[ccp4bb]

Xie Jiabao schrieb: Hi, Can anyone direct me to a program that calculates a protein cavity's dimensions (average) and not just its volume? Thanks in advance, Xie http://loschmidt.chemi.muni.cz/caver/ The program is called caver. -- Justin Lecher Institute for Neuroscience and Biophysics

Re: [ccp4bb] dry shipper on airplaine

Here I must disagree slightly with Preben. I once mentioned 'Twelve Monkeys' to the personnel at the check-in counter to lighten the mood (They didn't like the fumes coming out from the dewar). I really believe it helped them understand what was NOT in the dewar. And we were allowed to board the

[ccp4bb] Postdoctoral position in Brighton, UK

UNIVERSITY OF SUSSEX School of Life Sciences Department of Chemistry and Biochemistry Postdoctoral Research Assistant in Protein Crystallography Applications are invited for a three year Postdoctoral position, funded by the MRC,

[ccp4bb] Making a Poly ala model

Dear All, Can anyone recommend a windows/PC-friendly program (website?) to convert a PDB file into a poly-Ala model? Thanks a lot! Matt Matthew J. Bottomley, Ph.D. Senior Research Biochemist IRBM / MRL-Rome Notice: Thi

[ccp4bb] FW: Making a Poly ala model

OK - found it, thanks! Matt Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Doh

[ccp4bb] Siemens Multiwire Area Detector X-1000 available

To All at CCP4BB: We have a Siemens X-1000 Multiwire Area Detector to give away. It has been manufactured by Siemens Analytical X-ray Instruments Inc. in Madison, Wisconsin, USA. Equipment available includes multiwire area detector X-1000 itself, its Position Decoding Circuit, the 4-circle

Re: [ccp4bb] Making a Poly ala model

If you have perl installed, just use this script to convert as many files as you want once by typing : perl mutala.pl myfile.pdb myfile2.pdb etc Bottomley, Matthew wrote: Dear All, Can anyone recommend a windows/PC-friendly program (website?) to convert a PDB file into a poly-Ala model? Th

Re: [ccp4bb] Making a Poly ala model

Within PyMOL: remove polymer and not name N+CA+C+O+CB alter polymer, resn="ALA" save polyALA.pdb Cheers, Warren -- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Bottomley, Matthew Sent: Thursday, May 29, 2008 5:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Making a Poly al

[ccp4bb] mutation to cysteines

Dear All, Sorry for a non-CCP4 question. I intend to mutate a couple of residues to cysteines(so that they form a disulphide linkage) in a certain region of my protein. Could I please be directed to program(s) that would reliably let me do that, prior to primer designing? Thanks in advance, Amit

Re: [ccp4bb] mutation to cysteines

Hi Amit You can try MODIP http://caps.ncbs.res.in/dsdbase//dsdbase.html, which give you the stereochemical possibility of disulphide linkage between the residues. Not sure about the success rate based on the result from this database. hope this helps VK Kabaleeswaran Venkataraman Arise,

[ccp4bb] Well-paid crystallography postdoc position in Oslo

I have a 2-year postdoctoral research fellowship available in my group (financed by the Norwegian Research Council, project title "Postgenome glycomics: The structures, interactions, and functions of complex sugars attached to proteins and lipids"). The position is available immediately, but the s

Re: [ccp4bb] mutation to cysteines

Try the program disulfide by design: http://www.ehscenter.org/dbd/ Its easy to install (at least on windows) and to run. You put in a PDB file and the program will look in the structure where disulphide bonds are possible. It also ranks the candidates in energies. Finally, it can generate a PDB f

[ccp4bb] thermofluor - Thermal Shifts - Tm and Delta Tm

Hello, we want to use the thermofluor thermal shift assay to screen for buffers that our proteins are happy in. Reading around the subject, I am a bit unclear as to what to be looking for with regard to a stabilizing affect. Initially, we thought, the higher the Tm, then the more stabilizing the

Re: [ccp4bb] mutation to cysteines

amit sharma wrote: Dear All, Sorry for a non-CCP4 question. I intend to mutate a couple of residues to cysteines(so that they form a disulphide linkage) in a certain region of my protein. Could I please be directed to program(s) that would reliably let me do that, prior to primer designing?

[ccp4bb] waaay off topic...

...but I know you'll come through. I'm looking for recommendations for a good textbook covering fluorescence spectroscopy. Thanks in advance. Pat --- Patrick J. Loll, Ph. D.

Re: [ccp4bb] waaay off topic...

A good book is: Principles of Fluorescence Spectroscopy Joeseph R Lakowicz Roopa Thapar On Thu, May 29, 2008 1:16 pm, Patrick Loll wrote: > ...but I know you'll come through. > > I'm looking for recommendations for a good textbook covering > fluorescence spectroscopy. > > Thanks in advance. >

Re: [ccp4bb] insect expression system

Thanks to all that replied. You might find this useful. The question was: How to select an insect expression system for mammalian/viral glycoproteins? The following is a summary of the replies. *1. Baculovirus system* 1) For most proteins, the level of expression is far greater with bacuovir

[ccp4bb] hkl to mtz with anomalous data

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello everyone, we have been trying to convert an unmerged hkl-file to mtz such that the labels F+/F- or F/DANO (or I+/- etc respectively) are calculated, and failed so far. We would appreciate a hint towards the correct program/ options to use.