[Xplor-nih] parallel marvin

[John Kuszewski]

On May 12, 2008, at 7:26 PM, David A. Horita wrote:

> If I have a reasonable homology model, can I use it to start with?   
> How do I do this?

You could, but I'd avoid it if at all possible.  If Marvin's able to  
converge without starting from a homology model, you're that much  
more certain of the structure in the end.

But if you're having trouble converging, you could try replacing the  
network analysis that's done during the initialMatch script with a  
structure-based filter, using your homology model.  I haven't had to  
do this myself in the cases I've tried, but I could put something  
together.  It shouldn't be a problem, but there are a few different  
ways to implement it, and I'm not sure which would be best.  I'll  
send out a separate announcement with the code later.

One last point, though, is that you could use your homology model to  
help you score how well the network filter and so forth are working.   
Take a look at the CVN example, and you'll see references to  
"referenceStructure" in the initMatch and summarizePass scripts.   
Replace the filename there with the filename of your homology model's  
PDB, and it'll give you some interesting statistics in the headers of  
your .peaks and .shiftAssignments files.

Hope this helps.

--JK