[ccp4bb] How to calculate compactness of a structure

Dear ALL, I wonder if there is a way to calculate the compactness of a macromolecule structure. Is the ratio of surface area to volume a good indicator? Another question is, how can I calculate Matthews coefficient of a domain of a protein or one part of a complex? I welcome and appreciate an

Re: [ccp4bb] How to create electrostatic surface of modified DNA by APBS?

gt; > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: bshaa...@bgu.ac.il > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > > _______

[ccp4bb] How to create electrostatic surface of modified DNA by APBS?

Dear all: I'm having a problem create the electrostatic surface for a DNA chain containing several modified nucleotides. APBS could not identify those residues and reported them as unassigned. What should I do to solve this problem? Thanks a lot and best, Xiaoming

[ccp4bb] Problem with making a continuous nucleic acid chain

Dear all: I am facing a display issue in pymol. In my structure, there is a nucleic acid chain with some monomers which are modified nucleotides built in scketcher of ccp4 suite. However, When I showed the structure in pymol as cartoon, the nucleic acid chain was discontinuous where the monomer

[ccp4bb] Problem with making covalent bonds in phenix by LINK or edits file

Dear all: I am encountering a problem. I built a monomer model which is a modified nucleotide with Sketcher in ccp4 suite and generated the .cif file of this monomer. However, I could not make it bind with other nucleotides in the nucleic acid chain. I have tried to write LINK lines into PDB fi