[ccp4bb] Fwd: Re: [ccp4bb] SUMMARY: scala and xds data

Well, there's one one very good reason to scale XDS data with scala: scala prints out per-image statistics, which are fantastically useful. My particular favourite: the scaling B-factor, which is as direct a read-out of dose (i.e. decay) as we have: 1A^2 per MGy. (Lots and lots of cave

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 a

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

Re: [ccp4bb] Shifting twin fraction with refinement - finally zero

A few comments - you dont give your cell dimensions but if they are more or less the same for the P212121 and P43 21 2 I dont see how a 43 set of absences can turn into a 21 set .. However if there is non-crystallographic translation, then absences an mislead.. Is that true for you - Tw

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 pr

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

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 wit

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 ___

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 > > -

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 co

Re: [ccp4bb] Please remove me from this list

If you take a look into the header of your mail, you will find following three lines: List-Help: , List-Subscribe: List-Unsubscribe: <

[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 prote

[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) Accep

[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 lis

[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 det

[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

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 re

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. Unfortuna

[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 centrifug

Re: [ccp4bb] X-Ray films

Indiana Jones and the Kingdom of the Crystal Skull? "Nothing shocks me, I'm a scientist". Flip harry powell wrote: Hi Not a question about films for recording X-rays on, but a question about films about X-rays, Crystallography and related subjects! I was wondering what ccp4bbers favourite m