[phenixbb] phenix.refine problem CIF generated by PRODRG

Lucas Bleicher lbleicher at yahoo.com
Thu Mar 15 08:44:09 PDT 2007

--- Nicholas Noinaj <noinaj at uky.edu> escreveu:

> if all else fails, have you tried getting parameters
> for your ligand from the PRODRG Server and using
> that for inputing the ligand parameters into
> phenix.refine directly when you setup the refinement
> job?  (I think i have done this before???)
> here is the website in case you aren't familiar...
> http://davapc1.bioch.dundee.ac.uk/programs/prodrg/

The message was not directed to me, but as PRODRG was
cited, I'd like to comment on that.

I have been using the PRODRG server to generate
parameters for my ligands for some time. When I use
the CIF file on refmac it works perfectly. However, if
I use the same file on phenix.refine the ligand
becomes very distorted. I could do all protein
refinement on phenix.refine and then run some cycles
of refinement on refmac to do ligand refinement, but
I'd really like to do all the refinement in phenix,
which, for my cases, seems to produce much better
results than refmac. Does anybody faced a problem like
this? If so, did you succeeded in correcting it?

Lucas Bleicher

Fale com seus amigos  de graça com o novo Yahoo! Messenger 

More information about the phenixbb mailing list