[ccp4bb] Zn+2 proteases

Dear All I have a questions about the Zn+2 proteases (Thermolysin based Zn+2 site) As Zinc is trouble metal when it comes to test the activity. Which is better substitute for it. Is MgCl2 or MncCl2 Why one is preferred over the other. best Jiri

[ccp4bb] Electrostatic Potential: Poisson-Boltzmann criteria

Hi I am just calculating the Electrostatic Potential, and I wanted to know your opinion which force field is better.What is criteria to choose and not to choose the pKA... best Jiri

Re: [ccp4bb] Van der waals force

# > Bruno P. Klaholz > Centre for Integrative Biology > Institute of Genetics and of Molecular and Cellular Biology > 67404 ILLKIRCH > FRANCE > http://igbmc.fr/Klaholz > > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK > <CCP4BB

[ccp4bb] Van der waals force

Hi I just have a basic question if the Van der waals interaction will exist between the hydrophobic residues or it can also be contributed by the polar residues as well. What distance is required for the Van der waals interaction. best Jiri

[ccp4bb] Electrostatic Potential: Poisson-Boltzmann

Hi I am calculating the Electrostatic Potential of my protein. But there were few flexible region with high B-factor and I deleted that part of the protein and then recalculated it. But there I can see a big change.As I have a structure in the presence and the absence of the peptide and the these

[ccp4bb] drawing of peptide interaction

Hi I wanted to draw a peptide interaction in the catalytic site together with side chain of the enzyme. What is a good program to do that, or web based service. I see the LIGPLOT and I am wondering if there are some other alternatives of that. best Jiri

[ccp4bb] prodrg in coot

Dear members I am wondering how to activate the prodrg tool in coot. Does it has to be purchased to get licence??. If I made the ligand in ligand builder and click apply, it gives window info no cprogrg not found. I am using the coot 0.8.4 from the ccp4 site. Does the enhanced ligand tools has to

[ccp4bb] ligand with out space group information

Hi I have model of ligand molecule and it does not open in coot. Its not a crystal structure. I can view it in the pymol or chimera but not in the coot. It gives error that it does not have any space group information. Is there is a way to open it in coot. best Jiri

[ccp4bb] surface area

Hi I am comparing some protein complex with PISA analysis. Can someone make a note what is difference between interface area and buried surface area. I think buried surface area also include the interface area + the area encloses with in the protein. Does it make sense to mentioned the interface

[ccp4bb] case study of peptides

Hi I am looking for some literature or the structure of the metallopeptidases where the substrate bound with the ezyme but with shifted P2-P1-P1'-P2' cleavage site. May be some theoretical case study is there. Best Jiri

[ccp4bb] secondary structure assignment to PDB file

Hi Is there any tool that can assign secondary structure to the PDB file. The problem is if I used different modelling tools, there are regions in the protein which does not remain consistent and looks different in different application. best J. Vitali

Re: [ccp4bb] Visualize symmetry operations

Hi Aaron may be this tool can be helpful https://symd.nci.nih.gov/ or in the pymol there is script https://pymolwiki.org/index.php/Symmetry_Axis Visualizing the transformation between two selections/objects https://pymolwiki.org/index.php/RotationAxis PDB has a symmetry browser

[ccp4bb] intrasubunit rotation axis

Hi All I am interested to measure the symmetry axis of individual sub-unit (chain A & chain B) along with the symmetry axis of the heterdimer (AB). Each chain is also 2 fold axis, and I can measure by removing 1 chain and measure for the other and then combine all the symmetry axis in the 1 PDB

[ccp4bb] Symmetry axes

Dear All can some one advise that how to calculate/draw the symmetry axes on the structure. On the deposited structure one can do in the Jmol by selecting the symmetry option but how to do it off line. best Jiri

[ccp4bb] good images

Dear All I am making the images of the structure in the CCP4MG, I want to ask which format is best for good quality images JPEG or TIFF and what dpi is best. I add the legends in corel draw. If somebody have useful tips or suggestions. best Jiri

[ccp4bb] cutaway view of the electrostatic potential

Hi All I am trying to make images of the electrostatic surface of structure. I don't know how to make a cutaway view in this representation. I don't see any option in the CCP4MG. Is thiere any tutorial for this in chimera or other programs?? best J. Vitali