Re: [ccp4bb] "modeling" flexible ends on proteins

2014-10-22 Thread Min-Kyu Cho
Hi, For loops, there are servers like SuperLooper http://bioinf-applied.charite.de/superlooper/ ModLoop http://modbase.compbio.ucsf.edu/modloop/ FALC-Loop http://falc-loop.seoklab.org/ (seems to be down) If you want model flexible region itself, there is a program called flex

Re: [ccp4bb] Yeast membrane protein extraction

2014-10-22 Thread John Lee
Hi Theresa, I totally agree with the bead beater idea. Good reference for recipe (pg.699-701): Overexpression and Purification of Integral Membrane Proteins in Yeast Franklin A. Hays,*,1 Zygy Roe-Zurz,† and Robert M. Stroud -John On Wed, Oct 8, 2014 at 7:25 AM, Theresa Hsu wrote: > Dear

[ccp4bb] Postdoc positions in chromatin structural biology

2014-10-22 Thread Song Tan
Postdoctoral Positions in Chromatin Structural Biology Postdoctoral positions are available in the Tan Laboratory at Penn State to determine the structures of epigenetic chromatin enzymes and factors on their own or in complex with nucleosomes. These chromatin enzymes include single polypeptide

Re: [ccp4bb] Calculating over all bend in a DNA

2014-10-22 Thread Sasha Pausch
Hello CCP4bb, Based on suggestions from the members of CCP4bb, I used program Curves+ to check the bend (angle) in DNA. I have given my DNA which has two strands and 13 bases each as an input. I got an output file where I can see other parameters inferred from the structure. But I am getting a

[ccp4bb] "modeling" flexible ends on proteins

2014-10-22 Thread Tommi Kajander
Hi All, Would anyone know a software to model (just with some kind of random coil) the amino acid chain for the assumed flexible disorderd regions between domains, or at one end of protein? just for illustrative purposes. Thanks! Tommi

Re: [ccp4bb] Calculating over all bend in a DNA

2014-10-22 Thread Mooers, Blaine H.M. (HSC)
Hi Sasha, You can also use Richard Lavery's webservice for Curves+ ( http://gbio-pbil.ibcp.fr/cgi/Curves_plus/ ) and visualize the curve of the helical axis in 3D in a molecular graphics program. In addition, you can do a normal vector analysis similar to the one suggested by Tim Gruene by ru

Re: [ccp4bb] a more intelligent mapsig question

2014-10-22 Thread Eleanor Dodson
You have a gris 48 48 304 so need map 0 47 0 47 0 303 I guess. It should work I thought with asymm unit though Eleanor On 20 October 2014 15:22, Scott Horowitz wrote: > Hi all, > > Now that I have mapsig running, I am getting an error message that I am > confused by. The maps I am using are ano

Re: [ccp4bb] Calculating over all bend in a DNA

2014-10-22 Thread Valerie Pye
Hi Sasha - you can use 3DNA: http://x3dna.org/; http://w3dna.rutgers.edu/ HTH, val On 21 October 2014 20:53, Sasha Pausch wrote: > Hello CCP4bb, > > May I know how can we calculate or use any server which can calculate the > overall bend in a DNA (crystal structure)? > >

[ccp4bb] Fwd: Re: [ccp4bb] Calculating over all bend in a DNA

2014-10-22 Thread Tim Gruene
Dear Sasha, dear all, I meant 'two _sets_ of three atoms each'. Thanks to Mark for pointing this out to me. Best, Tim Forwarded Message Subject: Re: [ccp4bb] Calculating over all bend in a DNA Date: Wed, 22 Oct 2014 10:50:10 +0200 From: Tim Gruene Reply-To: Tim Gruene To: C

Re: [ccp4bb] Calculating over all bend in a DNA

2014-10-22 Thread Tim Gruene
Dear Sasha, you can select two pairs of three corresponding atoms at either end of the stand and calculate the plane normal of each set. The angle between the normals would be the overall bend. Best, Tim On 10/21/2014 09:53 PM, Sasha Pausch wrote: > Hello CCP4bb, > > May I know how can we calcu