Same sequence PDBs with slightly altered structures give very different networks

[Former user]

Hi,

I'm a grad student using Bio3D to create a DCCM/do a correlation analysis on an MD trajectory. My question is, what is the function of the PDB in the process? Does it just provide the coordinates for the generation of the DCCM? I ask because when I use PDBs of slightly different structure, with the same DCDs and same sequence, I get different net and net.cut under the same conditions. I just want to be clear on the function of the PDB for the correlation? Can I just use the MD trajectory(dcd) to create my network?

Thank you, Jacob

[Xinqiu Yao]

DCCM calculation (i.e. using dccm() function) does not require PDB. See help(dccm) for details.

Having a PDB can help to select atoms for subsequent analysis. For example, if the DCD contains all atoms but only C-alpha atoms are wanted for DCCM, using a PDB matching the topology of the DCD and the atom.select() function, you can locate C-alpha atoms in the DCD data. Of course, if the DCD only contains atoms to be used for DCCM analysis (e.g. C-alpha atoms), you can call dccm(dcd) directly without a PDB.

Let me know if you have more questions.