the scientific community. Please send resume (pdf preferred) to Dr. Jasmine Young at pdbj...@rcsb.rutgers.edu.
[ccp4bb] error during mrbump installation
Hi, I am trying to install mrbump on a 32 bit ubuntu linux desktop (kernel: 2.6.31-22-generic, python 2.4, 2.5 and 2.6 tested). When executing python setup.py after extracting mrbump-0.4.4, I get the following error messages: setup.py:269: DeprecationWarning: os.popen4 is deprecated. Use the subprocess module. i,o=os.popen4(dot -V) Traceback (most recent call last): File setup.py, line 452, in module install.check_dependencies(log) File setup.py, line 285, in check_dependencies installed=string.split(version_cur, .) UnboundLocalError: local variable 'version_cur' referenced before assignment Am I using the wrong version of python? Which one do I need to install? The manual states Python version 2.3 or later ... Thanks! Michael
Re: [ccp4bb] Effect of NCS on estimate of data:parameter ratio
Hi Ian, First, constraints are just a special case of restraints in the limit of infinite weights, in fact one way of getting constraints is simply to use restraints with very large weights (though not too large that you get rounding problems). These 'pseudo-constraints' will be indistinguishable in effect from the 'real thing'. So why treat restraints and constraints differently as far as the statistics are concerned: the difference is purely one of implementation. In practice this is not true, of course. If you impose infinitely strong NCS restraints, any change to a thusly restrained parameter by the refinement program will make the target function infinite, so effectively your model will never change. This is very different from the behaviour under NCS constraints and the resulting models in these two cases will in fact be very easily distinguishable. --Gerard ** Gerard J. Kleywegt Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] Effect of NCS on estimate of data:parameter ratio
I agree with Gerard. Example: it's unlikely to achieve a result of rigid-body refinement (when you refine six rotation/translation parameters) by replacing it with refining individual coordinates using infinitely large weights for restraints. Pavel. On 9/22/10 1:46 PM, Gerard DVD Kleywegt wrote: Hi Ian, First, constraints are just a special case of restraints in the limit of infinite weights, in fact one way of getting constraints is simply to use restraints with very large weights (though not too large that you get rounding problems). These 'pseudo-constraints' will be indistinguishable in effect from the 'real thing'. So why treat restraints and constraints differently as far as the statistics are concerned: the difference is purely one of implementation. In practice this is not true, of course. If you impose infinitely strong NCS restraints, any change to a thusly restrained parameter by the refinement program will make the target function infinite, so effectively your model will never change. This is very different from the behaviour under NCS constraints and the resulting models in these two cases will in fact be very easily distinguishable. --Gerard ** Gerard J. Kleywegt Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
[ccp4bb] iMosflm can't read images
I had trouble adding image files into iMosflm (1.0.4) GUI running on our in-house Linux machine (64-bit, Fedoro). It complained about the filenames: * FATAL ERROR * Image filenames must be of the form ABCDE_###.ext or ABCDE-###.ext where the initial string can be up to 40 characters long and must be separated from a 3 digit number by a _ or -, and the extension (ext) can be up to 8 characters long. The filenames are actually following the convention Mosflm required. The same image files were readable by iMosflm on Linux machine at the synchrotron station. Is anything wrong with our iMosflm installation, configuration...? Thanks for your help. Huiying _ Huiying Li, Ph. D Department of Molecular Biology and Biochemistry University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu
[ccp4bb] Assistant Professor faculty position at the University of Kentucky
The Department of Molecular and Cellular Biochemistry invites applications for a tenure track faculty position at the Assistant Professor level. The successful candidate must possess a Ph.D., M.D., or equivalent degree and have an active research program using structural methods to address questions of biomedical relevance. We are particularly interested in candidates that use X-ray crystallography as their major technique and whose research interests complement existing departmental programs including, but not limited to the areas of diabetes, cardiovascular disease, neuroscience, and cancer. Preference will be given to candidates with a record of scholarly achievement in membrane protein structural biology. The successful candidate will benefit from a stimulating and collaborative environment within the department and a strong graduate program. Competitive startup funds and salary as well as access to state-of-the-art facilities including in-house X-ray crystallography equipment, access to the SER-CAT beamline at the Advanced Photon Source in Chicago and appropriate space will be offered in a new 185,000 sq. ft. research building. Evaluation of applicants will begin October 2010. Interested applicants should visit http://medicine.mc.uky.edu/biochemreference to access the online faculty application. Required application materials include curriculum vitae, a description of your current and future research program, and three letters of reference. Inquires may also be sent to MCBX Faculty Search Committee at bioc...@uky.edu or call 859-323-5549. For further information about the Department, visit: www.mc.uky.edu/biochemistry The University of Kentucky is an equal opportunity employer and encourages applications from minorities and women.
[ccp4bb] macbook pro 13
Dear colleagues, We want to buy a macbook pro 13. It has Nvidia Geforce 320M graphics. Has anyone tried this computer and graphics with coot, O and Pymol and what is the performance? We would appreciate all suggestions. Mike Colaneri
