On 17 May 2012 21:27, Eleanor Dodson wrote:
> I am not familiar with CNS restraints, but whatever the program restraints
> are - if you do a omit map, or just set the occupancies of the metal and
> its surroundings to 0.00 and do a few cycles of refinement, I believe any
> model bias will disappe
I am not familiar with CNS restraints, but whatever the program restraints
are - if you do a omit map, or just set the occupancies of the metal and
its surroundings to 0.00 and do a few cycles of refinement, I believe any
model bias will disappear and what you see will be pretty accurate
descriptio
On Sat, 2012-05-12 at 08:48 -0400, Dave Roberts wrote:
> However, I just want to make sure the metal environment is not due to
> the fact that I did something wrong in my refinement script - thus
> making it tetrahedral because it was refined as tetrahedral.
...
> I don't use CCP4 for refinement,
Thanks for the replies. Yuri, yes, those were my exact concerns. This
is a molecular replacement structure, but that was done with an apo
structure, so I am certain the metal is there. My resolution is around
2.3 angstroms, which I think is OK for determining geometry.
I have done omit maps
Hi Dave,
I sounds to me like you are worried about 2 separate things here.
A: Am I affecting the geometry of the coordination sites with a restraint file
that is innacurate?
B:Are my electron density maps biased, and what I am seeing is not really there?
AFAIU, if you have a restraint file that
It depends on what is in the restraints file(s). In refmac, I believe only
the bond lengths are restrained, but only if you identify specific
metal-lagand links. Otherwise, there are no bond length or angle restraints.
Roger Rowlett
On May 12, 2012 8:48 AM, "Dave Roberts" wrote:
> Hello
>
> I ha
Hello
I have a protein structure I've been working on (seemingly forever),
which includes a bound metal. In fact, I have the same structure with
different metals bound (that's it's job, so it's not a surprise).
My question is this - the metals I'm talking about now are Ni+2, Cd+2,
and eithe
