Dear Crystallographers,
is there a ccp4 program--or otherwise--which can compute ca-ca
distances of corresponding residues between two superposed structures?
You mean to produce something like this?
http://xray.bmc.uu.se/usf/pics/distplot_1chr.gif
That can be done with LSQMAN - http://xray.b
On 11/28/2011 10:22 PM, Jacob Keller wrote:
Dear Crystallographers,
is there a ccp4 program--or otherwise--which can compute ca-ca
distances of corresponding residues between two superposed structures?
Jacob
Dont you get that from SSM and lsqkab (you have to turn on - list atom
distances or s
Dear Crystallographers,
Thanks very much for all who responded to my request. Below is a
compiled list of the various ways to skin this crystallographic cat!
Jacob
-Moleman ca plot distance-CCP4's superpose-distance matrix analysis,
e.g. http://www.csb.yale.edu/userguides/datamanip/ddmp/ddmp_descri
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Hash: SHA1
Dear Jacob,
Coot prints this information to the terminal, so you can start coot and
'tee' its output into a file.
Tim
On 11/28/2011 11:53 PM, Jacob Keller wrote:
> Let me refine my question (sorry for my lack of clarity): is there a
> program that w
The program:
http://sb20.lbl.gov/berry/for/pdbdist2b.for
does this.
If you run it by the wrapper pdbd2b:
echo 'Find distances greater than threshold between corresponding atoms in 2
PDB files'
echo 'Usage: pdbd2b file1 file2 startres# [thresh]'
pdbdist2b
On Nov 28, 2011, at 4:03 PM, Jacob Keller wrote:
Let me refine my question (sorry for my lack of clarity): is there a
program that will output the distances between the corresponding ca's
of a superposition on a residue-by-residue basis, and not just a
global RMSD value (doubtless these numbers
Hi Jacob,
This sounds like what you get from ddmp (
http://www.csb.yale.edu/userguides/datamanip/ddmp/ddmp_descrip.html ).
Good Luck,
-bob
On Mon, Nov 28, 2011 at 5:22 PM, Jacob Keller
wrote:
> Dear Crystallographers,
>
> is there a ccp4 program--or otherwise--which can compute ca-ca
> distances
CCP4's superpose does this.
It produces a table like this, but only for residues that are used in
the alignment.
.-..-.
|Query| Dist.(A) | Target|
|-++-|
| + A:ARG 10 ||H+ A:GLN 223 |
| + A:ARG
Let me refine my question (sorry for my lack of clarity): is there a
program that will output the distances between the corresponding ca's
of a superposition on a residue-by-residue basis, and not just a
global RMSD value (doubtless these numbers are part of the
superposition algorithm itself)? I w
Hi Jacob,
I used Moleman to do that once (http://xray.bmc.uu.se/usf/moleman2_man.html
)
The Distance LIst command is probably what you are looking for.
Mario Sanches
On Mon, Nov 28, 2011 at 5:22 PM, Jacob Keller <
j-kell...@fsm.northwestern.edu> wrote:
> Dear Crystallographers,
>
> is there
I'd say you have to look into the USF toolbox e.g. Moleman2
You want to calculate rmsd's there's an option for that.
Jürgen
On Nov 28, 2011, at 5:22 PM, Jacob Keller wrote:
Dear Crystallographers,
is there a ccp4 program--or otherwise--which can compute ca-ca
distances of corresponding residues
Dear Crystallographers,
is there a ccp4 program--or otherwise--which can compute ca-ca
distances of corresponding residues between two superposed structures?
Jacob
--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
emai
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