[ccp4bb] TCEP effect on protein

Hi all, My protein is relatively pure except the dimer. i used 10 mM TCEP to reduce it (directly added 1 M TCEP to make final volume of 10mM and kept at room temperature for 10 mins] then i dialysed the protein sample to remove TCEP [dialysis buffer is Na acetate pH 4.0]. On performing SDS PAGE a

[ccp4bb] structures with distinct substrate conformations

My literature search is not going so well. can anyone think of examples of the same substrate (not oxidized/reduced, intermediates or analogs) bound to the same enzyme (not mutants) binding site, but with one moiety adopting a drastically different conformation between different structures/dataset

Re: [ccp4bb] Calculation of the net charge of an electrostatic surface for secondary structural elements

Le 25 mars 2010 à 16:43, Tim Gruene a écrit : > Hello Rebecca, > > this is merely a guess, but I think, it should work. > > As you calculate the electrostatic surface potential in pymol, it uses apbs. > apbs, if I remember correctly creates an intermediate PDB-file where the > B-factor column i

Re: [ccp4bb] AW: [ccp4bb] 'Mushroom' shipping dewar for Rigaku pucks

Uups: We're using MVE SC 4/2V. Dirk Original-Nachricht > Datum: Thu, 25 Mar 2010 08:33:40 +0100 > Von: Dirk Reinert > An: CCP4BB@JISCMAIL.AC.UK > Betreff: [ccp4bb] AW: [ccp4bb] \'Mushroom\' shipping dewar for Rigaku pucks > Hi Todd, > > In case no one answered: We have several

[ccp4bb] A postdoc position is available

A postdoc position in membrane protein structural biology is available in the Biomolecular Research Laboratory (BMR) at the Paul Scherrer Institute, Switzerland. The successful candidate will work on the production, characterization, crystallization and structure determination of the serotonin

Re: [ccp4bb] Editing mesh in pymol?

One option is to use the map_double command to make a finer mesh, e.g., map_double mymap.map, -1 The maps produced by CCP4 by default are typically too coarse. Cheers. On 3/25/2010 12:00 PM, Paul Lindblom wrote: Hi everybody, can anybody tell me how to increase the number of lines in a m

[ccp4bb] Editing mesh in pymol?

Hi everybody, can anybody tell me how to increase the number of lines in a mesh, when I generated a electron density map in pymol? My mesh has to much space between the lines. The command "min mesh spacing" doesn't work, though I'm not sure, if this the right command at all. Thanks, P.

Re: [ccp4bb] Calculation of the net charge of an electrostatic surface for secondary structural elements

Hello Rebecca, this is merely a guess, but I think, it should work. As you calculate the electrostatic surface potential in pymol, it uses apbs. apbs, if I remember correctly creates an intermediate PDB-file where the B-factor column is replaced with the partial charge of that atom. So if you ca

Re: [ccp4bb] ccp4 vs. phenix special position atoms

Hi Pavel, you should add to the explanation what /==1 and !=1 are, as the majority of people don't know. / == : equal != : not equal Maia / / Pavel Afonine wrote: Hi Regina, this subject was discussed on PHENIX bulletin board some time ago: http://www.phenix-online.org/pipermail/phenixbb

[ccp4bb] Calculation of the net charge of an electrostatic surface for secondary structural elements

Dear CPP4 community, I am in search of a program that will calculate the net charge of an electrostatic surface formed by individual secondary structural elements (versus the entire protein) of a structure: for example, the net charge of the electrostatic surface of helices 2 and 3 versus, say

Re: [ccp4bb] R merge and R init

What XPREP (and some other programs) calls Rint is the same as Rmerge and is given by 100Sum|I-|/Sum(I) where the sums are calculated over all reflections with more than one equivalent (symmetry equivalents and identical indices), I is the intensity of an individual reflection and is the mean int

[ccp4bb] summary: Display X-ray images in windows

Thanks to everyone who answered. There are many ways to display the images. Summarized here are the answers: - "adxv" http://www.scripps.edu/~arvai/adxv.html Run it with the option "-nopixmap" if you are using it inside an NX client - -

Re: [ccp4bb] 2,3-butanediol

One thing I found with 2,3-Butanediol was for some crystallizations you can make it up a cryo solution with it at 12% and then put a thin layer it on top of the crystal droplet in a sitting drop well. Then you can loop the crystal and pull it up through the cryo layer - then out and to N2(l). J

[ccp4bb] N-term sequencing facility

Hi all, can anyone recommend an N-terminal sequencing facility in Germany, or nearby in Europe, which does seqquencing of PVDF blotted protein? Perhaps replies off-board are best and I can post a summary anyone interested. Thanks in advance, Tim Keys PhD Student Medizinische Hochschule Hannove

[ccp4bb] AW: [ccp4bb] 'Mushroom' shipping dewar for Rigaku pucks

Hi Todd, In case no one answered: We have several of those MVE dry shippers and sometimes use them to store Rigaku pucks. The racks do not fit in nicely. You have to use some force to get them into the shipper, but it works. Cheers, Dirk --- Dr. Dirk Reinert Boehringer Ingelheim Pharma GmbH & C