Re: [ccp4bb] Nucplot manual

Hello, I could access the site http://www.biochem.ucl.ac.uk/bsm/nucplot/contents.html without problems. Maybe it was down for some time? Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Thu, 6 Nov 2008, Raja Dey wrote: Dear Fri

[ccp4bb] Opinions on Crystal Imaging Systems

Dear CCP4BB community, We are looking into acquiring a crystal imaging system. I'm keen to learn about personal preferences and experiences, perhaps with some technical performance specifics. Points of interest include (but are not limited to) * quality of images (focussing depth, lightin

[ccp4bb] Nucplot manual

Dear Friends, Can anyone provide me the manual of nucplot as .pdf or .doc file? Thanking you in advance... Raja Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

[ccp4bb] Postdoctoral position at the University of Liverpool: De Novo phasing using long X-ray wavelengths

Postdoctoral position available in the School of Biological Sciences, University of Liverpool DE NOVO PHASING USING LONG X-RAY WAVELENGTHS Salary: £30,594 pa Duration: 1 year initially Closing Date: 26 November 2008 Start date: Immediately available Sulphur anomalous scattering is a la

Re: [ccp4bb] differentiating cation and anions in high resolution structures

Dear Kristof, The following literature can be a start point for you. /Acta Cryst./ (2003). D*59*, 32-37 Is the bond-valence method able to identify metal atoms in protein structures? P. Müller

Re: [ccp4bb] differentiating cation and anions in high resolution structures

Kristof, I don't know of such programs, but it wouldn't surprise me that distang could be jiggered to do what you want. The ribosome folks surely have dealt with this. No matter what program you use (or if you do it "by hand"), let the chemistry guide you: Na+ peaks will be weaker (only 10 elec

Re: [ccp4bb] hydrophobic surface representation

In the paper "Computational analyses of the surface properties of protein-protein interfaces" Acta Cryst. (2007). D63, 50-57, it is described how to do it using a GRID-type hydrophobic potential in CCP4MG. However, I could not find the corresponding menus in CCP4MG when I (quickly) tried. Mic

[ccp4bb] differentiating cation and anions in high resolution structures

Dear all, I'm looking for some means (literature references,.. possible programs) to differentiate between cations (Na+), anions (e.g. Cl-) and water molecules in high resolution protein/DNA structures, based on B-factors, distances, coordination, etc.. Does anyone has got an idea of what's

[ccp4bb] Postdoc position in industry - Syngenta, Bracknell

I would like to draw your attention to this post : Crystallography postdoc with Syngenta Crystallography postdoc Jealott's Hill, Bracknell, Berkshire Syngenta is a world-leading agribusiness committed to sustainable agriculture through innovati

Re: [ccp4bb] sugar ligand refinement in coot

Hi Lei, You can make a new library using Libcheck in CCP4 or eLBOW in Phenix . Then you can handle your ligands in Coot. Of course , the new PDB file for the GLC-GLC can be obtained from PDB or you can make it by libcheck yourself. Good luck! liu Petr Kolenko wrote: Hi Lei. As I expect, you u

Re: [ccp4bb] hydrophobic surface representation

Hi! To my knowledge one could use the program GRID available on http://www.moldiscovery.com/soft_grid.php to calculate the hydrophobic molecular-interaction field on the surface of the protein. But I guess it comes with a small license fee for academic users. Best Regards, Madhu Sebastiano P

Re: [ccp4bb] hydrophobic surface representation

At the bottom of the page http://cmgm.stanford.edu/classes/grasp/ is the code how to colour code hydrophobic residues with GRASP - this is not a calculation, I'm afraid, just colour coding. As far as I know GRASP does not have a web-interface. You can install grasp in a Windows installation wi

[ccp4bb] hydrophobic surface representation

Hi all, I'd love to have a surface representation of my structure in which I plot the hydrophobic exposed residues. A bit like an electrostatic potential plotted onto the surface, but rather than hydrophilic, an hydrophobic one. Is there a nice web server or a program that does that or you guys ju

Re: [ccp4bb] sugar ligand refinement in coot

Hi Lei. As I expect, you use REFMAC for structure refinement. This link should help you to connect in principle any atoms between residues (or ligands as well). http://www.ccp4.ac.uk/html/refmac5/files/coordinates.html#pdb_link You can also find many examples of different LINKs in the PDB rec