Re: [ccp4bb] Two kinds of solvent-accessible-surface ?

s correspond to "reentrant" surfaces as defined by Fred Richards. Best regards, Nadir Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-964 University of Lorraine, Nancy School of Science and Technology and School of Medicine 9, Avenue de la Foret de Haye

Re: [ccp4bb] crystal structures of enzymes with catalytic mutants

Hi Dusan, I tried OCA (http://oca.weizmann.ac.il/oca-bin/ocamain) and entered the keywords: inactive enzyme substrate complex. I got five hits, including mutants (pdf here attached). Best, Nadir Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-964 Univer

Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex

. I can conclude the data is exact and correct up to the second decimal. Enjoy! Nadir Mrabet -- Pr. Nadir T. Mrabet Structural & Molecular Biochemistry Ngere - INSERM UMR 954 University of Lorraine, Nancy School of Sciences and Technology & School of Medicine 9, Aven

Re: [ccp4bb] future of MolProbity?

Hi Oliver, Thank you for bringing this issue to my (our) attention. I have already sent a support mail to David because I believe MolProbity is very useful for both research and teaching. Best regards, Nadir Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U

Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?

. Nadir Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies & 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:

Re: [ccp4bb] [Proteopedia] announcement: course on Proteopedia with JSmol

Dear Angel, Jaime and Joel, Proteopedia is great work, but I am unlucky as I won't be able to visit you at Alcalà. This makes me think it would be great to have a web seminar on the topic. Thanks, Jaime! Enjoy your meeting in Madrid and around. Best regards, Nadir Pr. Nadir T. M

Re: [ccp4bb] Guard columns from FPLC

most aggregates if not all. HTH, Nadir Mrabet Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies & School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex Fran

Re: [ccp4bb] areaimol and hydrogens

Jose, Your are most probably right. Atoms used for ASA calculations are "unified atoms" as their vdW radii incorporate light atoms (hydrogens) which, by and large, crystallographers don't see. Adding extra H atoms is likely to end up in miscalculations. Nadir Mrabet Pr.

Re: [ccp4bb] H-Bond Energy Vs. Length/Geometry/Charge?

doing that and that is a real challenge far from being trivial. Best , Nadir Mrabet Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-964 University of Lorraine, Nancy School of Science and Technology and School of Medicine 9, Avenue de la Foret de Haye 54500

Re: [ccp4bb] metal chelation

probably need several washes but it works! Also be aware that EDTA binds well to several proteins. HTH, Nadir Mrabet Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies & School of Medicine 9, Aven

Re: [ccp4bb] repulsive effects of arginine

Resonance was to be understood exactly as meaning all the bonds are averaged between both types (single and double bonds). Furthermore, fluctuations in the immediate environment will affect electron distribution with time, as proteins exist in a dynamic state. Nadir Mrabet Pr. Nadir T. Mrabet

Re: [ccp4bb] repulsive effects of arginine

all the guanidinium group so that it is not punctual as is the case for lys NZ. H-bonds also solvate charges. Are you stating that asp can in no way be entrapped between the arginines? Recall arg-asp interactions in proteins are "hot spots". Cheers, Nadir Pr. Nadir T. Mrabet

Re: [ccp4bb] repulsive effects of arginine

Yes, indeed Andrey. And this results from resonance (tautomerization) of the guanidinium group. Regards, Nadir Mrabet Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies & School of Medicine 9

Re: [ccp4bb] AW: [ccp4bb] repulsive effects of arginine

Dear Jan, Is there a possibility for bifurcated salt bridges/H-bonds where the Asp would be entrapped between the two arginines, in which case, repulsive effects would not take place ? Cheers, Nadir Mrabet Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U

[ccp4bb] Re : Re: [ccp4bb] visualizing protein-protein interface

Google 2D-GraLab. Very good at showing detailed interface contacts along protein sequences. To my knowledge, there is no way to include a non protein ligand. But the source code is available on request and if you succeed to modify the program, please let us know. HTH, Nadir Mrabet Pr

Re: [ccp4bb] Modelling Software for beta turn design

://dunbrack.fccc.edu/molide/) and do the exercise in local mode. Best of luck, Nadir Mrabet Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies & School of Medicine 9, Avenue de la Foret de Haye

Re: [ccp4bb] Hydrophobic contacts

the short-range type, unlike uniform materials and/or industry-synthesized organic molecules. Best regards, Nadir Mrabet Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies & School of Me

Re: [ccp4bb] Backbone hydrogen bonds in protein

d this is far from being trivial. Best, Nadir Mrabet Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies & School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-l

Re: [ccp4bb] Hydrophobic contacts

Sorry, a bit late here (2:00 AM) after a long day. I meant (for CH2/CH2 contacts!): Dij < 1.8 + 1.8 + 2x1.4 = 6.4 Ang. Best, Nadir Mrabet Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Techn

Re: [ccp4bb] Hydrophobic contacts

If you take R(H2O) = 1.4 Ang, then 1.8 + 1.8 + 2x1.4 = 5.0 Ang. 8 Ang is far too much for CH2/CH2! HTH, Nadir Mrabet Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies & School of Medicine

[ccp4bb] Recent IUPAC definition of the hydrogen bond

IUPAC, Publication date (Web): 8 July 2011 Defining the hydrogen bond: An account (IUPAC Technical Report)*" Thanks for your input and interest. Greetings, Nadir Mrabet -- Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School o

Re: [ccp4bb] Off Topic- Cystine Detection

y 394 (2009) 147–158. HTH, Nadir Mrabet Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 University of Lorraine, Nancy School of Sciences and Technologies & School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France

Re: [ccp4bb] DSSP and PDB secondary structure assignments

OK, but you don't specify that Promotif uses DSSP for that purpose, right? -- Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-954 Nancy University, School of Medicine 9, Avenue Foret de Haye, BP 184 F-54500 Vandoeuvre-les-Nancy (France) Tel : +33 (0)3 83 68

Re: [ccp4bb] X-PLOR

Thanks Francisco. Nicolas, thanks also for your feedback. In fact, I had already downloaded the X-PLOR manual, but I needed some more details on the H-atoms optimization procedure. That was for the purpose of a teaching work on a 1995 paper. Best regards, Nadir Pr. Nadir T. Mrabet

[ccp4bb] X-PLOR

Hi, Could someone explain to me the scientific details of the protocols used in X-PLOR to (1) build explicit hydrogen atoms onto X-ray structures and (2) optimize their positions? Many thanks in advance. Greetings, Nadir -- Pr. Nadir T. Mrabet Structural& Molecular Biochemi

Re: [ccp4bb] protein structure for high schoolers

I would suggest MolProbity along with KiNG (on Firefox!) would be most appropriate (http://kinemage.biochem.duke.edu/). HTH, Nadir Pr. Nadir T. Mrabet Structural& Molecular Biochemistry N-gere - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 5

Re: [ccp4bb] Metal won't strip from IMAC

. If you reduce the pH, say to 5.2-5.5, not only you make adsorption less stronger (hence, column capacity may drop down), but you will at the same time prevent cysteine oxidation. You can also increase [imidazole] in the equilibration buffer to reduce adsorption. HTH, Nadir Pr. Nadir T. Mrabet

Re: [ccp4bb] How to assess geometry in a model?

Along you can consider also using MolProbity online. Best, Nadir Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 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

Re: [ccp4bb] Description of a newly solved structure

I would also suggest using MolProbity to assess structure quality. Best, Nadir Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +3

[ccp4bb]

Hi, We have been receiving several spam mail from this person. Any way to stop that quickly? Thanks, Nadir Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-N

Re: [ccp4bb] projecting SC value on protein surface

Hi Pavlina, I suggest you have a look at http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:GRASP2. Runs on Windows. HTH Nadir Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de

Re: [ccp4bb] off-topic: 2 peaks on Cation

In your original mail (2011-02-18; 18:45 GMT), you wrote: "Possibly deamidation of the protein, in particluar one or more lysines" Hence, my comment was based on your own writing, that is deamiDation. Wishing you a better week. Nadir Pr. Nadir T. Mrabet Structural& Molecula

Re: [ccp4bb] off-topic: 2 peaks on Cation

Typo! I actually meant deamidation. Nadir Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 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)3.83.68.3

Re: [ccp4bb] off-topic: 2 peaks on Cation

Given no info on the protein, it can be anything. Is it recombinant? Which host? etc. Oxydation (cys, met) is also a possibility By the way, deamination concerns asn and gln, not lys. Best, Nadir Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 N

Re: [ccp4bb] Singapore Research, facts and comments?

Have a look at A* (http://www.a-star.edu.sg/). Best, Nadir -- Pr. Nadir T. Mrabet Structural & Molecular Biochemistry INSERM U-954 UHP - Nancy 1, School of Medicine 54505 Vandoeuvre-les-Nancy Cedex France Tel : +33 (0)3.83.68.32.73 Fax : +33 (0)3.83.68.32.79 E-mail : nadir.mra...@medecine

Re: [ccp4bb] What is the simplest method to analytically compute the Solvent-Accessible Surface Area of a given atom in a protein?

It can go both ways: If you increase atom radii by adding that of the probe (e.g. 1.4 A° for a water probe) and calculate the "molecular surface" using a zero probe with atom radii as previously defined (Ri +1.4 A°), the area you get is that of the accessible surface. Pr. Nadir

Re: [ccp4bb] What is the simplest method to analytically compute the Solvent-Accessible Surface Area of a given atom in a protein?

first. How could I get the Varshney code? Best regards, Nadir Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 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:

Re: [ccp4bb] on the same note

cleophilic attack). It is recommanded to avoid hi pH and the presence of metal ions. HTH, Nadir -- Pr. Nadir T. Mrabet Structural & Molecular Biochemistry INSERM U-954 UHP - Nancy 1, School of Medicine 54505 Vandoeuvre-les-Nancy Cedex France Tel : +33 (0)3.83.68.32.73 Fax : +33 (0)3.83.6

Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues

. Nadir T. Mrabet Structural & Molecular Biochemistry INSERM U-954 UHP - Nancy 1, School of Medicine 54505 Vandoeuvre-les-Nancy Cedex France Tel : +33 (0)3.83.68.32.73 Fax : +33 (0)3.83.68.32.79 E-mail : nadir.mra...@medecine.uhp-nancy.fr Selon Buz Barstow : > Dear All, > > I&#x

Re: [ccp4bb] Removing a tight binding ligand

Hi, It could help if you said what your ligand is. Nadir Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 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:

Re: [ccp4bb] Native Gel Theory and Practice

, ABB, AAB). Nadir Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 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: Nadir.Mr

Re: [ccp4bb] Native Gel Theory and Practice

You actually need both data to infer stoechiometry and subunit composition. Nadir Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 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

Re: [ccp4bb] Query - inhibitor screening by fluorescence based assay.

t know you system. Note however that binding (1) might be non specific and (2) need not correlate with enzyme inhibition. Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-l

Re: [ccp4bb] Ion exchange protein lost

Human gcsf has a pI ~ 6. As Ursula suggests you might be better off with anion exchange. There are protocols that show you can both refold and purify onto such column type. Nadir Pr. Nadir T. Mrabet Structural& Molecular Biochemistry Nutrigenex - INSERM U-954 Nancy University, Schoo

Re: [ccp4bb] How could I Extract Iron from Protein?

I would go for DTPA and acid pH. Better than dialysis, I would use IEX and flush le bound protein with a buffer with as low a pH as possible with 10-100 mM DTPA, then wash with no DTPA, and elute le protein with clean (e.g. treated with Chelex) salt. HTH, Pr. Nadir T. Mrabet Structural

Re: [ccp4bb] linux question

You may want to consider CD-bootable Puppy Linux (http://en.wikipedia.org/wiki/Puppy_Linux). HTH, Nadir -- Pr. Nadir T. Mrabet Structural & Molecular Biochemistry INSERM U-954 UHP - Nancy 1, School of Medicine 54505 Vandoeuvre-les-Nancy Cedex France Tel : +33 (0)3.83.68.32.73 Fax : +3

Re: [ccp4bb] pdb-l: [mockeldri...@yahoo.com: Retraction of 12 Structures]

) by both crystallographers and modelers, but also by curators at the rcsb.. Regards, Nadir Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex Fr

Re: [ccp4bb] best linux for laptops?

You may want to consider as well: 1/ Cygwin (runs within Windows), or 2/ puppy linux (www.puppylinux.org/; runs with own boot CD regardless of OS -eg WinXP- installed on laptop). There is no issue I am aware of with drivers. Nadir Mrabet Pr. Nadir T. Mrabet Cellular & Molecular Biochemi

Re: [ccp4bb] Van der Waals contacts

of balance. Nadir Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM U-954 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-m

Re: [ccp4bb] structure <-> function

Ok, now we can perhaps debate of another problem. With a multiple choice question that has more than one acceptably good answer, is it "convergent", or rather "independent", evolution? This multiple choice question is open for discussion. Greetings, Nadir Pr. Nadir T

Re: [ccp4bb] Glycerol as metal chelator?

I wouldn't use a pH of 9 when dealing with metal cations in solution. By and large, metal hydroxides precipitate at alkaline pH. HTH Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184

Re: [ccp4bb] Van der Waals Interaction Distances

049* *20.298* *-0.006* *1.90* *0.042* *23.776* *-0.005* *1.95* *0.036* *27.742* *-0.005* *2.00* *0.031* *32.252* *-0.004* -- Pr. Nadir T. Mrabet Cellular & Molecular Bioch

Re: [ccp4bb] PDB protein strucutrues as screen saver

Hi, You may want to have a look at http://www.luminorum.com/html/luminorum_ltd___extras.html. hth Nadir -- 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-N

Re: [ccp4bb] protocol for harvesting proteins from bacterial periplasmic space

depleted of Me2+ (easily seen with Cu2+). Moreover, it is always possible to add some Me2+ to your extract prior to IMAC. All this was published long ago (Biochemistry. 31: 2690-2702, 1992). Nadir -- Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM U-724 Nancy Univer

Re: [ccp4bb] [OFF TOPIC] his-tag doesn't bind

by coordination bond formation to a metal-chelate. Coordination bond lentghs decrease (and binding improves) as ionic strength increases, so a 1-2 M salt concentration in you buffer may turn out to be appropriate. HTH, Nadir Mrabet -- Pr. Nadir T. Mrabet Cellular & Molecular Bioch

Re: [ccp4bb] 3D modeling program

I agree with Gerard regarding "homology", but then it becomes significantly more problematic when you deal with "remote homology". Nadir Mrabet -- Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM U-724 UHP - Nancy 1, School of Medicine 54505 Vandoeuvre-le

Re: [ccp4bb] 3D modeling program

ary constraint(s). Nadir Mrabet -- Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM U-724 UHP - Nancy 1, School of Medicine 54505 Vandoeuvre-les-Nancy Cedex France Tel : +33 (0)3.83.68.32.73 Fax : +33 (0)3.83.68.32.79 E-mail : [EMAIL PROTECTED] Selon Dima Klenchin <[EMAIL PROT

Re: [ccp4bb] Definition of salt bridge

5 Angs. Nadir Mrabet 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-mai

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 PROTE

Re: [ccp4bb] off-topic: Enzymology textbook recommendations?

Alan Fersht: Enzyme structure and mechanism. Definitely! Nadir Mrabet -- 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: +3

Re: [ccp4bb] Ammonium citrate tribasic buffer

Henderson-Hasselbalch equation must be written in terms of activities rather than concentrations, otherwise it is totally useless. Nadir Mrabet Selon "William G. Scott" <[EMAIL PROTECTED]>: > There are 3 pKa's for citric acid: > > 3.15, 4.77, and 5.19 > > so

Re: [ccp4bb] Na Acetate Buffer

aOH]))". Greetings, Nadir -- 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)3.83.68.32.7

Re: [ccp4bb] Na Acetate Buffer

expect you can ever achieve such a repeatability using a pH-meter. HTH, Nadir Mrabet -- 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 Franc

Re: [ccp4bb] Imidazole's ability to chelate metal ions

Well, I happen to lecture on this... The bible is "Data for biochemical research", Dawson et al., Oxford University Press. Should be available in most biochemistry labs, if not in the library. Cheers, Nadir -- Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM

Re: [ccp4bb] Imidazole's ability to chelate metal ions

uffer (pKa 7.0) or else results from competitive elution from an IMAC column. What should be done depends on your exact conditions. hth, Nadir -- Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM U-724 Nancy University, School of Medicine 9, Avenue de la Foret de Hay

Re: [ccp4bb] pH gradient in Mono Q

required and sufficient volumes of buffer A. Again, I ask the question: Did Matthew ever mentioned before he intended to perform a CHROMATOFOCUSING experiment? Nadir -- Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM U-724 Nancy University, School of Medicine 9, Avenu

Re: [ccp4bb] pH gradient in Mono Q

4.76). An equimolar (50mM) mixture of these with Buffer A titrated to 8.0 and Buffer titrated to 4.0 has been shown (in my hands) to yield a very linear gradient (must not be too steep, though). Matthew's question does not seem to concern chromatofocusing. Hth, Nadir -- Pr. Nadir

Re: [ccp4bb] 3D model building without CRT monitor

be the one and only crt from Viewsonic (but only 19"). Cheers, Nadir -- 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 Phon

Re: [ccp4bb] crashing-out protein eluted from Nickel column

fer, e.g. 6.5 or even 6.0 (try and see) so that you dont need to go beyond 100 mM imidazole in your elution buffer (as mentioned earlier, you must ajust the pH of the latter as required with extra HCl). Best, Nadir Mrabet -- Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSER

Re: [ccp4bb] Primary source for detergent properties

Hi, The only published compendium on detergents still available (to my knowledge) is http://www.merckbiosciences.co.uk/docs/docs/LIT/CB0068_M.pdf. No phase diagrams though. Regards, Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM U-724 UHP - Nancy 1, School of Medi

Re: [ccp4bb] questions about hydrophobic core

the other hand, taking away even residues that display very little ASA (< 5%) would certainly leave you with genuine core residues. Hope this helps. Greetings, Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM U-724 UHP - Nancy 1, School of Medicine Avenue de la

Re: [ccp4bb] Nature policy update regarding source code

Hi, I believe such requirements concern only "Nature Methods" rather than "Nature" by and large. Regards, Nadir Mrabet Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM U-724 UHP - Nancy 1, School of Medicine Avenue de la Foret de Haye, BP 184

Re: [ccp4bb] PCB buffer and MMT buffer

calculation using the Henderson-Hasselbach equation must refer to activities and not concentrations. Given this, expect a phosphate buffer pH to increase by 0.3-0.4 units upon a 10-fold dilution (That is from 1.0M to 0.1M in the referenced paper). Regards, Pr. Nadir T. Mrabet Cellular & Molec