Hi Jürgen,
it should properly take symmetry into account. I would be very surprised if
it doesn't.
Pavel
On Sun, Nov 18, 2012 at 9:14 AM, Bosch, Juergen wrote:
> Hi Pavel,
>
> does this also work for symmetry related atoms ?
>
> Jürgen
>
> ..
> Jürgen Bosch
> Johns Hopkins
On 11/17/2012 03:04 PM, Rex Palmer wrote:
I would like to specify a target atom in a pdb file and then isolate
all atoms within a given distance of the target. The selected atoms
are then to be placed in a new pdb file.
AWKward BASHing:
#! /bin/bash
read x y z <<<$(awk '{if(substr($0,1,4)=="A
Of course (sort of):
Extensions->Maps->Export Local Map Fragment
B
This is nice. Can it do the same for the map?
Thanks
Jim Brannigan
On 18 November 2012 15:52, Bernhard C. Lohkamp wrote:
In Coot:
Centre on the atom/place of interest.
Extensions->Modelling->New Molecule by Sphere
then se
In O, the command is called symm_sphere.
http://xray.bmc.uu.se/alwyn/A-Z_of_O/everything_s.html#anchor536668
James
On Nov 18, 2012, at 10:14 AM, Bosch, Juergen wrote:
> Hi Pavel,
>
> does this also work for symmetry related atoms ?
>
> Jürgen
>
> ..
> Jürgen Bosch
> Joh
Hi Pavel,
does this also work for symmetry related atoms ?
Jürgen
..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +
In Coot:
Centre on the atom/place of interest.
Extensions->Modelling->New Molecule by Sphere
then select the molecule and sphere radius.
B
I would like to specify a target atom in a pdb file and then isolate all atoms
within a given distance of the target. The selected atoms are then to be
Hi Rex,
as easy as:
phenix.pdb_atom_selection model.pdb "within(3, chain L and resseq 9 and
name CA)" --write-pdb-file=cut.pdb
which in the above example selects all atoms within 3 A from CA atom in
chain A of residue number 9, and writes them into cut.pdb file.
Pavel
On Sat, Nov 17, 2012 at 1
Hi Rex,
> I would like to specify a target atom in a pdb file and then isolate all
> atoms within a given distance of the target. The selected atoms are then to
> be placed in a new pdb file.
> Any suggestions please.
This is simple to do in PyMOL. After loading your structure just use
the mouse
Hi,
You can do this with MOLMOL. The official page from Wuthrich's group seems
to be no longer supported. You can find it on the web from several other
websites. For example: (http://pjf.net/science/molmol.html), (
http://blog.louic.nl/?p=397).
1) SelectAtom '#1:10@CA' (Structure 1, residue 10,
I would like to specify a target atom in a pdb file and then isolate all atoms
within a given distance of the target. The selected atoms are then to be placed
in a new pdb file.
Any suggestions please.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestea
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