Charlie - can you point me to an example to test?
Eleanor
On 16 April 2018 at 23:57, Daniel M. Himmel, Ph. D. wrote:
> Have you tried using the CNS script rmsd.inp? You can explicitly list
> the atoms to superimpose and set "coord_fit=true;".
>
> -Daniel
>
>
> On Mon, Apr 16, 2018 at 3:30 PM,
Have you tried using the CNS script rmsd.inp? You can explicitly list
the atoms to superimpose and set "coord_fit=true;".
-Daniel
On Mon, Apr 16, 2018 at 3:30 PM, Carter, Charlie wrote:
> I think I’ve asked this question before and I was pointed in a number of
> unsuitable (for various reason
On 04/02/15 17:21, Robert Byrne wrote:
The 'LSQ Superpose’ in Coot can superpose nucleic acids, but it is seemingly
not possible to define non-contiguous selections.
Admittedly there's no clicky-clicky interface, but you can do it and
it's described in the manual.
https://www2.mrc-lmb.cam.
I noticed the same problem with more recent versions of CCP4 (up to and
including 6.5.001) but failed to report it….
It seems that the problem occurs regardless of the atoms chosen for selection -
main, side or all - and with both v2 and v3 PDB files.
The 'LSQ Superpose’ in Coot can superpose
Dear Charlie,
could it be related to that furanose atoms now have primes (') instead
of asterisks (*) in their names?
Best,
Tim
On 02/04/2015 05:30 PM, Carter, Charlie wrote:
> I'm (still) using ccp4.6.1.1.
>
> Scripts that used to superimpose one tRNA on another now all return the error
>
>
Charlie,
Most probably this indicates a problem with your PDB file, either a format or
things like misplaced or absent residue name etc. If you can send me your files
and exact command that you run, I can have a look into this.
In future, if you see a message like "report to developer" please s
Can you send more details? the log file? the pdb
On 30 May 2014 22:54, Carter, Charlie wrote:
> This is a bizarre problem. I'm trying to superimpose multiple
> conformations of the same protein using segments I expect not to change.
> LSQKAB bails with this error each time:
>
> *** RWBROOK err
On 30/12/13 04:10, Doeke Hekstra wrote:
Hi All,
I would like to superimpose a query chain (moving frame) from a rather large
PDB file (~50 chains) to a target frame specified by a chain in a reference PDB
file.
echo "FIT RESIDUE CA 2 TO 63 CHAIN $CHAIN" >> lsqkab.conf
echo "MATCH
Hi All,
I would like to superimpose a query chain (moving frame) from a rather large
PDB file (~50 chains) to a target frame specified by a chain in a reference PDB
file.
echo "FIT RESIDUE CA 2 TO 63 CHAIN $CHAIN" >> lsqkab.conf
echo "MATCH RESIDUE CA 2 TO 63 CHAIN A" >> lsqkab.conf
Dear Norman,
That did the trick! And was easy to do...
Thanks a lot,
Anita
Dear Anita
You could try adding the following additional line of input:
rotate matrix 1 0 0 0 1 0 0 0 1
This multiplies the data in XYZINM by the identity matrix (so that
the data should be unchanged) but has the
Hi David,
On Tue, Dec 23, 2008 at 10:31:28AM -0500, Borhani, David wrote:
> Hi Clemens,
>
> Thanks for all your tests; the scripts/keywords you used to run LSQKAB
> with these test systems would help to clarify what may be going right
> vs. going wrong.
That was just a simple run with
lsqkab
, as your examples clearly point out!
Dave
P.S. - I'm not sure I understand the problem that Wangsa mentions, but
it may be related to the 3- vs. 4-character atom name match.
> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On
> Behalf
Dear all,
oops - due to some disk/network issues on my side, the final edits of
my email got lost. Sorry for reposting this again (corrected):
On Mon, Dec 22, 2008 at 02:58:31PM -0500, Borhani, David wrote:
> I think the LSQKAB change at Line 291(old)/Line 300(new) DOES introduce
> new and possib
Hi Dave,
On Mon, Dec 22, 2008 at 02:58:31PM -0500, Borhani, David wrote:
> I think the LSQKAB change at Line 291(old)/Line 300(new) DOES introduce
> new and possibly incorrect logic.
Very possible, but ...
> I haven't looked at all the code, but this one change does seem to
> substitute a check
NY 10036
> david.borh...@deshawresearch.com
> 212-478-0698
> http://www.deshawresearch.com
>
> > -Original Message-
> > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On
> > Behalf Of Kevin Cowtan
> > Sent: Monday, December 22, 2008 11:39 AM
reet, 39th Floor
New York, NY 10036
david.borh...@deshawresearch.com
212-478-0698
http://www.deshawresearch.com
> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On
> Behalf Of Kevin Cowtan
> Sent: Monday, December 22, 2008 11:39 AM
> To: CC
In case it helps, you can see the diffs between the 6.0.2 version and
the 6.1 version here:
http://www.ccp4.ac.uk/ccp4bin/viewcvs/ccp4/src/lsqkab.f.diff?r1=text&tr1=1.51&r2=text&tr2=1.42.2.2&diff_format=h
The obvious changes seem to be some code from Clemens to make sure that
insertion codes m
Hi Tim,
Not a stupid question at all. This is how I came to think that version
6.0 uses atoms with alternative conformations:
If I do the same superposition (with a pdb file that contains
alternative conformations) with LSQKAB version 6.0 and 6.1:
1) Version 6.0 reports 110 atoms "to be refi
Not using lsqkab very often, this might be a stupid question: How do you
know that version 6.0 _DOES_ include multiple conformations? Maybe it only
does not report their omission?
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On M
Why not start your script with
pdbset xyzin ...
OCC UP ALWAYS OCC_RESET 1.0
BFAC ALWAYS B_reset 20
end
acob Corn wrote:
Dear everyone,
I'm attempting to do a large scripted pairwise alignment of
theoretical models to calculate rmsd over a pre-determined residue
range, but the PDBs that I'm u
Thanks to everyone for the suggestions. It appears that just adding a
bfactor and occupancy flag is the way to go (eg - there's no way to make
lsqkab less finicky). Since I'm just hacking this together and
grep/sedding out the pairwise rmsds to pipe to another program, I'd
prefer to use the eas
Jacob, lsqman from USF will be happy without B and Q, and you can pick
the set of atoms that you want to align. I think that you can run it in
script mode, as well.
Kevin
Jacob Corn wrote:
Dear everyone,
I'm attempting to do a large scripted pairwise alignment of theoretical
models to calcu
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