Re: [ccp4bb] Rfree and unaccounted density

Dear Vineet Following points shall be kept in mind. 1.If you have been able to model most of the protein into the electron density, then its a bit strange. your refinement parameters suggest that refinement is still away from convergence. 2.You might be trapped in local minima, and in this case

[ccp4bb] University of Auckland - Lecturer in Structural Biology

Lecturer in Structural Biology School of Biological Sciences Auckland Vacancy Number: A618-07L Applications are invited for a tenured position as Lecturer in Structural Biology. You should have state-of-the-art skills and a publication record in structural biology, preferably in X-ray crys

Re: [ccp4bb] covalently bonded Ligand fit

In Coot (0.3.2 and later) you could also try the following: - center on the serine to be phosphorylated - click Extensions->Phosphorylate this residue and Coot will sort out phosphorylation, renumbering etc in no time. JED -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PR

[ccp4bb] MS for verification of protein constructs

I wonder if anyone would care to share experiences/ideas/biases that relate to the use of mass spectrometry to verify the identity of protein constructs used for crystallization. Our experience with different MS facilities has been checquered. Specifically: What's the current thinking on

Re: [ccp4bb] MS for verification of protein constructs

I second Dr. Loll's question, and would like to be CC'd in whatever MS tips, including service-providers, are sent. I have been having a bit of a debacle with a certain MS service provider. Jacob Keller ==Original message text=== On Wed, 05 Sep 2007 11:41:52 am CDT Patri

[ccp4bb] few organophophates coordiantes

Hi, Thanks for the reply to my earlier query. I am looking for the coordinates of few organophosphates which can bond covalently to protein as follows . 1) Para-oxon: O,O-Diethyl-O-para-nitrophenyl phosphate 2) Sarin: 2-(fluoro-methyl-phosphoryl)oxypropane 3) Soman: 3-(fluoro-methyl-phosphoryl)o

Re: [ccp4bb] few organophophates coordiantes

Hi Sam: You can define a SMILES string, put that in coot, and it will create coordinates. Similarly, within phenix, you can do this with elbow.builder and then optimize is either with built-in forcefields or with an external QM program. It will give you a reasonable (usually) cif file that you

Re: [ccp4bb] MS for verification of protein constructs

If you have a very pure protein sample, you'll want to use an ESI-ion trap for analyzing proteins of that size. It should be possible to get an exact mass (i.e. within a single Da). It's possible, but very rare, to get exact masses of proteins up to 100 kDa using ESI-ion trap instruments. If you

Re: [ccp4bb] MS for verification of protein constructs

... all these are correct indeed - but ESI-TOF is also a nice solution, especially coupled to an LC system. My understanding was that MALDI-TOF is better for smaller fragments, accuracy can be about 10 Dalton ... for more info there is a useful short review of the use of ms techniques for s

Re: [ccp4bb] MS for verification of protein constructs

Hiya For verification purposes we almost always N-terminal sequence (we are fortunate in that we have such a facility on site so that the samples can be turned round fast) - old technology but good and solid! We then usually combine these data with a Mass Spectra (MALDI-ToF-Tof - on site - is

Re: [ccp4bb] MS for verification of protein constructs

Hello, While I am not a professional MS person, I have had the privilege of working with many MS scientists and some knowledge has rubbed off despite my best efforts to stay benighted. All the correct information in the post below is therefore credited to the MS community whereas all the errors