Dear list,
In my structure there are some residues in alternative conformations that I
would like to refine. I have mostly run Phenix for refinement but recently, I
have switched to Refmac and since I have no much of experience I dig into the
ccp4 archive and found some tips from Eleanor
Certainly Elenaor. Here are a few:
# typical lysozyme
% refmac_occupancy_setup.com 193l.pdb
occupancy refine
occupancy group id 1 chain A residue 1 alt A
occupancy group id 2 chain A residue 1 alt B
occupancy group id 3 chain A residue 59 alt A
occupancy group id 4 chain A residue 59 alt B
James - could you send me a few examples to add to the documentation?
Lockdown means I cant easily access my own examples - all trapped on the
lab desktop..
Eleanor
On Mon, 7 Jun 2021 at 17:18, James Holton wrote:
> I wrote a script for auto-generating occupancy refinement relationships
> for
I wrote a script for auto-generating occupancy refinement relationships
for refmac. It is perhaps not as sophisticated as what phenix does
internally, but it gets common things right, like if you have a 2-headed
side chains or partial-occupancy metals.
In GUI2 the Advanced box allows you to do that
eg RESO 10 3 say if you wanted to restrict resolution..
Eleanor
On Mon, 7 Jun 2021 at 11:35, Marina Gárdonyi <
marina@pharmazie.uni-marburg.de> wrote:
> Hi,
>
> I didn't know that I can also enter keywords without a file! That is a
> good note,
Hi,
I didn't know that I can also enter keywords without a file! That is a
good note, thank you!!
Best regards,
Marina
Zitat von Jon Cooper :
Hello, the keywords can be entered in refmac gui (in one of the
dropdown things), so you don't need a file, as such, but it's useful
to keep a
Hello, the keywords can be entered in refmac gui (in one of the dropdown
things), so you don't need a file, as such, but it's useful to keep a record.
Sent from ProtonMail mobile
Original Message
On 5 Jun 2021, 16:39, Marina Gárdonyi wrote:
> Hello everyone,
>
> I am trying
here is an extract from the documentation.
is it a help?
i will try to find examples.
eleanor
This keyword defines number of cycles of refinement.
Occupancy refinement (version 5.6.0037) from Tidied up
occupancy group id chain ... residue
atom alt
or
occupancy group id chain ...
Hello everyone,
I am trying to refine structures with Refmac.
The problem is that nobody from my working group is familiar with this
programm. They are using Phenix exclusively.
That's why I need your help. I would like to refine the occupancy. I
know that I need a keyword file for this,
