Dear Garib,
Thank you very much. I will try the keyword.
> Your case: Do you see some sort of modulation of intensities in your images?
> Something like weak strong intensities along c axis? Or do you see elongated
> peaks in the images.
Sorry I'm not sure what "modulation of intensities in imag
Dear Yamashita
Refmac indeed does not apply vdw repulsions (antibumping restraints) if the sum
of occupancies is less than 1 and atoms do not belong to the same residue with
the same alt code. It means that if you have two or more molecules each with
occupancy less than 0.5 then there will be n
Dear Garib,
Sorry I'm a little confused.
As Eleanor said, Is it true that Refmac doesn't apply vdw restraints
if the sum of the atoms occupancies is <= 1?
> If you want to deal with translational disorder (e.g. you have a modulated
> crystal then there is another way.
In my data, there are crys
OK, I see. I looked at my log-files, and I also have about 30
restraints for for VDW_symm. Then I looked at another structure with no
packing issues, and the corresponding numbers is ~90. What I am saying
is that the number of restraints that you have appears to be reasonable.
It seems that cla
In refmac you can remove vdw interactions between chains using the following
command
It is an example:
vdwr exclude between chains A B
or between resdues:
vdwr exclude between residues first residue 123 chain A second residue 155
chain B
Regards
Garib
On 8 Dec 2010, at 16:09, Keitaro Yama
At the moment there is no way of telling refmac to ignore clashes between
symmetry related atoms.
Is there any reason you would want to do that? Perhaps there are other ways of
solving the problem you would like to solve.
I can add a keyword to force to ignore these clashes if there is sufficien
As far as I know there are no repulsions restraints applied if the sum
of the atoms occupancies is <=1.0. If one atom is fully occupied. and
another partial then there will be a restraint.
Eleanor
On 12/08/2010 04:45 PM, Keitaro Yamashita wrote:
Dear Ed,
These tables were reported by Refmac5
Dear Ed,
These tables were reported by Refmac5:
Before refinement,
---
Restraint type N restraints Rms Delta Av(Sigma)
.
VDW repulsions: symmetry: refined_atoms 38 0.232
On Thu, 2010-12-09 at 01:09 +0900, Keitaro Yamashita wrote:
> When I tried to refine using Refmac5, the output told many vdw
> repulsions with symmetry mates
What do you mean by that? I had a similar situation recently, and there
are many records in the log file that say something like this
IN
Dear all,
I'm refining complex structure against X-ray diffraction data with
packing disorder.
(Some domains overlap with their symmetry mates (4-fold), so their
occupancies are set to 0.25)
I'd like to know whether refinement programs can exclude any
interaction among symmetry mates from geometr
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