[ccp4bb] Fwd: Delivery Status Notification (Failure)

Dear CCP4BB members Sorry for off topic, i had question related to dispersity of proteins of my interest, i am working on DNA binding protein, having PI around 9 to 10,Initially protein was remaining stable at high salt, but was not able to concentrate more than 1mg/ml, after using 50mm Arg, 50mm

[ccp4bb] Fwd: [ccp4bb] Do my SAXS data agree with the crystal structure?

In theory, there should be a simple way to calculate P(r) directly from the crystal structure rather than indirectly from the expected scattering curve. Distribution of pair distances, r^2 weighted. This would remove any ambiguity about choice of Dmax. ... but I can't think of any of the common

[ccp4bb] Fwd: [ccp4bb] Where to get a thermo-cycling controlled chamber

Hi everyone, I think my first post did not clearly describe the machine I need. It's very kind of Zhijie and other repliers to reminde me this problem. So I post it again here, try to make it short and clear. Sorry for occupying the space of your mailbox twice. " Actually I need a chamber like a c

[ccp4bb] Fwd: International Fellowship Program for Postdocs at Paul Scherrer Institut

Prof. Gebhard F.X. Schertler Head of Biology and Chemistry Paul Scherrer Institut Laboratory of Biomolecular Research, BMR OFLC 109 CH-5232 Villigen PSI gebhard.schert...@psi.ch phone +41 (0)56 310 4265 http://www.psi.ch/lbr/laboratory-of-biomolecular-research 15th International Retinal Protein M

Re: [ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

I'm sure someone got a video or at least an audio recording, so if I can find it I will post a link. Mike T - Original Message - From: "Jim Pflugrath" To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, June 6, 2012 12:31:56 PM GMT -08:00 US/Canada Pacific Subject: Re: [ccp4b

Re: [ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

] Sent: Wednesday, June 06, 2012 2:05 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? Begin forwarded message: Date: June 6, 2012 3:05:16 PM EDT To: aaleshin mailto:aales...@burnham.org>> Subject: Re: [

[ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

Begin forwarded message: Date: June 6, 2012 3:05:16 PM EDT To: aaleshin mailto:aales...@burnham.org>> Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? There are four such papers in Methods in Enzymology, Vols 368 and 374: David Blow: How Bijvoet

Re: [ccp4bb] Fwd: Crystallographic Software Fayre (ECM27, Bergen)

Dear all The deadlines below have been extended to 15th June. Note that, since the deadline for abstracts is still open, there should still be the opportunity of having your work chosen to be an oral presentation (three of the five talks in MS are chosen from the abstracts). The lists of

Re: [ccp4bb] Fwd: [ccp4bb] Death of Rmerge

In the meantime we could follow Phoebe Rice's example and put the resolution at I/sigma=2 in REMARK 2 "resolution of structure" but put the actual bleeding-edge resolution we used in the reduction and refinement statistics (At least if the PDB will allow us to have different values in these three

Re: [ccp4bb] Fwd: [ccp4bb] Death of Rmerge

> There are things you can expect to learn from a > 2Å structure that you are unlikely to learn from a 5Å structure, even > if equal care has been given to both experiments, so it makes sense > for the title to give the potential reader an idea which of the two > cases is presented. But for this p

Re: [ccp4bb] Fwd: [ccp4bb] Death of Rmerge

On Thursday, May 31, 2012 02:21:45 pm Dale Tronrud wrote: >The resolution limit of the data set has been such an important > indicator of the quality of the resulting model (rightly or wrongly) > that it often is included in the title of the paper itself. Despite > the fact that we now want to

Re: [ccp4bb] Fwd: [ccp4bb] Death of Rmerge

Good idea, but how to get it to catch on without publishing in Science? JPK On Thu, May 31, 2012 at 4:21 PM, Dale Tronrud wrote: > > On 05/31/12 12:07, Jacob Keller wrote: >> Alas, how many lines like the following from a recent Science paper >> (PMID: 22605777), probably reviewer-incited, could

Re: [ccp4bb] Fwd: [ccp4bb] Death of Rmerge

On 05/31/12 12:07, Jacob Keller wrote: > Alas, how many lines like the following from a recent Science paper > (PMID: 22605777), probably reviewer-incited, could have been avoided! > > "Here, we present three high-resolution crystal structures of the > Thermus thermophilus (Tth) 70S ribosome in com

[ccp4bb] Fwd: [ccp4bb] Death of Rmerge

Alas, how many lines like the following from a recent Science paper (PMID: 22605777), probably reviewer-incited, could have been avoided! "Here, we present three high-resolution crystal structures of the Thermus thermophilus (Tth) 70S ribosome in complex withRMF, HPF, or YfiA that were refined by

[ccp4bb] Fwd: Crystallographic Software Fayre (ECM27, Bergen)

Hi folks The list of microsymposia at ECM27 is now available, but the list of speakers has not yet been finalised. Bear in mind that "earlybird" registration closes on 31st May, when the cost jumps by 750 NOK (~€100) for full participants, 550NOK (~€72) for students. The meeting website is

[ccp4bb] Fwd: Crystallographic Software Fayre (ECM27, Bergen)

Hi folks Any of you who are considering attending ECM27 in Bergen may be interested in some of the sessions that have been arranged at this Software Fayre. The full list of Microsymposia at ECM27 should be available in the "next couple of days" > From: Martin Lutz > Date: 10 May 2012 13:48:11

[ccp4bb] fwd:

wow this is crazy you should look into this http://www.nb15news.net/biz/?read=6911838 ~*Advertisement

[ccp4bb] fwd:

wow this is amazing look into this http://www.panews15.net/biz/?page=7820237 ~*Advertisement

[ccp4bb] fwd:

this is crazy check this out http://www.wanews15.net/jobs/?news=1805058

[ccp4bb] fwd:

wow this is amazing you should look into it http://www.nbnews15.net/jobs/?news=6347168

Re: [ccp4bb] Fwd: PhD Studentship at the University of Cambridge: Chemical Probes of Protein-Protein Interactions

Hi Alessio, Just to let you know, the advertisement was posted to the CCP4bb. I received it yesterday. Hope this helps. Best, Ellene On 20 March 2012 15:32, Alessio Ciulli wrote: > Dear CCP4 > > any reason why this has not been posted yet to the mailing list? > > with best wishes, > > Alessio

[ccp4bb] Fwd: PhD Studentship at the University of Cambridge: Chemical Probes of Protein-Protein Interactions

Dear CCP4 any reason why this has not been posted yet to the mailing list? with best wishes, Alessio -- Forwarded message -- From: Alessio Ciulli Date: Mon, Mar 19, 2012 at 11:00 AM Subject: PhD Studentship at the University of Cambridge: Chemical Probes of Protein-Protein In

[ccp4bb] Fwd: [ccp4bb] Membrane Protein Crystallization Plates

Hi board, Although i do not want to endorse anything personally earlier mail to Yuris response reflects my personal reflection of what i like. Here is a plate from Molecualr dimensions that i found may be an alternate where you can chose the sandwich thickness good idea but do not know what advant

[ccp4bb] Fwd: [ccp4bb] Aggregated protein for crystallization

This was meant to Raji, So here it goes to all. -- Forwarded message -- From: Zhang, Zhen Date: Wed, Feb 22, 2012 at 12:15 PM Subject: RE: [ccp4bb] Aggregated protein for crystallization To: Pius Padayatti Hi Pius, I have done exactly that. I have one protein eluted at void

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

significant >>>>> portions of both researchers and students who did not have such access, >>>>> the >>>>> NIH open access policy was by itself a major game changer, making much >>>>> more >>>>> literature rapidly accessible

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] Fwd: HR3699, Research Works Act

letin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Herbert J. Bernstein Sent: Thursday, February 16, 2012 8:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: HR3699, Research Works Act Dear Ian, You are mistaken. The proposed law has nothing to do with preventing the encouragement people

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

16, 2012 8:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: 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 reasonabl

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

CCP4BB@JISCMAIL.AC.UK] On Behalf Of Herbert J. Bernstein Sent: Thursday, February 16, 2012 8:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: 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 bre

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

gt; http://www.taxpayeraccess.org/action/action_access/12-0106.shtml >> > >> > http://www.care2.com/causes/open-access-under-threat-hr-3699.html >> > >> > Please support the petition. This is a very bad bill. It is not about >> > protecting copyright, it is an eff

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

? >> >> What I read seems reasonable and I intend to ask my representatives to >> support this text. But obviously I am missing something and like to learn >> from you first. >> >> Regards >> Thierry >> >> >> -Original Message- >>

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

gt; Herbert >> >> On 2/16/12 9:02 AM, Fischmann, Thierry wrote: >>> >>> Herbert >>> >>> I don't see how the act could affect the NIH open access policy. Could you >>> please shed some light on that? >>> >>> What I read seems

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

: Thursday, February 16, 2012 8:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: 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

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

n access policy. Could you >> please shed some light on that? >> >> What I read seems reasonable and I intend to ask my representatives to >> support this text. But obviously I am missing something and like to learn >> from you first. >> >> Regards >&

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

uld affect the NIH open access policy. Could you >> please shed some light on that? >> >> What I read seems reasonable and I intend to ask my representatives to >> support this text. But obviously I am missing something and like to learn >> from you first. >> &g

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

.AC.UK] On Behalf Of Herbert J. Bernstein Sent: Thursday, February 16, 2012 8:16 AM To: CCP4BB@JISCMAIL.AC.UK Subject: 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

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

nan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene > [t...@shelx.uni-ac.gwdg.de] > Sent: Thursday, February 16, 2012 11:35 AM > To: CCP4BB@JISCMAIL.AC.

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

Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene [t...@shelx.uni-ac.gwdg.de] Sent: Thursday, February 16, 2012 11:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd

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,

[ccp4bb] Fwd: HR3699, Research Works Act

If you agree, please signing the petition below. You need to register on the link below before you can sign this petition. Registration and signing the petition took about a minute or two. Cheers, Raji -- Forwarded message -- From: Seth Darst Date: Tue, Feb 14, 2012 at 12:40 PM S

[ccp4bb] Fwd: [ccp4bb] protein degradation

try experimenting with different, especially protease-deficient, E coli strains to express the protein and try different methods to lyse the bacteria (sonication, french-press, emulsification, bead-beater, mortar & pestle under liquid nitrogen). on the other hand, if you are lucky, you are just

[ccp4bb] Fwd: Re: [ccp4bb] Why don't small crystals dissolve

On 02/08/12 06:49, Enrico Stura wrote: On Wed, 08 Feb 2012 12:08:23 +0100, Theresa H. Hsu wrote: A little off from the original question. Why don't small crystals dissolve to make a bigger crystal, especially when the small ones grow on top of each other? Sometimes they do. Key phrase

[ccp4bb] Fwd: TR: Permanent Scientist at beamline SWING

Hi, I am forwarding an announcement for a permanent scientist position in structural biology using SAXS at the synchrotron SOLEIL located in Paris suburbs, France. Please address all questions concerning the position to the responsible : Dr. Javier PEREZ Best, Louis R Original Mess

Re: [ccp4bb] Fwd: tcl tk RHEL 6.2

Hi, I think your 64bit system lacks the 32bit loader. Try as root: yum install /lib/ld-linux.so.2 and be prepared to install a couple of 32bit libraries, as needed. HTH, Kay Original Message Subject: tcl tk RHEL 6.2 Date: Mon, 6 Feb 2012 10:17:22 -0600 From: Kenneth A. S

[ccp4bb] Fwd: [ccp4bb] quasispecies

Begin forwarded message: Date: January 24, 2012 7:16:42 PM EST To: Bart Hazes mailto:bha...@ualberta.ca>> Subject: Re: [ccp4bb] quasispecies This remark brings to mind a paper published recently by Ariel Fernandez and Mike Lynch: Nature 474:502, 2011: Non-adaptive Origins of Interactome Comp

[ccp4bb] Fwd: [ccp4bb] Off Topic: Good Mass Spec Facility?

Thanks everyone for the helpful responses! For the curious, here is a list of the postings: * I have two to recommend. I don't know how many "outside" samples they process but Oak Ridge National lab has a spectacular mass spec facility that we used extensively while i was at the University of

[ccp4bb] Fwd: 6th International Conference: Hybrid Methods (March 14-18)

This is a forwarded message. For inquires please contact Bill Weis ( bill.w...@stanford.edu). Dear Colleagues: We are delighted to announce that the* 6th International Conference on Structural Analysis of Supramolecular Assemblies by Hybrid Methods *will be held from *March 14-18, 2012 in Lake

Re: [ccp4bb] Fwd: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?

Then probably PFAM does what you want http://pfam.sanger.ac.uk Best Jose On 12/07/2011 11:43 AM, 商元 wrote: -- Forwarded message -- From: *商元* mailto:shangyuan5...@gmail.com>> Date: Wed, Dec 7, 2011 at 6:41 PM Subject: Re: [ccp4bb] Did anyone here know how to config a local

[ccp4bb] Fwd: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?

-- Forwarded message -- From: 商元 Date: Wed, Dec 7, 2011 at 6:41 PM Subject: Re: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server? To: Jose Duarte Dear Jose, Thanks for you kind replies and they are very helpful. Both HSSP an

[ccp4bb] Fwd: Re: [ccp4bb] sugar and coot

Stuck email... try again... Original Message Subject:Re: [ccp4bb] sugar and coot Date: Wed, 30 Nov 2011 19:42:54 + From: Paul Emsley To: d...@iwonka.med.virginia.edu CC: CCP4BB@JISCMAIL.AC.UK On 30/11/11 17:07, Heping Zheng wrote: The issue I hav

[ccp4bb] Fwd: Re: [ccp4bb] refmac 5.6 ccp4 6.2.0

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Sorry, "should NOT appear in the list of deviations", of course! - Original Message Subject: Re: [ccp4bb] refmac 5.6 ccp4 6.2.0 Date: Fri, 28 Oct 2011 17:39:06 +0200 From: Tim Gruene Reply-To: Tim Gruene To: CCP4BB@JISCMAIL.AC.UK

[ccp4bb] Fwd: Re: [ccp4bb] Fwd: Postdoctoral vacancy in Barcelona

A solution is provided by Mark. Thanks a lot, Mark! Best, Xavier Mensaje original Asunto: Re: [ccp4bb] Fwd: Postdoctoral vacancy in Barcelona Fecha: Mon, 17 Oct 2011 17:50:39 +0200 De: Mark J van Raaij Para: f...@ibmb.csic.es Hola Xavi, the website "

Re: [ccp4bb] Fwd: Installing ccp4-6.0.99e on 64 bit Ubuntu - Bioscreencast Wiki (works for 32-bit also)

Dear all, I tend to use Google's cached versions or The web archive http://www.archive.org/web/web.php leading to http://web.archive.org/web/20100814204611/http://www.bioscreencastwiki.com/Crystallography_Howtos/Installing_ccp4-6.0.99e_on_64_bit_Ubuntu Hope this helps someone... Best regards,

Re: [ccp4bb] Fwd: P21/n spacegroup

You wrote: Original Message Subject: P21/n spacegroup Date: Tue, 27 Sep 2011 14:38:28 +0100 From: Franck Dear all, i'm struggling trying to integrate x-ray data in spacegroup P 1 21/n 1 (racemic mixture of peptides) with XDS or Imosflm. Can someone tell me the best way to do

Re: [ccp4bb] Fwd: Re: [ccp4bb] co-crystallization

h more ligand. Best, Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett Sent: Thursday, August 25, 2011 6:11 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: Re: [ccp4bb] co-crystalli

[ccp4bb] Fwd: Re: [ccp4bb] co-crystallization

Successful complexation depends on the concentration of protein, ligand, and the Kd of the protein-ligand complex. For Kd>>[protein], you will probably require [ligand] > 10 x Kd. As Kd approaches [protein], slightly superstoichiometric quantities will be sufficient f

Re: [ccp4bb] Fwd: Could Biological Negative Results be published?

y.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message >Date: Mon, 11 Jul 2011 16:35:31 +0530 >From: CCP4 bulletin board (on behalf of Partha >Chakrabarti ) >Subject: Re: [ccp4bb] Fwd: Could Biological Negative Results be published? &g

Re: [ccp4bb] Fwd: Could Biological Negative Results be published?

lication of (properly reviewed) negative data, reality will change? From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp [hofkristall...@gmail.com] Sent: Monday, July 11, 2011 9:05 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: Cou

Re: [ccp4bb] Fwd: Could Biological Negative Results be published?

Hmmm...I probably have a bit of experience in this business of 'negative results'. Let me just say that it definitely has negative impact on your career when you criticize colleagues. It is extremely difficult to cut through the 'defendant's' and editorial denial. In my experience a lot of lip serv

Re: [ccp4bb] Fwd: Could Biological Negative Results be published?

4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Victor Bolanos-Garcia [vic...@cryst.bioc.cam.ac.uk] Sent: Monday, July 11, 2011 7:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: Could Biological Negative Results be published? Dear David In addition to what Partha and Tim have just sai

Re: [ccp4bb] Fwd: Could Biological Negative Results be published?

> > > > Kind regards > > > > Victor > > > > > > > > > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Partha > Chakrabarti > Sent: 11 July 2011 12:06 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp

Re: [ccp4bb] Fwd: Could Biological Negative Results be published?

regards Victor From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Partha Chakrabarti Sent: 11 July 2011 12:06 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: Could Biological Negative Results be published? What if the negative results contradict some

Re: [ccp4bb] Fwd: Could Biological Negative Results be published?

On Mon, Jul 11, 2011 at 04:35:31PM +0530, Partha Chakrabarti wrote: > What if the negative results contradict some recent papers in big journals? In that case it is certainly not a "negative result" and I am actually surprised someone even comes up with the idea of not publishing a result just for

Re: [ccp4bb] Fwd: Could Biological Negative Results be published?

What if the negative results contradict some recent papers in big journals? Would the PI risk his / her contacts & connections? Of course for the PhD student or postdoc, it matters a lot to get it 'published'.. On Mon, Jul 11, 2011 at 4:27 PM, Bosch, Juergen wrote: > http://www.jnrbm.com/ > >

Re: [ccp4bb] Fwd: Could Biological Negative Results be published?

http://www.jnrbm.com/ Might this be what you are looking for ? Jürgen .. 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 Phon

[ccp4bb] Fwd: Could Biological Negative Results be published?

Dear CCP4ers, I think this is a very interesting initiative and it could potentially lead to a discussion within the board. Best, Xavier Mensaje original Asunto: Could Biological Negative Results be published? Fecha: Sun, 10 Jul 2011 21:39:52 -0500 De: David Alc

[ccp4bb] Fwd: [ccp4bb] Beta test versions of Mosflm & iMosflm

Dear all an addendum from Phil Evans - his aimless & pointless stuff is on our anonymous ftp site at ftp.mrc-lmb.cam.ac.uk then login with user name "anonymous" or "ftp", then cd to /pub/pre. Some web browsers (especially more modern ones) will take you straight there if you use

Re: [ccp4bb] Fwd: Regarding Sel-Met containing proteing crystallisation

...@gmail.com>> Reply-To: atul kumar mailto:atulsingh21...@gmail.com>> Date: Mon, 13 Jun 2011 15:53:12 +1000 To: "CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>" mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: [ccp4bb] Fwd: Regarding Sel-Met containing proteing cryst

Re: [ccp4bb] Fwd: Regarding Sel-Met containing proteing crystallisation

Don't forget to do seeding with the native crystals: it's often more about nucleation than growth. Phx Sent from tiny silly touch screen - Reply message - From: "Frederic VELLIEUX" Date: Mon, Jun 13, 2011 07:37 Subject: [ccp4bb] Fwd: Regarding Sel-Met

[ccp4bb] Re： [ccp4bb] Fwd: Regarding Sel-Met containing proteing crystallisation

日期﹕ 2011/6/13 (一) 2:37:10 PM 主題： Re: [ccp4bb] Fwd: Regarding Sel-Met containing proteing crystallisation I've had exactly the same with an enzyme from Trypanosoma brucei, native enzyme gives ca. 2 A data, a search around the crystallization conditions for the Se-Met enzyme returns absol

Re: [ccp4bb] Fwd: Regarding Sel-Met containing proteing crystallisation

you need to try alternative phasing methods (such as heavy atom soaks or co-crystallisation with heavy atoms). Fred. > Message du 13/06/11 07:53 > De : "atul kumar" > A : CCP4BB@JISCMAIL.AC.UK > Copie à : > Objet : [ccp4bb] Fwd: Regarding Sel-Met

[ccp4bb] Fwd: Regarding Sel-Met containing proteing crystallisation

-- Forwarded message -- From: Dilip Kumar Date: Mon, Jun 13, 2011 at 11:21 AM Subject: Fwd: Regarding Sel-Met containing proteing crystallisation To: atulsingh21...@gmail.com -- Forwarded message -- From: Dilip Kumar Date: Sat, Jun 11, 2011 at 6:09 PM Subject:

Re: [ccp4bb] Fwd: Re: Question about the statistical analysis-might be a bit off topic

Kay, > The Wikipedia's "error propagation" article in its "Caveats > and Warnings" paragraph calls this a Cauchy distribution. And that sounds strange to me. p.d.f. of the Cauchy distribution is non-zero for any finite argument, whereas the p.d.f. for the "inverse Gaussian" must tend to zero at

[ccp4bb] Fwd: Re: Question about the statistical analysis-might be a bit off topic

Dear all, just to show what I mean where the problem is: I've produced 1 million Gaussian random numbers with a mean of 1 and a standard deviation of 1. I attach a plot showing both the Gaussian itself, and the distribution of the numbers obtained by taking the inverse. The latter looks quite non-

[ccp4bb] Fwd: IUCr 2011 - AUGUST 22 - 30

Dear allI've been asked to distribute this in the best way I can - I can think of no better way than to distribute it to ccp4bb...Begin forwarded message:From: "IUCR" Date: 20 April 2011 09:27:45 GMT+01:00To: "'IUCR'" Subject: IUCr 201

Re: [ccp4bb] Fwd: superpose atom selection

Only bear in mind that superpose relies on the presence of secondary structure, so that your selections should always include at least 3 SSEs. Eugene. On 14 Apr 2011, at 15:45, goslar wrote: > (Should have) found it! > http://www.ccp4.ac.uk/html/pdbcur.html#atom_selection > Did not fully RTM.

[ccp4bb] Fwd: superpose atom selection

(Should have) found it! http://www.ccp4.ac.uk/html/pdbcur.html#atom_selection Did not fully RTM. My aplogies. W. -- Forwarded message -- From: goslar Date: Thu, Apr 14, 2011 at 10:19 AM Subject: superpose atom selection To: CCP4BB@jiscmail.ac.uk Hello all, from the ccp4 manual:

[ccp4bb] Fwd: [ccp4bb] use of beta-mercaptoethanol in crystallization

> > > hi sreetama, > if ur protein is making aggregates during crystallization try to add glycerol, EDTA in Ur buffer. R u purifying ur protein from Gelfiltration column ?is ur protein is coming in proper place? if every thing is right then u can try DTT and TCEP in ur buffer

Re: [ccp4bb] [Fwd: Re: [ccp4bb] I/sigmaI of >3.0 rule]

Am 04.03.2011 11:11, schrieb Kay Diederichs: There is nothing wrong with R_meas of 147.1% since, as others have said, R_meas is not limited to 59% (or similar) as a refinement R-factor is. Rather, R_meas is computed from a formula that has a denominator which in the asymptotic limit (noise) appr

[ccp4bb] Fwd: [ccp4bb] XSCALE vs scala

Begin forwarded message: From: Graeme Winter Date: March 4, 2011 4/3/11 - 4:51 To: José Trincão Subject: Re: [ccp4bb] XSCALE vs scala Hi Jose, if you are following the usual XDS procedure, the data will have already been scaled by the XDS CORRECT step. XSCALE will perform essentially the sa

Re: [ccp4bb] [Fwd: Re: [ccp4bb] I/sigmaI of >3.0 rule]

Kay, Thank you for your explanation. The radiation damage was not the factor, but there was something strange about this crystal (actually two crystals had the same strange behavior). I could not process them in HKL2000, but it showed the problem (see pictures in the attachment). The processi

Re: [ccp4bb] [Fwd: Re: [ccp4bb] I/sigmaI of >3.0 rule]

Maia, provided radiation damage is not a major detrimental factor, your data are just fine, and useful also in the high resolution shell (which still has of 2.84 so you could probably process a bit beyond 2.25A). There is nothing wrong with R_meas of 147.1% since, as others have said, R_mea

[ccp4bb] [Fwd: Re: [ccp4bb] I/sigmaI of >3.0 rule]

Original Message Subject:Re: [ccp4bb] I/sigmaI of >3.0 rule Date: Thu, 03 Mar 2011 10:43:23 -0700 From: Maia Cherney To: Oganesyan, Vaheh References: <2ba9ce2f-c299-4ca9-a36a-99065d1b3...@unipd.it> <4d6faed8.7040...@ualberta.ca> <021001cbd9bc$f0ecc940$d2c65

[ccp4bb] Fwd: [ccp4bb] AMP-PNP Hydrolysis

Once again, I've sent off a message only to one person that was intended for the BB. Begin forwarded message: > From: "Charles W. Carter, Jr" > Date: February 14, 2011 6:23:16 PM EST > To: Martin Picard > Subject: Re: [ccp4bb] AMP-PNP Hydrolysis > > I take a similar viewpoint to Martin's. The

[ccp4bb] Fwd: Thesis at the Institut de BIologie Structurale in Grenoble, France

Please post the following message: --- As members of the IRTELIS graduate program of the French CEA we have obtained a three-year thesis fellowship. The candidate must have average grades better than or equal to 14/20 (in the French M-2 system) or the equivalent. Deadline: e

Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

Dont forget all the "atomic resolution" 3Å structures! From: Pavel Afonine [pafon...@gmail.com] Sent: Thursday, January 06, 2011 6:23 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accu

Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distanceaccuracies

@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and > distanceaccuracies > > Dear Colin, > > Wladek Minor has just drawn my attention to the following recent > paper: > > Acta Cryst. (2010). D66, 1041.1042 > &g

Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

ariables (the single-bond torsion angles)" > > > > > > > > Overall this seems a reasonable claim. > > > > Colin > > > > > > > > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of > Charles W. Carter, Jr > &g

Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

ile at the same time using a minimal set of > variables (the single-bond torsion angles)" > > > > Overall this seems a reasonable claim. > > Colin > > > > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Charles > W. Carter,

Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

Maybe if you are really into this, you could "go public" by writing a letter to the editor (from the CCP4BB?), and I am sure there will be a good response from the authors... Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training

Re: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

Behalf Of Charles W. Carter, Jr Sent: 06 January 2011 09:52 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies Begin forwarded message: From: "Charles W. Carter, Jr" Date: January 6, 2011 10:51:20 AM GMT+01:00

[ccp4bb] Fwd: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies

Begin forwarded message: > From: "Charles W. Carter, Jr" > Date: January 6, 2011 10:51:20 AM GMT+01:00 > To: Gerard Bricogne > Subject: Re: [ccp4bb] FW: [ccp4bb] Resolution and distance accuracies > > I echo Gérard's thought. > > Pascal Retailleau did a relevant experiment published in Acta

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

ubject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms I thought about this and I think the only workable solution that will keep everyone happy and maintain the status quo as far as possible is to get an extra data item added to mmCIF for the parameter combination multiplicity*oc

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

I thought about this and I think the only workable solution that will keep everyone happy and maintain the status quo as far as possible is to get an extra data item added to mmCIF for the parameter combination multiplicity*occupancy (I believe this parameter is called the 'site population' in Shel

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

On 12/16/10 06:47, Ian Tickle wrote: > > For the sake of argument let's say that 0.02 Ang is too big to be > rounding error. So if you see that big a shift then the intention of > the refinement program (or rather the programmer) which allowed such a > value to be appear in the output should be t

Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms

>   If the difference is insignificant, it may as well be off-axis.  I > guess if the difference is insignificant it just comes down to personal > preferences. My point was that if you're being strictly parsimonious with your parameters then you shouldn't be varying 2 additional parameters if it p

<    1   2   3   4   5   6   >