One option would be molrep
molrep -m -mx
Of course it assumes that your two structures have overall similar
structures and no substantial conformational changes.
As the question posed, I think, it does not have solution (only
approximations). Almost all programs assume either atom labe
So it's really a non-CCP4 non-solution...
--G
On Fri, 26 Feb 2010, Pavel Afonine wrote:
On 2/26/10 8:35 AM, Gerard DVD Kleywegt wrote:
Nope - LSQMAN would still be looking for stretches of sequentially ordered
residues and would only match atoms with identical names (" CB " with " CB
", for
On 2/26/10 8:35 AM, Gerard DVD Kleywegt wrote:
Nope - LSQMAN would still be looking for stretches of sequentially
ordered residues and would only match atoms with identical names (" CB
" with " CB ", for instance).
--G
PS: Brownie points for the non-phenix solution, though!
A non-CCP4 (PHE
Nope - LSQMAN would still be looking for stretches of sequentially ordered
residues and would only match atoms with identical names (" CB " with " CB ",
for instance).
--G
PS: Brownie points for the non-phenix solution, though!
On Fri, 26 Feb 2010, J?rgen Bosch wrote:
How about LSQMAN ?
w
eficient at the moment, but that seems worth trying.
Steve
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Gerard DVD Kleywegt
Sent: Friday, February 26, 2010 10:50 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3D fitting
But it still won't
How about LSQMAN ?
with ATOM_types Side_chain ?
That should do the trick.
Jürgen
P.S. sorry it's not really a CCP4 related program, but I use it very
frequently in conjunction with the CCP4 suite :-)
On Feb 26, 2010, at 11:22 AM, Ed Pozharski wrote:
On Fri, 2010-02-26 at 16:50 +0100, Gera
On Fri, 2010-02-26 at 16:50 +0100, Gerard DVD Kleywegt wrote:
> But it still won't solve Miri's problem. I think what she is asking
> for is a
> program that detects which atoms should be matched to which,
> irrespective of
> their names (i.e., not assuming they are called " CA ") and order
> (i.
mail.ac.uk] On Behalf Of
Gerard DVD Kleywegt
Sent: Friday, February 26, 2010 10:50 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3D fitting
But it still won't solve Miri's problem. I think what she is asking for
is a
program that detects which atoms should be matched to which,
ir
Perhaps supcomb could do this:
http://www.embl-hamburg.de/ExternalInfo/Research/Sax/supcomb.html
Quoting Gerard DVD Kleywegt :
But it still won't solve Miri's problem. I think what she is asking
for is a program that detects which atoms should be matched to
which, irrespective of their nam
But it still won't solve Miri's problem. I think what she is asking for is a
program that detects which atoms should be matched to which, irrespective of
their names (i.e., not assuming they are called " CA ") and order (i.e., not
nicely sequential such as amino-acid residues), and then applies
SSM is also available in Coot and CCP4MG of course...
Eleanor Dodson wrote:
would ssm serve your purpose?
eleanor
ebi or ccp4i
Miri Hirshberg wrote:
Sun., Jan. 17th 2010
EBI
Greetings,
I am looking for a 3D structure superposition program which takes
two structures and superpose them ba
would ssm serve your purpose?
eleanor
ebi or ccp4i
Miri Hirshberg wrote:
Sun., Jan. 17th 2010
EBI
Greetings,
I am looking for a 3D structure superposition program which takes
two structures and superpose them based only on the coordinates X,Y,Z
regardless of of residue/atoms name.
(both f
PISA will do that - an EBI service or available less prettily from ccp4i
Eleanot
Miri Hirshberg wrote:
Sun., Jan. 17th 2010
EBI
Greetings,
I am looking for a 3D structure superposition program which takes
two structures and superpose them based only on the coordinates X,Y,Z
regardless of of re
In ccp4i select "Coordinate utilities/Superpose"
And then on the first menu select "Superpose using secondary structure
matching".
It will automatically superpose based on fold rather than atom
alignment. (This is the same software as used at the EBI for what used
to be called MSDfold).
Mi
The Matchmaker utility in Chimera is another good one:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html
On Sun, Jan 17, 2010 at 12:54 PM, Miri Hirshberg wrote:
> Sun., Jan. 17th 2010
> EBI
>
> Greetings,
>
> I am looking for a 3D structure superposition program
Hi Miri,
you can do this (and more) using a tool from PHENIX:
phenix.superpose_pdbs [pdb_file_fixed] [pdb_file_moving] [parameter_file]
A couple of examples:
phenix.superpose_pdbs fixed.pdb moving.pdb selection_fixed="chain A and
name CA" selection_moving="chain B and name CA"
phenix.superp
Sun., Jan. 17th 2010
EBI
Greetings,
I am looking for a 3D structure superposition program which takes
two structures and superpose them based only on the coordinates X,Y,Z
regardless of of residue/atoms name.
(both files are in PDB format)
Thanks
Miri
Dr M
17 matches
Mail list logo
