Re: [ccp4bb] crystals of 1D

In case you are using a "standard" purification protocol (with, say, two purification steps and a polishing gel filtration) you might also try adding yet another purification step, no matter how pure your sample looks on SDS-PAGE. Tim -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr.

[ccp4bb] molprobity in coot: BL WARNING:: reduce didnt run ok, so stop here!

Hello, I just installed Wincoot 0.6.1 and reduce/probe as well, and tested with several PDB files for probe/clash validation. For some PDBs it worked perfectly; but for my own model, it did not work and I have the following message: . Found 0 hydrogens (0 hets) S

Re: [ccp4bb] Solvent accessible regions of the channel (Pore)

Hello Muhammad, The comments thus far are spot on, but the choice depends on your objective. If you are looking for the probable substrate trajectory, CAVER (though I'd suggest MOLE http://mole.chemi.muni.cz/web/), but these lack detail of the solvent accessible surface. If you want fast render

Re: [ccp4bb] crystals of 1D

Have you tested how well they diffract? You should do that first. Sometimes small, ugly looking crystals can give good data. ho

Re: [ccp4bb] crystals of 1D

Hi, Have you also considered substituting the components of your initial crystallization hit. For example, you can substitute the original PEG with others PEGs. You can also systematically replace the cations (CaCl2, MgCl2, etc) and anions (CaCl2, CaOAc, etc) from the original conditions. This a

[ccp4bb] PDBe to retire the OCA search system in October 2010

Dear PDBe users, The Protein Data Bank in Europe (PDBe; pdbe.org) will retire the OCA search system in October 2010. Users and developers relying on this service are advised to direct their links to the OCA site at the Weizmann Institute instead - http://oca.weizmann.ac.il/oca-bin/ocamain De

Re: [ccp4bb] Solvent accessible regions of the channel (Pore)

Hi Bashir, In Pymol: 1. Show---Surface (will generate surface around the protein) 2. Setting-Surface---Cavities & Pockets Only. (will show only Cavities inside) 3. Use cavity_cull command to set the filter for cavities. (eg. set cavity_cull, 40) Manish -- Manish Chandra Pathak,

Re: [ccp4bb] crystals of 1D

Hi, i'm not sure if you try just seeding in your original condition. If yes, you could try matrix seeding. Another option would be addtitves or the silver bullets from McPherson. Sometimes sitting drop vs. hanging drop make a difference. Mutations at the surface are quite often an excellent alt

Re: [ccp4bb] Possible sulphate

A reasonably strong peak on the S atom in an anomalous difference Fourier map. From: Rex Palmer Reply-To: Rex Palmer Date: Wed, 7 Apr 2010 09:00:59 -0500 To: Conversation: [ccp4bb] Possible sulphate Subject: [ccp4bb] Possible sulphate What seems to be a possi

Re: [ccp4bb] Solvent accessible regions of the channel (Pore)

Dear Muhammed, HOLLOW (http://hollow.sourceforge.net) probably is OK. You can find a nice example at figure 2 of Ujwal et al., PNAS vol15(46), 17742-17747 (the interior surface of the mVDAC1 channel) HTH Jose Miguel --

[ccp4bb] crystals of 1D

Hi All, I am dealing with a protein that crystallizes in 1D. The broom stick crystals does not yield with any improvement w.r.t their dimension. I have tried using different concentration of salt, ppt and pH around the parent condition, even tried seeding and temperature changing. However, any

Re: [ccp4bb] Third CCP4 workshop in USA, at APS, June 10-17

Dear Colleagues, This is a third and final call for applications for the third annual CCP4 school: "From data collection to structure refinement and beyond" which will be held at Advanced Photon Source, USA. Application deadline has been extended from Friday, April 9 to Tuesday, April 12.

Re: [ccp4bb] Solvent accessible regions of the channel (Pore)

Caver? http://loschmidt.chemi.muni.cz/caver/ cheers, charlie

Re: [ccp4bb] Possible sulphate

Rex Palmer wrote: What seems to be a possible sulphate has been identified in our electron density. What steps could/should be taken to confirm or consolidate this assignment that would satisfy referees? Rex Palmer Birkbeck College Geometry of the interactions (and the shape of the electron d

[ccp4bb] Crystallization Teaching dvd

Does anyone have a dvd depicting protein crystallization including setting up microplates and hanging/sitting drops that would be suitable for teaching purposes? Rex Palmer Birkbeck College

[ccp4bb] Possible sulphate

What seems to be a possible sulphate has been identified in our electron density. What steps could/should be taken to confirm or consolidate this assignment that would satisfy referees? Rex Palmer Birkbeck College

[ccp4bb] Solvent accessible regions of the channel (Pore)

Dear all; Can anybody help me how I can make the solvent accessible surface(inside) of the channel(pore)by pymol, or by any other programme. Thanks in Advance -- Muhammad Bashir Khan Department for Biomolecular Structural Chemistry Max F. Perutz Laboratories University of Vienna Campus Vienna B

[ccp4bb] Waters from Coote

Is there a preferred type of density map to use with Coote for identifying waters? Rex Palmer Birkbeck College

[ccp4bb] Postdoctoral Position at PSI

We currently have an opening for a postdoctoral fellow in integrated structural biology, c.f. http://www.psi.ch/pa/offenestellen/Wissenschaft/2219 Michel O. Steinmetz (Biomolecular Research) Clemens Schulze-Briese (Swiss Light Source) Paul Scherrer Institut 5232 Villigen - PSI SWITZERLAND