Re: [ccp4bb] sigma cutoff for fitting waters in model
I am a bit out of touch with the discussion, and this may have been mentioned already. It is important to remember that Sigma is an OVERALL value for the whole map, whereas one is looking for local solutions when fitting any density. Stuff on the surface of the molecule ought to be contoured at a lower level than in the ore, and this applies to protein as well as waters. Eleanor Ed Pozharski wrote: On Wed, 2010-04-21 at 17:21 -0700, James Holton wrote: The 0.3% chance of a peak being above 3 sigmas assumes that the histogram of electron density values is Gaussian. It is not! In fact, it is a funny-looking bimodal distribution (the peaks are protein and solvent regions). Indeed! That's why it is a bizarre argument. In fact, standard deviation is rather meaningless unless one is dealing with univariate distribution. For bimodal distributions, changes of standard deviation are uninterpretable (without looking at the distribution, that is) since they can be due to both shifts and redistribution. Cheers, Ed.
Re: [ccp4bb] Rsym problems...maybe???
No - no - no! Probably you should have integrated to a higher resolution! Eleanor Daniel Bonsor wrote: Hello again. At first I was not worry but maybe now I am. I have completed a structure and submitted to the PDB. They queried my Rsym value in the highest resolution bin, 2.5-2.37A (may I dare say it 100%). I was not worried at the time as I had: 99.4% completeness Mean(I/sdI) of 2.5 and a redundancy of 11 (which would explain the high Rsym) Space group I422 My Rpim in this shell is 30%. Should I reduce the resolution and start from scratch again or is everything fine and dandy and I should stop worrying?
Re: [ccp4bb] YATQ (yet another twinning question) - may involve pirates
A general point often overlooked, the Rfactor from twinned refinement at least with SHELX and REFMAC do not use exactly the same formulation as an Rfactor for a mono-crystal and seems consistently lower than expected.. my impression is that they cannot be compared easily. And there may be a problem with the FreeR set which should reflect the twinning pairs. I belive PHENIX deals with this properly, but it is not nec so for CCP4. You need to assign the Free sets in the highest conceivable Laue group then extend them to the lowerr spacegroup. Eleanor Garib Murshudov wrote: I am getting in habit of writing double emails. I would say that refmac overestimates at early stages and truncate underestimates (it is just an intuition, not based on theoretical or empriical results) Garib On 23 Apr 2010, at 23:16, Ethan Merritt wrote: In a nutshell = Is there a way to make solve/resolve behave reasonably if the data is twinned? Is there a recommended alternative path to clean up and maybe even auto-trace a map with 4-fold NCS but twinned data? Maybe Pirate/Buccaneer? In detail = I'm fighting with a structure that is probably/maybe in P4(2). 2.6A data 98% complete Rmerge = 0.07 in P4 Rmerge = 0.16 in P422(note the disturbingly low value) Pointless is 88% confident it's P4(2). Laue GroupLklhd NetZc Zc+ Zc-CCCC- Rmeas R- = 1 P 4/m *** 0.916 4.68 9.36 4.67 0.94 0.47 0.09 0.30 10 P 4/m m m 0.000 6.83 6.83 0.00 0.68 0.00 0.20 0.00 Truncate says the data is twinned, with a twinning fraction of 0.25. That is consistent with the bad-but-not-awful Rmerge in P422, right? I have a promising initial MR solution in P4(2) with four monomers in the a.s.u. It refines to R/Rfree = 0.36/0.38 in refmac but only if I enable the twinned data option. Twinning fraction refines to Twin fractions=0.4322 0.5678 My thought was to use the 4-fold NCS and solvent flattening in resolve to clean up and ideally auto-trace into the initial mediocre maps. The resolution is not great, but the 4-fold NCS should help a lot. Unfortunately, so far as I can figure out resolve ignores the twinning and is stuck dealing with R 0.60 and extremely poor maps. I tried de-twinning the data, but this was not a great success. Should I believe the truncate estimate of 25% twinning fraction or the refmac estimate of 43%? Neither? In any case, feeding the supposedly detwinned data to either refmac or resolve produces worse results that I was getting before attempted detwinning. Any advice? -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [ccp4bb] programmatic symmetry mate generation
James Stroud wrote: Hello All, I want to programmatically generate the symmetry mates for a molecule and write out the files containing the symmetry related molecules. I'm resisting the urge to reinvent the wheel. What is the best way to do this? I'd prefer to do it within a python program using an open source library, but I'd settle for scripting an external program if that is the only option. James Well - pdbset will do it.. E
Re: [ccp4bb] sigma cutoff for fitting waters in model
Eleanor, Do you have a rationale for assuming a lower uncertainty on the surface than in the core? I ask this because I did once look at the variation of the local RMSD of a difference Fourier, i.e. w(mFo-DFc) with w=2 for acentrics, w=1 for centrics, and I didn't find any obvious correlation with the location of the protein/solvent regions. The variation seemed to be just random and pretty well what one would expect given the sample size of the locally-defined region used to compute the uncertainty. Cheers -- Ian On Mon, Apr 26, 2010 at 9:42 AM, Eleanor Dodson c...@ysbl.york.ac.uk wrote: I am a bit out of touch with the discussion, and this may have been mentioned already. It is important to remember that Sigma is an OVERALL value for the whole map, whereas one is looking for local solutions when fitting any density. Stuff on the surface of the molecule ought to be contoured at a lower level than in the ore, and this applies to protein as well as waters. Eleanor Ed Pozharski wrote: On Wed, 2010-04-21 at 17:21 -0700, James Holton wrote: The 0.3% chance of a peak being above 3 sigmas assumes that the histogram of electron density values is Gaussian. It is not! In fact, it is a funny-looking bimodal distribution (the peaks are protein and solvent regions). Indeed! That's why it is a bizarre argument. In fact, standard deviation is rather meaningless unless one is dealing with univariate distribution. For bimodal distributions, changes of standard deviation are uninterpretable (without looking at the distribution, that is) since they can be due to both shifts and redistribution. Cheers, Ed.
Re: [ccp4bb] Please remove me from this list
Please remove me from this list. Thank you, Anne-Marie -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Randy Byrne Sent: Sunday, April 25, 2010 6:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Please remove me from this list __ This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the originator of the message. Any views expressed in this message are those of the individual sender, except where the sender specifies and with authority, states them to be the views of Malvern Instruments. http://www.malvern.com __
Re: [ccp4bb] Please remove me from this list
Although not as dramatic, there is a simple, private, method one can use to unsubscribe, and it possesses the additional merit of actually doing what you want: http://www.ccp4.ac.uk/ccp4bb.php Colapietro, Anne-Marie wrote: Please remove me from this list. Thank you, Anne-Marie -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Randy Byrne Sent: Sunday, April 25, 2010 6:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Please remove me from this list __ This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the originator of the message. Any views expressed in this message are those of the individual sender, except where the sender specifies and with authority, states them to be the views of Malvern Instruments. http://www.malvern.com __
Re: [ccp4bb] MacBookPro problems
Hi Jürgen, the Zalman is o.k. on a Nvidia 380. I just wrote an email to the vendor. Am 23.04.10 17:43, schrieb Jürgen Bosch: Yeah, send your Zalman vendor a nice email and let them exchange your DVI adapter. Had that problem too - alternatively you can scavenge one DVI adapter from another computer and test it. I wouldn't be surprised if it works, that's how I figured it out. Jürgen On Apr 23, 2010, at 9:37 AM, Joachim Reichelt wrote: Dear all, I just got a MacBookPro. I have two questions: How to get the keyboard shortcuts in coot or pymol up, e.g. altF to open the file dialog. and whenever I connect a zalman 220 (stereo ready) monitor to the mac using a miniDisplayPort to DVI adapter, the monitor is not recognized and so it is completely dark. The Mac does not show the monitor in the dialogues but an error message. -- Joachim - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ --
Re: [ccp4bb] Please remove me from this list
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[ccp4bb] Crystallography service available from Scripps FL
Dear crystallographers, Macromolecular X-ray crystallography core of Scripps FL offers equipment and resources to scientists outside (academic and industrial) of our campus by providing crystallographic analysis of their chosen biological macromolecules. We offer full service by performing protein crystallization, X-ray diffraction data collection (both in-house and at Argonne National Laboratory) and processing, phasing, crystallographic refinement, model building, and visualization. The following is a highlight of resources and instruments; 1. Minstrel III imager and RoboIncubators 2. TTP LabTech mosquito crystallization robot 3. Innovadyne 96+8 crystallization robot 4. EmeraldÂs Matrix Maker 5. SER-CAT (APS) access 6. Rigaku MicroMax-007 HFM X-ray generator 7. Proteros Free Mounting System (FMS) 8. Mar345dtb image plate detectors 9. Computer clusters for data collection and processing For more information, please refer to our website at http://crystallography.florida.scripps.edu or contact us at crystallogra...@scripps.edu
[ccp4bb] EMBO Practical Course Computational aspects of protein structure determination and analysis: from data to structure to function
Now open for registration: EMBO Practical Course 'Computational aspects of protein structure determination and analysis: from data to structure to function' Dates: 6-10 September 2010 Venue: EMBL-EBI, Hinxton, Cambridge, CB10 1SD, UK Registration Deadline: 23 July 2010 - 12 noon (GMT) Acceptance Notification Date: 30 July 2010 - 12 noon (GMT) This course is aimed at PhD students and post-docs working on the collection and analysis of protein structure data. The goal is to provide them with insight into the protein structure determination process, how to critically assess the quality of data from models and also provide expertise in the analysis of protein structure data with a view to predicting protein function. Course outline and details: http://www.ebi.ac.uk/training/handson/course_100906_structures.html Course programme: http://www.ebi.ac.uk/training/handson/course_100906_structures_programme.html Please forward this announcement to anyone who might be interested in attending the course. Thanks! --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk http://www.ebi.ac.uk/pdbe/ Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
[ccp4bb] Help with Bayes's theorem
I thought some of you would enjoy a little conditional probability discussion found in the NY Times today, since this is a big part of crystallography nowadays. I'm always on the lookout for good ways to teach Bayes's theorem. http://opinionator.blogs.nytimes.com/2010/04/25/chances-are/ Jim
Re: [ccp4bb] Unsubscribe
Please remove me from this list unsubscribe From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Randy Byrne [randy.by...@malvern.com] Sent: Sunday, April 25, 2010 7:38 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Please remove me from this list Thank you. Best regards, Randy Byrne Malvern Instruments Inc. 117 Flanders Road Westborough, MA 01581-1042 Tel: 508-768-6415 Fax: 508-768-6403 Help Desk: support...@malvern.com http://www.malvern.com Malvern’s web site http://www.malvern.com/malvernmovie An exciting 4 minute overview of Malvern http://www.malvernevents.comMalvern’s Interactive Learning Center __ This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the originator of the message. Any views expressed in this message are those of the individual sender, except where the sender specifies and with authority, states them to be the views of Malvern Instruments. http://www.malvern.com __
[ccp4bb] Schroder et al. DEN potential
All - I am trying to intuitively understand the concept of the DEN (deformable elastic network) function for low resolution X-ray crystallography in Schroder et al. (Levitt Brunger) recent Letter to Nature (Vol 464, 22 April 2010). Is this (conceptually anyway) analogous to an experimentally determined NOE distance restraint between some parts of a structure in an NMR refinement, except here using distance restraints from homologous structures determined at high resolution? I am trying to think of a way to describe it to students without the math. That may be impossible but I'd like to try! I should probably have posted this to CNSbb but I don't currently belong- sorry. Thanks Laurie Betts UNC
[ccp4bb] please unsubscribe
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[ccp4bb] Please recommend a microscope for crystallography
hello everyone I really appreciate it if anyone can recommend a microscope for crystallography. I am looking at manual one ( without any fancy motor driven stage or fancy digital camera-computer stuff) , but need have the trinocular for a simple digital camera to take photo I was using leica MZ6, but I feel the zoom level is a little bit low. another thing is I need some space between the object lense and the cover plate so that I can use tool to manipulate crystals thanks a lot for your help lei _ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_3
Re: [ccp4bb] Help with Bayes's theorem
Bayes Theorem can help well informed patients too. They just need to know how good their doctors are! 1. After reading the NYT you know that 1/3 of the time your doctor is going to tell you that you have better than a 90% chance of breast cancer if you have a positive mammogram. 2. After reading the NYT, you know that 0.8% of women your age get breast cancer. 2. After a chat at the hair salon, you were surprised to learn that about 2.5% of women who had mammograms and don't have breast cancer were needlessly scared shitless when their doctors told them they had a 90% chance of having breast cancer. 3. You take a mammogram and your doctor tells you that you have a 90% chance of breast cancer. What is your real chance of breast cancer after this mammogram? p(H|E) = (pH * pE|H) / pE = (pH * pE|H) / (pH * pE|H + pE|H' * pH') = (0.008 * 1/3) / ((0.008 * 1/3) + (0.025 * 0.992)) = 9.4% Who needs an MD? James On Apr 26, 2010, at 12:30 PM, Jim Pflugrath wrote: I'm always on the lookout for good ways to teach Bayes's theorem.
Re: [ccp4bb] programmatic symmetry mate generation
Hi James, The symmetry copies of a molecule asymmetric unit can be saved to a new PDB file using the saveunitcell.py Python script with Chimera. http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts It uses the CRYST1 record in the PDB file to determine the symmetry group. Unfortunately as mentioned in the script you need to use Chimera as the Python interpreter, which you may not be willing to do -- but you can just call out to the command-line version of Chimera (also documented in the script) via os.system() or whatnot. There is also a sym command in Chimera which can generate symmetry mates from a wide spectrum of possible criteria. A Python script to call sym is just: from chimera import runCommand runCommand(sym options you want) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
[ccp4bb]
Dhabaleswar Patra M.Vijayan's Lab Molecular Biophysics Unit Indian Institute Of Science Bangalore,Karnataka-560012 Mobile- +919980369860 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
[ccp4bb] Sonication e.coli parameters
Hi All, Our protein is expressed as inclusion bodies ibn e.coli W3110 cells. we harvest the cells supend it in water [no buffer] and perform sonication to lyse the cells. we lyse the cells till our O.D is decreased to 1/3rd of original our starting O.D of suspension is about 250. then we centrifuge the abvoe suspencion at 12000 rpm to collect teh inclusion bodies. but we are not getting good yield and also inclusion bodies are not that pure. Do we need to add lysozyme prior to lysis. can anyone suggest a good method to lyse ecoli cells expressing protein in inclusion bodies. Thanks in anticipation meg
