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
I think I’ve asked this question before and I was pointed in a number of
unsuitable (for various reasons, including lack of access to the programs like
ccot) directions. Why can one not use lsqkab to superimpose the nucleic acid
portions of protein RNA complexes?
I’m asking now because I’ve fou
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
>
>
I'm (still) using ccp4.6.1.1.
Scripts that used to superimpose one tRNA on another now all return the error
YOU HAVE FAILED TO FIND ANY ATOMS TO FIT
I've looked high and low for a reason for this and failed. The pdb files
themselves look normal and behave well in PYMOL. They have CRYST1 cards
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
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 error: point code unitfunction
***1 -1022MMDB_F_Atom
*** file : 4ARC_rot
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
go.
Best regards,
Boaz
הודעה מקורית
מאת "Carter, Charlie"
תאריך: 03/11/2013 20:24 (GMT+02:00)
אל CCP4BB@JISCMAIL.AC.UK
נושא [ccp4bb] LSQKAB with trajectory files
I've just tried to use LSQKAB to transform an entire trajectory file that is a pdb file
I've just tried to use LSQKAB to transform an entire trajectory file that is a
pdb file with ENDMDL cards between models to a new orientation for the purpose
of making use of work with the new orientation.
LSQKAB returns with an error:
*** RWBROOK error: point code unitfunction
***
Dear All,
I am trying to superpose 2 chains from the same pdb file. I have
generated 2 separate pdb files, each with one chain, using PDBSET.
When I run LSQKAB with the 2 generated files (on UBUNTU 10.04, ccp4 6.2) it
fails to run. The 2 input files CONTAIN the columns for occupancie
Dear All,
I am trying to superpose 2 chains from the same pdb file. I have
generated 2 separate pdb files, each with one chain, using PDBSET.
When I run LSQKAB with the 2 generated files (on UBUNTU 10.04, ccp4 6.2) it
fails to run. The 2 input files CONTAIN the columns for occupancie
Dear All,
I am trying to superpose 2 chains from the same pdb file. I have
generated 2 separate pdb files, each with one chain, using PDBSET.
When I run LSQKAB with the 2 generated files (on UBUNTU 10.04, ccp4 6.2) it
fails to run. The 2 input files CONTAIN the columns for occupancie
side effect of forcing the
program to read in the XYZINF input file.
Norman
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf
Of Anita Lewit-Bentley
Sent: 16 March 2009 14:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] LSQKAB error
Dear all,
I am trying to compare several
Dear all,
I am trying to compare several related structures using LSQKAB. In
order to refine the superpositions, I'd like to use the option
"radius", to see the relative postion of certain residues within a
given distance from a common point.
The programme reads the commands OK:
" ALL A
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
Dear colleagues,
While using LSQKAB I have encountered what it seems a different behavior
between version 6.1 and 6.0.
If I superpose two structures with LSQKAB version 6.1 (included in
CCP4-6.1.0), residues with alternative conformations are not included
for the calculations. This is an exa
Hi everybody,
I wonder why in lsqkab, the glycine residues have a rms value for their
side chains which are non null
(the same calculation done with CNS give about the same results for the
rms calculation, but with
null value for the rms of glycine side chains).
thanks a lot
nathalie
--
Dr.
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
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 using have neither B-factor nor occupancy fields. Lsqkab is unhappy about this fact
(see below), and I'm wondering if there's
34 matches
Mail list logo
