Re: [ccp4bb] Definition of salt bridge

I am not sure where this was getting at, but i would just point out to you that continuum electrostatics (that you refer to) tend to overestimate the "desolvation" penalties (that is if you assume the whole protein interior has a dielectric of 2-4. while there may be other benefits for the

Re: [ccp4bb] How to improve twinning crystal in protein crystallization

You might want to try acetonitrile. annie Annie Hassell Glaxo Smithkline 5 Moore Drive RTP, NC 27709 919/483-3228 919/483-0368 (FAX) [EMAIL PROTECTED] "Heng Chiat Tai" <[EMAIL PROTECTED]> Sent by: "CCP4 bulletin board" 16-Oct-2008 16:15 Please respond to "Heng Chiat Tai" <[EMAIL PROTECT

[ccp4bb] How to improve twinning crystal in protein crystallization

Hi, I have a protein crystallized in 30% PEG8000/2000 mM NaCl/Tris pH 7.0. The crystal is not single but twinned long rod. I tried glycerol and dioxane, but it doesn't work. Try to change pH also same. Any suggestion? Any paper mention provide systematic strategy for solving this protein

Re: [ccp4bb] Definition of salt bridge

Hi Nader, By significant, I mean those interactions that withstand the normal structural fluctuations of the structure. In MD simulation, two ion-pairs at a distance of 8 A won't stay for long and will disappear early during the simulation. So, they cannot be considered as non-bonded interactions

Re: [ccp4bb] Definition of salt bridge

* Dear Francisco, 1.Transfer of a salt bridge from water to nonpolar environment costs ~10 - 16 kcal/mol (B. Honig and W. L. Hubell, 1984, PNAS 81, 5412-5416). 2.The energy penalty paid due to the desolvation of the charged residues may not be recovered by favorable interaction among the charged

Re: [ccp4bb] Definition of salt bridge

The problem lies with your definition of "significant". If it is non null, then any interaction is significant (dual-pan balance concept). Coulomb's energy is a function of 1/r^2, therefore at 8 Angs, it is still 15% of Emax. Even H-bonds are sometimes considered relevant up to 5 Angs. Nadir M

Re: [ccp4bb] Definition of salt bridge

Yes, it is electrostatic interaction. But when searching for a salt-bridge in a protein structure it won't be considered a significant non-bonded interactions at 8 A distance. Also, the electrostatic interaction extends beyond 8 A. For a significant interaction the distance need to be < 8A. Ibra

Re: [ccp4bb] Definition of salt bridge

-- Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM U-724 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: [EMAIL PROTECTED]

Re: [ccp4bb] Definition of salt bridge

Hi, You can find more information about salt-bridges in the following references: 1) Ion-pairs in Proteins. JMB, 168, 867-885 (1983) - Thornton 2) Investigation of Salt Bridge Stability in a Generalized Born solvent model. JCTC, 2, 115-127 (2006) - Carlos Simmerling 3) Evaluation of Salt Bri

[ccp4bb] Turbo in stereo

Hi all, First of all, let me apoligize for this off-topic question but I would like to use Turbo in stereo to build structures but unfortunately, I am unable to do so. I have stereo for pymol, coot and O but not for Turbo, which is my favourite program at the moment. I am running Ubuntu Hardy

Re: [ccp4bb] Definition of salt bridge

Dear Fransico, *Salt bridges are close range electrostatic interaction which depend on conformer population. *S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Thu, Oct 16, 2008 at 8:21 AM, Chavas Leo <[EMAIL PROTECTED]> wrote: > Dear Franci

[ccp4bb] Scientific computing position at AstraZeneca UK

Dear all, I would like to draw your attention to a scientific computing position currently open at AstraZeneca. This is a fixed term position in the Computational Chemistry group in Alderley Park to support the high-performance computing environment as part of the system administration team. J

Re: [ccp4bb] Poor electron density - polyAla or PolyGly?

Dear Joe one thing that has helped me a lot with similar problems is G. Kleywegt's SPASM - you make your best guess of the mainchain then add a total guess of the sidechains (say with mutate in COOT - choosing the top rotamer). Then you cut out the loop and run this in SPASM as a s

Re: [ccp4bb] Twinning for P31

People dont read the CCP4 documentation on twinning! Grrr PG P3 can have 3 twinning operators; and these are: k,h,-l ( or symm equiv) - if this is a crystallographic operator the PG becomes P321 -h,-k,l (or symm equiv) - if this is a crystallographic operator the PG becomes P6 -k,-h,-l (or sy

Re: [ccp4bb] Twinning for P31

Hi, I tried to processed it as P321. It seemed that it might be right. The Rmerge increased just a little. Then I used phenix.xtriage and sfcheck to check it. The results are as following: phenix.xtriage: Twinning and intensity statistics summary (acentric data): Statistics independent of twin