[ccp4bb] residues forming the surface of a cavity

Dear all,   Is there any CCP4 module/ other software/ web server which can determine which particular residues form the surface of a pocket/ binding-site in a protein? Thanks in advance, sreetama

Re: [ccp4bb] residues forming the surface of a cavity

On 10/04/2012 04:09 PM, sreetama das wrote: Dear all, Is there any CCP4 module/ other software/ web server which can determine which particular residues form the surface of a pocket/ binding-site in a protein? Do you mean "residues not far from any ligand atom"? And you know wher

Re: [ccp4bb] off topic: reproducing hits from organic solvents

Dear Peter, my guess is that isopropanol might have evaporated and, in general, that the concentration of PEG4000 might be higher that in the starting solution because of evaporation. I would try to decrease the isopropanol concentration, or even eliminate it. As a "cooker test" if you sm

Re: [ccp4bb] residues forming the surface of a cavity

Try PISA -- Eugene On 4 Oct 2012, at 08:09, sreetama das wrote: Dear all, Is there any CCP4 module/ other software/ web server which can determine which particular residues form the surface of a pocket/ binding-site in a protein? Thanks in advance, sreetama -- Scanned by iCr

Re: [ccp4bb] residues forming the surface of a cavity

You can also try the CASTP server On Thu, Oct 4, 2012 at 2:47 PM, wrote: > Try PISA > > -- Eugene > > On 4 Oct 2012, at 08:09, sreetama das wrote: > > Dear all, > Is there any CCP4 module/ other software/ web server which > can determine which particular residues form the sur

[ccp4bb] Postdoctoral position at the Membrane Protein Lab, Oxfordshire

Dear All, A 1 year position has become available for a Research Associate in the Membrane Protein Laboratory (MPL) for crystallisation, crystallographic and structure determination of a bacterial antibiotic transporter. The successful candidate will work on improving the crystals and solving th

Re: [ccp4bb] [OT]: Purification in ArcticExpress

Apologies for revisiting this topic but I wanted to post a summary of the responses for the compulsive archive searchers like me. Several people suggested the addition of ATP (5 mM) to the buffers either at lysis or once the protein is bound to the column (see ref: R. E. Joseph; A. H. Andreotti, P

[ccp4bb] On maps and doubts

Hello everyone, I would like to share my experience with one dataset and request some advice on which is the best way to prove a conformational change seen in a density map. The first issue arose when we were looking for an extra ribosomal factor added to a crystalized ribosome. After careful dat

Re: [ccp4bb] On maps and doubts

Try GraphEnt but you might have to recompile it for your size of proteins. That has helped me several times to see something that was barely there. Here's the link for the 'click-generation': http://utopia.duth.gr/~glykos/graphent.html Jürgen .. Jürgen Bosch Johns Hopkins Un

Re: [ccp4bb] Professor Dame Louise Johnson

I am very sorry to hear the sad news. Like innumerable others, I am very grateful to have had the opportunity to meet "The Prof. Johnson" of the classic Blundell & Johnson crystallography textbook. I met Prof. Johnson at Diamond a few years ago and immediately saw in her an inspiring, graceful and

Re: [ccp4bb] On maps and doubts

Dear Israel, I wonder why you do not see anything in your Fo-Fc (mFo-DFc?) maps, since the limit for a (n+1) * mFo - n * DFc map, when n approaches inifinity, is the mFo-DFc difference map. There is nothing wrong in going further like with 4mFo-3DFc maps, but you should bear in mind that they are