[ccp4bb] Group Leader position in Helsinki, Finland

2015-03-18 Thread Tommi Kajander
(Reposting this position as it didnt go to the jobs list..:) On behalf of the search committee (see links below): -- The Institute of Biotechnology is a leading European research institute within the University of Helsinki with a mission to increase knowledge in cross‐disciplinary biology an

[ccp4bb] PhD position in Durham

2015-03-18 Thread POHL E.
Project description Herbicide resistance of weeds is a major challenge for global food production. The situation becomes particularly severe when weeds become resistant to multiple modes of herbicide action (multiple herbicide resistance=MHR). This collaborative project between Durham University

Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box

2015-03-18 Thread Patrick Shaw Stewart
Hi Steve I have one more comment for this thread. The microbatch-under-oil method is very handy for anaerobic work: 1. You can keep the microbatch stock solutions in normal microtitre plates (polypropylene is best to reduce evaporation) for months, which hugely reduces the amount of degassing t

Re: [ccp4bb] Graphics cards for Coot, Pymol, Chimera on MacBook Pro Laptop

2015-03-18 Thread Xiao Lei
Hi Marc, I have a Macbook pro Mid 2009 model (with integrated graphics card) and I can run coot and pymol without any problem ( I haven't tested on Chimera), I do not think a discrete graphics is needed. However, for pymol I can not use the "stereo" function. I do not know if the discrete graphic

Re: [ccp4bb] OS X yosemite

2015-03-18 Thread Xiao Lei
Hi Mirek, I have to reinstall xquartz to get my ccp4 and coot working after upgrading to Yosemite from Mavericks. Xiao On Tue, Mar 17, 2015 at 4:30 PM, Cygler, Miroslaw wrote: > Hi, > I am thinking of upgrading the os on my mac to Yosemite. Are there any > known issues for crystallographic so

Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box

2015-03-18 Thread Edward A. Berry
Do you have evidence that the oil blocks diffusion of O2? O2 is a nonpolar molecule, generally much more soluble in oils than in water. I'm not sure about silicone oils, but I would think they also dissolve O2 readily. eab On 03/18/2015 08:02 AM, Patrick Shaw Stewart wrote: Hi Steve I have o

[ccp4bb] Antw: Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex

2015-03-18 Thread Matthias Barone
Hi, I just checked the PIC sever tim suggested. very nice indeed. If you only want to map different interfaces and the amino acids involved in, I suggest to run the pisa server, too. http://www.ebi.ac.uk/pdbe/pisa/ . I used it extensively to find out whether a certain set of crystal contacs lead

Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box

2015-03-18 Thread Julia Griese
Hi, As far as I can tell oil does not block diffusion of O2 whatsoever. You can keep larger volumes (≥1 ml) of solutions anoxic in air for several hours with dithionite (≥0.5%) to scavenge oxygen and a redox indicator dye such as phenosafranin to monitor the state of the solution. Small drops

Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box

2015-03-18 Thread Ronald E Stenkamp
I also wondered about the statement about oils blocking diffusion of O2. We had lots of trouble keeping things anaerobic in a glove box until we degassed the oils and waxes used to mount crystals in capillaries. We found that putting them under vacuum removed much of the dissolved oxygen. Th

Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box

2015-03-18 Thread Tristan Croll
It's a little complicated. It's true that oxygen is more soluble in most oils than in water - but in a high viscosity mineral oil the diffusion rate is orders of magnitude lower. So the combination of an oil overlay and a reducing agent in your buffer should protect your sample much longer than

Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box

2015-03-18 Thread Edward A. Berry
Actually I may have misunderstood the original post. Patrick never said oils block O2 diffusion: On 03/18/2015 09:47 AM, Edward A. Berry wrote: The microbatch-under-oil method is very handy for anaerobic work: (In a glove box, of course) 1. You can keep the microbatch stock

[ccp4bb] Mosquito Tips (4.5mm / 9.0mm)

2015-03-18 Thread Paul Smith
Hello CCP4, Sorry for the labware related post, but I think this is the right audience. I have 4 new reels of mosquito tips with 4.5mm pitch (for 384 well setups, TTP labtech part number 4150-03010). I only use 96well format, thus am looking to swap these for 9mm pitch (part number 4150-03020).

[ccp4bb] on openning the PDB file and the mtz file by Coot

2015-03-18 Thread Smith Liu
Dear All, When we by Coot open the PDB fle and the mtz file from the same refinement, the protein backbone (and the sidechains) and the electron density always fit automatically. Will you please tell me the mechanism of the Coot how the PDB file automatically fit the mtz file in its graphical