[ccp4bb] creating alternate conformations using PyMol

Hi all, I am working on generating alternate conformations for a particular loop region of a protein. I just want to move this region into different conformations in order to show the possible states it can occur in. Is there an easy way to do this in pymol which will help me rotate only

Re: [ccp4bb] Off-topic: coomassie linearity? SUMMARY

On 26 Sep 2008, at 08:20, Jacob Keller wrote: Hi All, thanks for the responses. It seems that coomassie linearity is not so bad after all, especially when measured by IR fluorescence (reference from Steve Darnell). Others mentioned silver stain, but it seems that silver has a narrower dyn

[ccp4bb] FACULTY POSITION IN X-RAY CRYSTALLOGRAPHY

FACULTY POSITION IN X-RAY CRYSTALLOGRAPHY Where: Department of Biochemistry and Molecular Biology Thomas Jefferson University in Philadelphia USA Job Description: The Department of Biochemistry and Molecular Biology at Thomas Jefferson University in Philadelphia invites applications for tenure-t

Re: [ccp4bb] losing zinc during crystallization

Hi Sue, I fully agree with Thierry, you might have to cyrstallize the protein under exclusion of dioxygen. There are many metallo proteins which have to be crystallized that way. But a first attempt might be the TCEP as already suggested by many others. If you need advice regarding crystalliza

Re: [ccp4bb] HydrophobiC interaction Chromo

Dear Meg, Please note that there are many ways to do HIC. Different resins result in different degrees of separation and it's unfortunately impossible to predict what would happen without trying it out. Which is why various companies sell HIC 'trial kits' - a few little columns packed with media s

Re: [ccp4bb] Off-topic: coomassie linearity? SUMMARY

Hi All, thanks for the responses. It seems that coomassie linearity is not so bad after all, especially when measured by IR fluorescence (reference from Steve Darnell). Others mentioned silver stain, but it seems that silver has a narrower dynamic range, even though more sensitive. Sypro and B

[ccp4bb] Research Associate (Staff Scientist ? Structural Biology & X-ray Science)

On behalf of Monica Wesley: Research Associate (Staff Scientist – Structural Biology & X-ray Science) Cornell High Energy Synchrotron Source ?The Macromolecular Diffraction Facility of the Cornell High-Energy Synchrotron Source (MacCHESS) is seeking to fill a staff scientist position. Applicant

[ccp4bb] deadline for applications for beamtime at BM14 -RUN oct-DEC 2008

Dear all, deadline for submission of proposals for beamtime at BM14 for beamtime at ESRF during Nov/Dec 2008 is next Friday 3rd october 2008 -get in your proposals now!. Beamline proposals can be submitted on-line from the BM14 webpages at http://www.bm14.ac.uk PLEASE r

Re: [ccp4bb] losing zinc during crystallization

Loss of a zinc at a dimer interface, triggered by formation of a disulfide bridge across the interface has already been observed for nitric oxide synthase. The 1st reported structure had the disulfide bridge: http://www.sciencemag.org/cgi/content/abstract/279/5359/2121 But 2 other groups indepen

Re: [ccp4bb] Reading the old literature / truncate / refinement programs

This goes back to my previous idea about using the Bayesian estimates ( & sig()) of I & sig(I) in the refinement instead of the measured ones. This would remove any objection to using negative observed intensities, though it's hard to see what exactly the objection is. Basically you're just moving

Re: [ccp4bb] TLS parameter representation

Hi Cedric TLSVIEW does that one. You will get the software from the web site http://pymmlib.sourceforge.net/tlsview/tlsview.html. Regards Abhik

Re: [ccp4bb] TLS parameter representation

The AXES keyword in tlsanl allows import and display in CCP4mg or MOLSCRIPT. TLSView from Jay Painter and Ethan Merritt can also do it. http://pymmlib.sourceforge.net/ Cheers Martyn On Fri, 2008-09-26 at 10:08 +0200, cedric bauvois wrote: > Dear All, > > i would like to know wether it's possibl

Re: [ccp4bb] HydrophobiC interaction Chromo

Hi Meg, ethanol is often used in a HIC elution buffer as it is good at breaking hydrophobic/hydrophoic interactions. (Detergents or isopropanol can be used to do the same thing). But, as with all things, tolerance to ethanol depends upon your protein. At pH 5, I would guess that Citrate or Acetat

[ccp4bb] TLS parameter representation

Dear All, i would like to know wether it's possible to represent graphically TLS-tensors obtained via refmac5 and how to procede? Best Regards. Cédric -- Dr. Cedric Bauvois Cristallographie des protéines Institut de Recherches Microbiologiques JM Wiame -IRMW Av E. Gryzon 1, 1070 Brussels (Belg

[ccp4bb] HydrophobiC interaction Chromo

Dear all, In continuation with my earlier mail on problem in cation exchange chromato, i was suggested to go for hydrobic interaction chromato [HIC] as an additional step. my protein is indeed a hydrophobic protein. we have sepharose 6 fast flow low sub resin and my protein has a pi of 5.8 -6.3