Re: [ccp4bb] journals with on-hold policy

If the work is funded by the NIH, you must deposit and release coordinates upon publication regardless of the journal's policy. http://grants.nih.gov/grants/guide/notice-files/not99-010.html Joe Becker Merck Research Labs -Original Message- From: CCP4 bulletin board [mailto:[EMAIL

[ccp4bb] EMBO Workshop on THE CHEMISTRY AND BIOCHEMISTRY OF CATALYSIS BY BIOLOGICAL SYSTEMS - 20 - 22 June 2007, EMBL Hamburg

Registration is now open for the EMBO Workshop on THE CHEMISTRY AND BIOCHEMISTRY OF CATALYSIS BY BIOLOGICAL SYSTEMS 20 - 22 June 2007, EMBL Hamburg http://www.embl-hamburg.de/workshops/2007/catalysis/ Registration deadline: 31st March 2007 Workshop aims: With the continuously emerging

Re: [ccp4bb] journals with on-hold policy

If you publish the paper a year from now, with no hold, will everyone be happy? -Original Message- From: CCP4 bulletin board on behalf of [EMAIL PROTECTED] Sent: Fri 2/16/2007 6:54 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] journals with on-hold policy Dear CCP4ers, This is a new

[ccp4bb] FW: scaling question

Hello: I am posting this question on behalf of my colleague. Thanks, Madhavi -Original Message- From: Romano, Keith Sent: Friday, February 16, 2007 10:43 AM To: Nalam, Madhavi Subject: FW: scaling question I am in the process of scaling synchrotron data with scalepack, and I am

Re: [ccp4bb] journals with on-hold policy

I think Martha Stewart's magazine has fairly liberal data deposition policies as well. _ Eric A. Toth, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology Marlene and Stewart Greenebaum Cancer Center University of Maryland

Re: [ccp4bb] pseudotranslation and dyads in NCS

To understand this one at least needs the P1 unit cell.. Operators 3 4 and 5 are almost the same rotation.. It is unlikely that they are all 2 folds? Eleanor Daniel Adams wrote: Hi bb, I am working on P1 dataset, SAD phasing resolution is 3.5 and trying to build model. However I am facing

[ccp4bb] on-hold policy - reasons why

Cheers, Many thanks to all of you who sent in the (mostly positive) helpful replies. A lot of folks asked why do we have to place the structure on hold - since this is a pretty typical example of how industrial crystallographers have to operate sometimes, I will attempt to explain. We have a

Re: [ccp4bb] Rfactor does not drop

Hey Emmanuel Typical R-factor for random structure will be above 57% and for initial MR model it will be somewhere between 40-50%. In your case, High R-factor might be due to many reasons. So check the data for any twining and also again check the Space group. Because sometime you will end up

[ccp4bb] crytstallographic software

Dear colleagues, I was wondering whether someone of you has reported/published new or improved crystallographic software somewhere else than Acta Cryst. It would be nice if you could share your experience with me. Topics might be: - quality of the journal - rapid publication - literate peers -

Re: [ccp4bb] Rfactor does not drop

Hi, I dare say with an R-factor of 0.64, your MR solution is simply wrong. Just into the blue, you could 1) try various MR-programs (phaser, molrep, amore...) 2) try a different search model 3) try your best model but start with subdomains or chop off possibly flexible parts 4) have a look

Re: [ccp4bb] Rfactor does not drop

Just an aside to this - I have had R factors 55% which then refine.. It is when they dont refine you are in trouble .. Eleanor Jiamu Du wrote: *Dear Prata:* First, I think you'd better check your subgroups. Maybe you got opposite hand of the data. Or change a model. When the Rfactor is

[ccp4bb] Advice on img proc software

Dear All: I am trying to make FFTs of images of assemblies of spheres and other shapes to explain diffraction, the usual thing. So far I do this through cumbersome cludges, and I bet there are better ways, and I am looking for free or cheap software to do this. I load the image into basic

Re: [ccp4bb] Advice on img proc software

Hi, You may want to have a look at ShaFFT: http://www.ibg.uu.se/static/exjobb/00/5.pdf (the undergraduate project write-up) You can download the program from ftp://xray.bmc.uu.se/pub/alwyn (file is shafft_export.tar) Cheers, Martin On Feb 19, 2007, at 4:35 AM, Bernhard Rupp wrote:

[ccp4bb] Fwd: [ccp4bb] pseudotranslation and dyads in NCS

-- Forwarded message -- From: Daniel Adams [EMAIL PROTECTED] Date: Feb 16, 2007 12:29 PM Subject: Re: [ccp4bb] pseudotranslation and dyads in NCS To: [EMAIL PROTECTED] My apology for not mentioning unit cell, The P1 unit cell is 74 91 116 109 105 90 Any suggestions or comments

Re: [ccp4bb] Advice on img proc software

Bernhard, I've used Matlab to calculate 2D FTs (eg, a Cowtan-esque FT of a cat). I'm sure you could come up with a way to do the phase coloring without too much sweat--the degree of flexibility available to you in this program is quite large. My university has a campus- wide license

[ccp4bb] ATP binding

Hello, This is another off-topic question. We are trying to purify a putative ATP-binding protein. What kind of beads or column would work best in this situation? Jena Biosciences sells a kit of four different ATP-Sepharose beads with different attachment points of the ATP to the solid

Re: [ccp4bb] Advice on img proc software

The mathcad image processing module is too expensive for my taste. My university has a campus- wide license for Matlab, so it's *free* for me... I have no idea of what it would cost to purchase. [reminder: never compare educational licensing with giving drugs to schoolchildren.] For

Re: [ccp4bb] crytstallographic software

As co-editor of J Appl Cryst, handling teaching/education and computer software mainly, J Appl Cryst is the appropriate journal in the IUCr series for publishing new software, improved software, tutorials, etc. We would strongly encourage you to submit such manuscripts to J Appl Cryst, both

Re: [ccp4bb] Rfactor does not drop

Hi Emmanuel, try MZ protocol (MZ = multi-zone) in phenix.refine. It does the smart rigid body refinement starting from a few low resolution reflections and ending up with using all data. In-between it does the maximum-likelihood bulk-solvent modeling and scaling. All together it results in a

Re: [ccp4bb] axis of unit cell change

Hi, Sam, I think you have the same crystal form as that which was reported. The screw axes are not assigned when you index and integrate your data. HKL2000 will assign the unit cell edges from shortest to longest for a, b, and c. You'll assign the screw axes when you scale the data. It

Re: [ccp4bb] crytstallographic software

Kevin Cowtan wrote: Acta D has for some reason a rather poor impact rating, and J. Appl. Cryst. a rather better one. There is no outlier rejection in the calculations for journal citation reports (eg: impact factors). Congratulations to: Spek AL, Single-crystal structure validation with

Re: [ccp4bb] axis of unit cell change

Hi, The point is to check where you have the non helicoidal 2fold axis (no extinction). I guess, it will be the 2-fold axis along your a parameter. Then, you have to reindex, because the convention is to choose the 2 fold axis along c. Goood luck, Claudine U Sam wrote: Hi I crystallized a

[ccp4bb] In CCP4, How to perform anneal?

Dear All: Only by using CCP4, how to perform anneal refinement ? Thanks -- Jiamu Du Key Laboratory of Proteomics Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS)