I am working on a data set of an T=4 icosahedron protein crystal, employing
molecular replacement methods.
I've consulted a professor, he told me that my crystal is in fact
isomorphous to the model so that there is no need for MR.
So I figured such command lines:
phenix.refine output.mtz model.p
Hi,
for each PDB file run:
phenix.pdb_interpretation model_1.pdb ligand.cif
phenix.pdb_interpretation model_2.pdb ligand.cif
...
phenix.pdb_interpretation model_N.pdb ligand.cif
and it will result in a buch of output files
model_1.pdb.geo
model_2.pdb.geo
...
model_N.pdb.geo
where each *.geo fil
Or eLBOW with a Python script. I can provide a start if you desire.
On Thu, Dec 2, 2010 at 9:29 AM, Bryan Lepore wrote:
> On Thu, Dec 2, 2010 at 12:17 PM, wrote:
>> get values for chosen torsion angles of ligand ...
>
> moleman with a script.
>
> -Bryan
>
--
Nigel W. Moriarty
Building 64R02
On Thu, Dec 2, 2010 at 12:17 PM, wrote:
> get values for chosen torsion angles of ligand ...
moleman with a script.
-Bryan
Dear All,
I have set of pdb files (few hundred), which contain the same ligand. I
would like to get values for chosen torsion angles of ligand. I know I can
do it manually (what would be painful and time consuming) but maybe someone
does know smarter and more automated way of doing it? I would
Summary attachment: BSG Details.doc
The preliminary programme for the BCA Spring Meeting 2011 at Keele is now
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at http://crystallography.org.uk/spring-meeting-2011 and registration is now
open.
The Programme Chair for BCA 2011 Keele is Arwen Pearson.
The main meeting takes place April
If you will replace link line with the following
LINKRC1 NAG A1003 ND2 ASN A 611NAG-ASN
Then it should be read by refmac and by coot. And restraints should be applied
properly
regards
Garib
On 2 Dec 2010, at 06:49, Dr. STEPHEN SIN-YIN, CHUI wrote:
>
I dont think that isnt the correct format for a LINKR record.
LINKRC LEU A -1 N CYG A 0LEU-CYG
LINKRC2 CYG A 0 N SER A 2
CYG-SER
It is like this - it points to a named LINK entry in your restraints
library eg LEU-CYGun refm
Easiest to follow the documentation..
http://www.ccp4.ac.uk/dist/html/dm_ncs_averaging.html
You get the matrices most easily by mapping A to B A to C etc using
lsqkab if you want to average over the A molecule..
Eleanor
On 12/01/2010 05:41 PM, Francis E Reyes wrote:
Hi all
I'm trying to f
On 02/12/10 06:49, Dr. STEPHEN SIN-YIN, CHUI wrote:
> Dear All,
>
> Please see the maps for the ASN residues of the protein, As suggested by
> colleague, they are NAG which are connected to the N atom of ASN413 & ASN611.
> I put the NAG molecule to those density and try to use the following command
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