[ccp4bb] Anion-Pi interaction in protein

2012-08-13 Thread Kavyashree Manjunath
Dear users, Has there been any instances where there is an anion-pi interaction in proteina. I found a density that could accommodate an acetate ion just above the aromatic ring of the tyrosine residue in the protein I am working on. I just came across an article regarding the anion-pi interaction

Re: [ccp4bb] determination of oligomerization state of protein

2012-08-13 Thread gauri misra
Hi, Try glutaraldehyde crosslinking of peaks you are obtaining from SEC individually and see if it gives you some idea. Best wishes Gauri

Re: [ccp4bb] Enhancing Crystal Quality

2012-08-13 Thread Sangeetha Vedula
Lucas, if your crystals diffract worse at room temp than cryoprotected, it looks like there may be radiation damage at room temperature, so you may need to cryoprotect. The change in osmotic pressure may be too much for your crystals when you're cryoprotecting the crystals by a sudden dunk. Also, d

Re: [ccp4bb] determination of oligomerization state of protein

2012-08-13 Thread Jim Fairman
Multi-Angle Light Scattering (MALS) coupled with an HPLC column attached to an analytical SEC column is my standard "go-to" method for determining molecular weights/oligomeric states of peaks from SEC runs. I've only ever used the detectors from Wyatt ( http://www.wyatt.com/solutions/hardware/hard

[ccp4bb] determination of oligomerization state of protein

2012-08-13 Thread Sangeetha Vedula
Hello all, I am working with a protein that is probably a hexamer based on homology with other proteins but when I ran it on an analytical size gel filtration column, I see multiple peaks. I would like to determine the exact oligomerization state of the mixture and have considered blue native gel

[ccp4bb] libcheck garbled small molecule in ccp4 6.3 but not in ccp4 6.2.2

2012-08-13 Thread hari jayaram
Hi, I just upgraded to the newest CCP4 version 6.3 and noticed that libcheck which coot uses to produce restraints from a SMILES string produces garbled coordinates in ccp4 version 6.3 , but the same SMILES string works just fine with CCP4 version 6.2. I tried to get it to fail on public molecule

Re: [ccp4bb] NADP binding protein without Rossmann fold.

2012-08-13 Thread Sudipta Bhattacharyya
Dear all, Thank you very much for your cooperation. Regards, Sudipta. Sudipta Bhattacharyya. Senior Research Fellow, Department of Biotechnology, Indian Institute of Technology Kharagpur, India.