[ccp4bb] How to calculate compactness of a structure

[Xiaoming Ren]

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 any advice! 

Thanks in advance,
Xiaoming



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

[Xiaoming Ren]

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

[Xiaoming Ren]

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 monomers are placed. I could not 
get a intact nucleic acid chain except setting the cartoon_nucleic_acid_mode 
value to 1, with the backbone passing through ribose C3' atoms.

I tried to add SEQRES lines into the pdb file according to the pdb instruction, 
but it doesn't work if I want the backbone to pass through phosphorus atoms.

May I get some suggestions from you? Although it's not a big problem, it's 
really painful.

Thanks a lot and best,
Xiaoming

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

[Xiaoming Ren]

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 file, and also 
edited .edits file for phenix.refine. In both conditions, phenix.refine works 
except that it wouldn't add covalent bonds between the residues as I expected.

I have used .edits file for covalent binding between residues before, and it 
worked well.

So there must be something wrong with my input files. But I couldn't fighure 
out where the problem is. 

Thanks a lot and best regards!
Xiaoming