Re: [ccp4bb] Validity of Ion Sites in PDB

2014-03-06 Thread Robbie Joosten
Dear Jacob, There are a lot of potential problems with ion validation, that make obtaining a reliable answer difficult. If you want to datamine ion validation results, you can use the ready-made WHAT_CHECK files in the PDBREPORT databank for original PDB files or in the PDB_REDO databank for th

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

2014-03-06 Thread Sabuj Pattanayek
Thanks! we're gonna test one of the lg's from b&h, one of our zalman's just died today. On Thu, Mar 6, 2014 at 6:06 PM, Shaun Lott wrote: > Thanks to everyone who responded, on and off the list. I thought I'd post > a quick summary. > > To clarify my question slightly (if belatedly) I'm specifi

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

2014-03-06 Thread Shaun Lott
Thanks to everyone who responded, on and off the list. I thought I'd post a quick summary. To clarify my question slightly (if belatedly) I'm specifically looking for a passive 3D solution to plug into my MacBook Pro whilst on sabbatical in the USA. I'll be using it for a mixture of 2D and 3D v

Re: [ccp4bb] Validity of Ion Sites in PDB

2014-03-06 Thread Talon Romain
Dear Jacob Keller, As you say, there is a number of methods used to assign, as correctly as possible, ions and water molecules: > depending of everything you know about the purification protocol of the molecule (every ions and compound which could have been seen by the target protein), > depe

Re: [ccp4bb] Validity of Ion Sites in PDB

2014-03-06 Thread Nat Echols
On Thu, Mar 6, 2014 at 11:45 AM, Keller, Jacob wrote: > I was curious whether there has been a rigorous evaluation of ion binding > sites in the structures in the pdb, by PDB-REDO or otherwise. I imagine > that there is a considerably broad spectrum of habits and rigor in > assigning solute blobs

Re: [ccp4bb] Validity of Ion Sites in PDB

2014-03-06 Thread David Schuller
Certainly some sites will be defined better than others by such criteria. I would hope that they are discussed in the publications relevant to the PDB submission. On 03/06/14 14:45, Keller, Jacob wrote: Dear Crystallographers, I was curious whether there has been a rigorous evaluation of io

[ccp4bb] Validity of Ion Sites in PDB

2014-03-06 Thread Keller, Jacob
Dear Crystallographers, I was curious whether there has been a rigorous evaluation of ion binding sites in the structures in the pdb, by PDB-REDO or otherwise. I imagine that there is a considerably broad spectrum of habits and rigor in assigning solute blobs to ion X or water, and in fact it w

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

2014-03-06 Thread David Roberts
Every now and then I pipe on this as well. We have Zalman monitors here - I bought them about 4 years ago - when you could not buy them any more in the states. I just bought them on Ebay - they came new in the box directly from China. The person did fed-ex shipping - did not cost any extra, a

Re: [ccp4bb] Efforts been made to solve protein (soluble) aggregation

2014-03-06 Thread Bosch, Juergen
Co expression of binding partner perhaps ? And then tagging the other protein partner ? Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708

[ccp4bb] WWTF-funded positions in the Life Sciences, hosted by the Max F. Perutz Laboratories (MFPL), Vienna

2014-03-06 Thread Kristina Djinovic Carugo
*WWTF-funded positions in the Life Sciences, hosted by the Max F. Perutz Laboratories (MFPL), Vienna, Austria* The Vienna Science and Technology Fund (*WWTF*) has launched a call for applications in the Life Sciences. The "Vienna Research Groups for Young Investigators" call by the City of V

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

2014-03-06 Thread Zhijie Li
I beg to differ on this: "Also, passive screens have a pol-filter in place, the fine lines of which you will observe on a white background, the more disturbing the closer the viewing distance to the screen is. So, for general office applications (writing text), the screens are less useful. " Our

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

2014-03-06 Thread mesters
Hi, this is probaly due to the transition from old TFT style to new IPS panel based monitors... Several new passive 3d monitors are hitting the market such as AOC d2769Vh and the Philips Gioco 278G4. Both are based on 27" IPS Monitor pa

Re: [ccp4bb] Efforts been made to solve protein (soluble) aggregation

2014-03-06 Thread Mark J van Raaij
Dear Wenhe, this sounds a bit like our struggles to solubly express and purify the dsRNA-binding avian reovirus sigmaA protein, please find the two papers here: http://www.ncbi.nlm.nih.gov/pubmed/?term=van+Raaij+MJ%2C+sigmaA The key to solving our problem was to realise the protein aggregated esp