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

Hi Edward, I just need to comment on this. To define contact atoms, you must use "solvated united atoms" that is atoms with implicit hydrogens where needed (united radius), this radius being further increased by that of a molecule of water. Why is that? In vacuum, it was shown that at a dist

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 University o

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-964 Uni

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

[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] 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

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 32 73 Fax : +

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.uhp-nan

Re: [ccp4bb] on the same note

Hi, There is no way you can compare NiNTA and GSH affinity supports. It is a lot easier to regenerate NiNTA. This has to do with the ligand, not the support. Kd is 10-100 times lower for GSH. GSH contains a "highly" reactive SH group if enough thiolate is present (oxydation and/or nucleophilic att

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

Hi, You first need a program to calculate ASA, e.g. Naccess. Once you have the ASA on a per-residue basis, you can plot a histogram, by e.g. feeding the data to a spreadsheet application of your choice. What is usually done is to list residues sequencewise vs. ASA. Best success, Nadir -- Pr. N

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 : +33 (0)3.83.

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] 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

I suspect everyone is refering to Rost's "twilight zone" in sequence similarity where homology modeling trials had better be avoided. If so, the "twilight zone" would rather correspond to any indefinite or transitional condition(s) with no applicable or ever relevant bin

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