Re: [IMP-users] Issue with Flexible Modeling Using PMI

[Ben Webb <>]

On 10/20/20 12:09 PM, Jake Sumner wrote:
> I have recently been trying to conduct flexible modeling using beads of 
> varying size for a particular protein. I have separated the protein into 
> 5 domains based on the PDB crystal structure, and I have already done 
> rigid body modeling to fit the domains to an EM map we have. However, I 
> seem to run into an issue when I try to do flexible modeling by creating 
> bead models using the topology file. Essentially, each of the domains is 
> coming directly from the PDB crystal structure, and I am creating beads 
> from the residues listed there and in the FASTA file. The beads are 
> created with a varying number of residues to reflect the size and 
> overall flexibility of the domain. When I set up the topology file in 
> this manner, and make sure to not invoke the rigid body or super rigid 
> body options, I get a structure warning from IMP saying it is making the 
> components flexible.

Right, if you do that there is nothing constraining your beads to 
continue looking like the input crystal structure. If that's your 
intention, then you can safely disregard the warning.

> However, I also get a warning that "No hierarchies 
> were passed to create_flexible_beads()".

Hmm, that seems wrong. I'm happy to look at your system, if you can send 
it to me, to see what's going on there.

	Ben
--
                      https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle