Re: [ccp4bb] PCB buffer and MMT buffer

Hi Jenny (and others), The buffer systems used in the PACT screen are described in the following paper by Janet Newman. /Acta Cryst./ (2004). D*60*, 610-612[ doi:10.1107/S0907444903029640 ] Novel buffer systems for macromolecular crystallizat

[ccp4bb] Post-Doctoral Position

dear BBers unfortunately, i have posted this ad a couple of times before. please contact pete about this position if you are interested. his email is [EMAIL PROTECTED] rick* * *Post-Doctoral Position in Single Particle Analysis.* We are looking for a suitably qualified candidate to fill

Re: [ccp4bb] PCB buffer and MMT buffer

Hi, These buffers are available from Molecular Dimensions Ltd. and Jena Biosciences. Regards Lesley -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of Jenny Sent: 30 January 2007 04:20 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] PCB buffer and MMT buffer Hi,

Re: [ccp4bb] First 96 wells plate

Hi, Its been a while since this was posted, but I was going through the "old" entries to see if I missed anything... See http://www.microplate.org/history/det_hist.htm Flip _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Wednesday, January

[ccp4bb] problem with anisotropic refinement using refmac

Hallo to all out there, I have a problem refining a structure against a 1.33 A resolution data set. Using REFMAC (version 5.2.0019, also tested version 5.3) with isotropic B-factor refinement resulted in an valid model with R / R(free) of 17.8 / 19.2%. To finish the model I tried to use anis

[ccp4bb] Drug Discovery Workshops in Oxford

We are holding an eCheminfo Drug Discovery Workshop week at the Chemical Research Laboratory, Oxford University the week of 25-29 June 2007.  The approach will be hands-on using an IT classroom and a set of workshops led by application scientists using leading drug discovery software packages. Each

[ccp4bb] peptide crystallization

Dear all, Can u suggest me about the peptide crystallization,some references.Should I try it with PEG or MPD.It is 10-15 residues long.Thanx in advance. S...

[ccp4bb] crystal

Dear all Sorry for unrelated query.I have crystallized a protein which is at 40% of MPD.But the problem is that I get several crystals but these are small.Thecrystals diffract upto 3A.I welcome any suggestion to make the crystals big enough to diffract at high resolution.What additives I can add??

Re: [ccp4bb] peptide crystallization

There was a brief discussion of this on the board last year. See: http://www.dl.ac.uk/list-archive-public/ccp4bb/msg18757.html Good luck kmj shivesh kumar wrote: Dear all, Can u suggest me about the peptide crystallization,some references.Should I try it with PEG or MPD.It is 10-15 residues

Re: [ccp4bb] problem with anisotropic refinement using refmac

>Hello Georg, Some of the atoms in your model are ending up with a negative value of U, hence the warning. You might want to look at any disorder associated with these atoms and refine their occupancies. If that doesnt help try tightening the restraints that you are using for refinement. They might

Re: [ccp4bb] problem with anisotropic refinement using refmac - Sacrosanct R-free

"...They might also get rectified when you use all of your data for refinement, meaning when you are not using any R free..." Sorry to go off on a little tangent here - but doesn't refining against ALL of your data generally mean that your RFree is no longer your "free" and cannot be used for c

Re: [ccp4bb] problem with anisotropic refinement using refmac - Sacrosanct R-free

I believe the recommended procedure is to refine against all data before submission, using the same set of parameters and weights as for the last refinement against the working set alone, after all why throw away 5% (or even 10% in some cases) of your hard-won data? The purpose of Rfree is 1) to c

Re: [ccp4bb] problem with anisotropic refinement using refmac - Sacrosanct R-free

Ian is right and, using the same logic, the most appropriate solution appears to be to use the Sigmaa estimates from the last refmac run (based on the free reflections). I thought there was a way to read these in from the MTZ but can't find it in the manual. If I understand it correctly, Sigmaa

Re: [ccp4bb] problem with anisotropic refinement using refmac - Sacrosanct R-free

>> "...They might >> also get rectified when you use all of your data for refinement, meaning >> when you are not using any R free..." >> >> > Sorry to go off on a little tangent here - but doesn't refining against > ALL > of your data generally mean that your RFree is no longer your "free" and > c

Re: [ccp4bb] ccp4bb on new site

On 21 Jan, Mario A. Bianchet wrote: > Agreed. include [ccp4bb] on the subject. I have no way to set to the > return-path, etc... in my mail-reader only "subject, sender, date, > to, cc, etc..." Procmail gives total flexibility in sorting and filtering email using a syntax that is reminisce

Re: [ccp4bb] problem with anisotropic refinement using refmac - Sacrosanct R-free

After reading Ian's message and the first followups: I think it's really important to keep the free-R set through the initial anisotropic refinements, especially at resolutions 1.3 - 1.5 A where anisotropic refinement may or may not be warranted. I've seen several instances where R dropped

Re: [ccp4bb] problem with anisotropic refinement using refmac

On Tuesday 30 January 2007 04:11, Georg Zocher wrote: > I have a problem refining a structure against a 1.33 A resolution data > [snip] > To finish the model I tried to use anisotropic refinement which should > be possible/reasonable because of an observable to parameter ratio of > about 2.8. Thi

[ccp4bb] Refmac5 site?

I'm in need of the source code for Refmac5 (latest version) to recompile with an increased number of atoms. It seems the refmac site is down. Does anyone know another location of the latest source, or the status of the refmac site? --paul -- Paul Paukstelis, Ph.D. Research Associate Institute

[ccp4bb] Colour surface by sequence conservation

I'm trying to colour a molecular surface by sequence conservation...(sorry, I think I incorrectly posted this to COOTBB the other day) I've figured out how to do it in GRASP - modify the B-factor column in the PDB file to represent the percentage conservation and then colour the surface by B-facto

Re: [ccp4bb] Refmac5 site?

Yes, I believe York were going to be off-line for a couple of days following some computer problems. The Refmac 5.3 source code is also available from our pre-release page: http://www.ccp4.ac.uk/prerelease_page.php As it happens, I updated it on Monday, so it is up-to-date. Cheers Martyn -O

Re: [ccp4bb] Colour surface by sequence conservation

It may be easier if you try the Consurf server (http://consurf.tau.ac.il). Best regards, Dante Neculai The ConSurf Server -Original Message- From: CCP4 bulletin board on behalf of Iain Kerr Sent: Tue 1/30/2007 6:17 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Colour surface by seque

Re: [ccp4bb] [COOT] [ccp4bb] Colour surface by sequence conservation

Of course, should have tried that BUT, it appears PROTSKIN has problems everytime it encounters a gap. It now complains about res. 296 in the same fashion (287-295 are missing from the coordinates) There must be a way around this...I could split all the different parts (ie. those separated

[ccp4bb] HKL2000

Does anyone know how to manually change the unit cell in HKL 2000 (I need to ½ one cell parameter). I thought I had done it before but I can not remember how I did it. Thanks Allen Sickmier Amgen MS 14-2A 1 Amgen Center Dr. Thousand Oaks, CA 91320-1789

[ccp4bb] Met auxotroph of C43/C41 cells

Hello, Does anyone know if a Met auxotroph derivative of C43 or C41 cells is available? Alternatively, has anyone successfully used a metabolic inhibition protocol for SeMet incorporation with these cells? Thanks, Ari