Re: [ccp4bb] Bicelle Crystallization in a Gryphon Robot

Sorry for self promotion but you might also consider the HILIDE method which is very similar to bicelle and sponge, only having fully solubilized protein:lipid:detergent complexes as input sample and therefore being fully compatible with regular liquid handling robotics. See Gourdon P et al 2011

Re: [ccp4bb] Bicelle Crystallization in a Gryphon Robot

there is one nice JOVE video and article from Jeff Abramson lab which was neat showing using mosquito to set up bicelle. No offense to Art people J Vis Exp. 2012 Jan 9;(59). pii: 3383. doi: 10.3791/3383. High-throughput Crystallization of Membrane Proteins Using the Lipidic Bicelle Method. Ujwal

Re: [ccp4bb] Bicelle Crystallization in a Gryphon Robot

Hello Cory, Unfortunately your Crystal Gryphon was not designed to work with all bicelle solutions. However, your Crystal Gryphon is easily upgradeable with our new LCP attachment. This will allow you to do LCP, Bicelle and Sponge Phase experiments. If you have any further questions about the

Re: [ccp4bb] Problem with COOT and MSE (SeMET ) residues

Do you use CCP4-6.2? I met the similar problem before. Try use the latest version of coot 0.7. On Wed, Feb 15, 2012 at 8:42 AM, Christopher Browning < christopher.brown...@epfl.ch> wrote: > Hi Laurie, > > > Not much, I did not get any useful feedback so I emailed Paul Emsley > directly. > > C

[ccp4bb] Bicelle Crystallization in a Gryphon Robot

Hello all; I am wondering if anyone has any experience getting a ARI Gryphon robot to pick up protein in a bicelle solution? The nano needle on our robot does not seem to want to suck the sample up in a variety of liquid class settings. Any suggestions out there on if this can be made to work? Ch

Re: [ccp4bb] Fwd: [ccp4bb] protein degradation

I agree with Mark, except that I wouldn't even try sonication, Triton or freeze/thaw cycles in that case. I'd look for emulsification (with a Homogenizer) in a cold room, but if you go quickly and gently with the French Press (either in a cold room or by using a cold piston) it might help. Don'

Re: [ccp4bb] surface residue mutation

Steve Kent has published a few more (at least 1 other) since HIV... 3ODV http://www.rcsb.org/pdb/explore/explore.do?structureId=3ODV Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography. Pentelute, B.L., Mandal, K., Gates, Z.P., Sawaya, M.R., Yeate

Re: [ccp4bb] Bond Length Outliers (correction)

Btw, re other sources of deviation: Molprobity does not report geometry deviations beyond CB. The RUN500 command from CCP4i does. BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale Tronrud Sent: Thursday, February 16, 2012 10:56 AM To: CCP4B

Re: [ccp4bb] Bond Length Outliers (correction)

Using the Protein Geometry Database (pgd.science.oregonstate.edu) I looked up all Arg residues in models with resolution of 1.3 A or better and found 5920 examples. The mean value of the O-C-N angle (and I'm assuming that the O and C atoms are in the Arg) is 122.6 deg with a sigma of 1.1 deg.

Re: [ccp4bb] Fwd: HR3699, Research Works Act

Dear Colleagues, If you want an excellent, painless transfer from journal to PUBMED, just stick to the IUCr journals. They do an excellent job of cooperating in the NIH open access policy with an automatic transfer of the clean refereeded and edited paper to PUBMED. Yes, the IUCr journal co

Re: [ccp4bb] Bond Length Outliers (correction)

Hi, If I remember correctly this angle is for the planarity of the peptide bond. Maybe you have a real deviation which might occur not so seldom than expected. You have a quite high resolution. If the density is really convincing then you may accept this outlier. Not every outlier is a mistake.

Re: [ccp4bb] Fwd: HR3699, Research Works Act

Dear Colleagues, Acta participates very nicely and fully in the NIH Open Access program. After one year of the normal restricted access any NIH-funded paper automatically enters the NIH open access system. The journals get to get their revenue when the paper is most in demand, but the com

Re: [ccp4bb] Fwd: HR3699, Research Works Act

Charlie, A much more balanced view than others have posted. NIH Open Access requirement is a vast overreach. I agree. HR 3699 appears to be as deeply flawed. It could be made better with amendments? Enrico. On Thu, 16 Feb 2012 17:06:24 +0100, Charles W. Carter, Jr wrote: For what it's

Re: [ccp4bb] Fwd: HR3699, Research Works Act

I am strongly in favour of Open Acess, but Open Access is not always helped by lack of money for editing etc. For example: Acta Crystallographica is not Open Acess. In one manner or another publishing must be financed. Libraries pay fees for the journals. The fees help the International Union o

[ccp4bb] Bond Length Outliers (correction)

Ahh yes, I looked at the wrong line. My Rmsd bond angle is 2.55 degrees (not bond length). MolProbity states that my only abnormal angle is 124.23 degrees between O--C--N of an Arg. Real Space Refinement does not change anything and Regularizing the zone completely distorts the backbone. Any sug

Re: [ccp4bb] Fwd: HR3699, Research Works Act

Pedro, Well it worked for me (and I see many others) without a zip code. I see that someone else typed "Bayreuth" in the zip code field - so I suspect you can type anything there! Cheers -- Ian On 16 February 2012 16:31, Pedro M. Matias wrote: > > Can non-US residents sign this petition? You

Re: [ccp4bb] Fwd: HR3699, Research Works Act

Can non-US residents sign this petition? You need a Whitehouse.gov account and in order to register you have to provide a U.S. (I presume) zipcode. At 15:37 16-02-2012, Ian Tickle wrote: Dear Herbert Thanks for your detailed explanation. I had missed the important point that it's the require

[ccp4bb] Bond Length Outliers

I am currently in the final steps of refining a 1.3A structure and am coming across a slight problem. According the the pdb file, I have an Rmsd bond length of 2.55. MolProbity identifies three outliers which correspond to the bond lengths of: Asp: C--O , bond length = 1.2A Arg: C--O , bond le

Re: [ccp4bb] Fwd: HR3699, Research Works Act

For what it's worth, my own experience with the issue of scholarly publication and open access is nuanced enough that perhaps my two-bits worth can add to this discussion. In short, I agree both with Ian's previous message and with Herbert, and feel that the incompatibility between them goes to

Re: [ccp4bb] Fwd: HR3699, Research Works Act

> Can non-US based scientists sign the petition, btw? Well there's nothing to stop you! It asks for your zip code, but I just left it blank and it accepted it. Cheers -- Ian

Re: [ccp4bb] Fwd: HR3699, Research Works Act

There was an op-ed piece in the NY Times last month about this issue written by Michael Eisen, a found of PLos: http://www.nytimes.com/2012/01/11/opinion/research-bought-then-paid-for.html?ref=carolynbmaloney On Feb 16, 2012, at 9:47 AM, Paula Salgado wrote: May I also suggest reading these:

Re: [ccp4bb] Fwd: HR3699, Research Works Act

May I also suggest reading these: https://intechweb.wordpress.com/2012/01/25/selected-reading-on-research-works-act-why-you-should-care/ https://intechweb.wordpress.com/2012/02/16/open-access-on-a-string-cut-it-and-it-will-grow-back/ Can non-US based scientists sign the petition, btw? There ar

Re: [ccp4bb] offtopic : Signed binaries in the next OS X

On Thu, Feb 16, 2012 at 7:17 AM, Francis E Reyes wrote: > The problem is not developers ensuring their identities by signing their > apps.  It's that there's now a (small) barrier for the end user in installing > unsigned apps. > > The implementation has yet to be seen, but will getting around t

Re: [ccp4bb] Fwd: HR3699, Research Works Act

Dear Herbert Thanks for your detailed explanation. I had missed the important point that it's the requirement on the authors to assent to open access after a year, which the proposed Bill seeks to abolish, that's critical here. I will go and sign the petition right now! Best wishes -- Ian On

Re: [ccp4bb] offtopic : Signed binaries in the next OS X

Hi Tim, we all get the "aschott notification" - I don't know her, but I do know about the CIPF, the Centro de Investigacion Principe Felipe in Valencia, Spain. This centre recently laid off an important number of researchers and I would guess she was one of them - so I doubt she will want anythi

Re: [ccp4bb] Fwd: HR3699, Research Works Act

The bill summary says: Research Works Act - Prohibits a federal agency from adopting, maintaining, continuing, or otherwise engaging in any policy, program, or other activity that: (1) causes, permits, or authorizes network dissemination of any private-sector research work without the prior c

Re: [ccp4bb] offtopic : Signed binaries in the next OS X

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Francis, not sure what you are trying to say. Many people have been securing their software e.g. with md5sums or PGP-signatures. Debian do that, and they do it for free as far as I know. You could sign your own software (for free) and then distri

Re: [ccp4bb] offtopic : Signed binaries in the next OS X

Hi Tim The problem is not developers ensuring their identities by signing their apps. It's that there's now a (small) barrier for the end user in installing unsigned apps. The implementation has yet to be seen, but will getting around this barrier simply be a pop up ("press OK if you reall

Re: [ccp4bb] REFMAC 5.7

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Morten, the 'external' keyword as e.g. exploited by Rob Nicholls' prosmart http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ Software->ProSmart could probably do that. The syntax reads like "exte dist first chain I resi 9 ins . atom N second ch

[ccp4bb] offtopic : Signed binaries in the next OS X

It seems that Apple is building a higher walled garden for OS X in the form of signed binaries. They're not mandating every app come from the appstore but instead have a level that allows developers to 'sign' their binaries with their own developer ID (which of course costs $99USD/year). Or the

Re: [ccp4bb] choice of wavelength

Hi Andrew, I completely agree and it is what I meant by "(assuming the full photon energy is captured)". If the fraction of photons counted goes up at longer wavelengths than the relative benefit of using longer wavelength is even more pronounced on Pilatus. So for native data sets the wavele

[ccp4bb] REFMAC 5.7

Dear board, How do I define base-pairing restraints in DNA in REFMAC 5.7? Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

Re: [ccp4bb] Fwd: HR3699, Research Works Act

Dear Ian, You are mistaken. The proposed law has nothing to do with preventing the encouragement people to break copyright law. It has everything to do with trying to kill the very reasonable NIH open access policy that properly balances the rights of publishers with the rights of authors and

Re: [ccp4bb] Fwd: HR3699, Research Works Act

Reading the H.R.3699 bill as put forward (http://thomas.loc.gov/cgi-bin/bdquery/z?d112:HR03699:@@@L&summ2=m&;) it seems to be about prohibiting US federal agencies from having policies which permit, authorise or require authors' assent to break the law of copyright in respect of published journal a

Re: [ccp4bb] Fwd: HR3699, Research Works Act

I signed, and I think so. Further information can be found here: http://www.guardian.co.uk/science/2012/feb/02/academics-boycott-publisher-elsevier On 16 Feb 2012, at 11:41, Boaz Shaanan wrote: > I initially thought that it had to do with a new Hampton Research thing. > > But can non-American

Re: [ccp4bb] Fwd: HR3699, Research Works Act

I initially thought that it had to do with a new Hampton Research thing. But can non-American citizens sign the petition too? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skyp

Re: [ccp4bb] Fwd: HR3699, Research Works Act

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Raji, maybe you could increase the number of supporters if you included a link to (a description of) the content of HR3699 - I will certainly not sign something only summarised by a few polemic sentences ;-) Cheers, Tim On 02/15/2012 11:53 PM,

Re: [ccp4bb] choice of wavelength

On 15 Feb 2012, at 23:55, Bart Hazes wrote: Diffracted intensity goes up by the cube of the wavelength, but so does absorption and I don't know exactly about radiation damage. One interesting point is that on image plate and CCD detectors the signal is also proportional to photon energy, s

Re: [ccp4bb] All-D World

I believe Eric is paraphrasing Genesis 3. It's all the serpent's fault. http://www.ic.unicamp.br/~stolfi/PUB/misc-misc/GenesysParody.html On 16/02/2012 02:39, Eric Bennett wrote: Jacob, I wish it were that cheery. Do

Re: [ccp4bb] DNA in coot

Le 15/02/12 11:36, Tim Gruene a écrit : > Hello Lisa, > > which version of coot do you use? Maybe it is outdated and that function > not yet properly implemented. I can confirm Bill's comment, and we work > with coot 0.6.2. > > Cheers, > Tim > > On 02/15/2012 09:01 AM, LISA wrote: >> Hi all, >

Re: [ccp4bb] choice of wavelength

Dear Colleagues, I think the following paper will be of particular interest for some aspects of this thread:- J. Appl. Cryst. (1984). 17, 118-119[ doi:10.1107/S0021889884011092 ] Optimum X-ray wavelength for protein crystallography U. W. Arndt Abstract: If the diffraction pattern from crystall