Re: [ccp4bb] Crystallisation video

2012-08-05 Thread Donald Damian Raymond
Hi, Our lab has a few videos on youtube that may be what you are looking for. http://www.youtube.com/user/JanetSmithLab See the Setting Crystal Trays video. -Donald On Aug 4, 2012, at 12:18 AM, Bret Church bret.chu...@sydney.edu.au wrote: Hi, Does anybody know of a video of setting up

[ccp4bb] Pairwise distance calculation

2012-08-05 Thread Zhou, Tongqing (NIH/VRC) [E]
Dear All, I am trying to obtain the pairwise Ca-distances between corresponding residues of two antibody light chains. CCP4 Superpose can output the distances in the log file, but the numbers seem to be wrong when examed by eye. Is there a way to calculate the pairwise distance between two

Re: [ccp4bb] Pairwise distance calculation

2012-08-05 Thread Boaz Shaanan
Hi, ProSmart (in 6.3.0) might be your friend here. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or

Re: [ccp4bb] OFF TOPIC: recommendations for High Pressure Homogenizers

2012-08-05 Thread Van Den Berg, Bert
My lab has had a C3 for almost 8 years now. It's very good for coli, not so good for yeast as 25-30 kpsi is in the extreme range of the instrument and you'll wear out seals etc pretty quickly. For those pressures you'll also need high pressure air. You'll also need to be fairly disciplined in

Re: [ccp4bb] OFF TOPIC: recommendations for High Pressure Homogenizers

2012-08-05 Thread Patrick Loll
We have an Avestin C5 that's about 10 yrs old, and pretty much everything that Bert said is also true for us. The instrument works great for bacteria; it can also break yeast, but the pressures required are at the upper limit of its capabilities, so everything needs to be in tip-top condition.

Re: [ccp4bb] Pairwise distance calculation

2012-08-05 Thread Eleanor Dodson
I am surprised if the numbers are wrong, maybe your chosen superposition isn't the same as that used for superpose - there are 2 methods available - are you using the secondary structure matching, or the assigned residue match? Eleanor dodson On 5 Aug 2012, at 15:17, Zhou, Tongqing (NIH/VRC)

Re: [ccp4bb] Fedora 16 CCP4-6.3.0 installation problem:

2012-08-05 Thread Tru Huynh
On Sat, Aug 04, 2012 at 07:27:29PM -0400, james09 pruza wrote: Dear All, Fedora 16 CCP4-6.3.0 installation problem: The configure output shows- zlib library not found. The package seems to be installed and latest as checked by yum install zlib Package zlib-1.2.5-6.fc16.x86_64 already