how about mean square deviation of the rmsd of each c alpha？
| |
Smith Liu
|
|
邮箱：smith_liu...@163.com
|
签名由 网易邮箱大师 定制
在2017年12月02日 22:48，Reza Khayat 写道：
Hi,
I'm analyzing the RMSD between 60 subunits of a virus. Can someone identify a
program that can generate a spread for the RMS
Hi,
I'm analyzing the RMSD between 60 subunits of a virus. Can someone identify a
program that can generate a spread for the RMSD between equivalent C-alpha
atoms? For example, the C-alpha atom for amino acid 39 may have RMSD values
from 0.1 to 1.5. Coot does a nice job of automatically detect
compar does this providing the sequence is the same.
amd you can get lsqkab to give you the full list but only i think for
those atoms you overlap..
eleanor
On 12/29/2010 01:52 PM, Michael Swan wrote:
Dear all,
I am having a bit of trouble finding a program to do an rmsd calculation and
give m
Michael,
I think something crudely resembling what you are asking can be done
with Chimera.
Load your two PDBs and run matchmaker
Tools > Structure Comparison > MatchMaker
In the dialog box that appears, under matching, there is a box that is
ticked by default "iterate by pruning long atom
Hello Mike,
I would recommend PyMOL. Consider this example:
# get structures from PDB
fetch 2j0s, async=0
fetch 2j0u, async=0
# remove alternative configurations
remove not alt +A
# select conformers with c-alpha atoms
select conf1, 2j0s and chain A and name CA
select conf2, 2j0u and chain A an
From:Michael Swan
Subject: rmsd calculation for all atoms.
Dear all,
I am having a bit of trouble finding a program to do an rmsd
calculation and
give me the differences between all the atoms in the structures.
I have two structures which are identical in the sense that one is
the apo
p
Dear all,
I am having a bit of trouble finding a program to do an rmsd calculation and
give me the differences between all the atoms in the structures.
I have two structures which are identical in the sense that one is the apo
protein and one is the bound structure. I would like to superimpose them
Jenny,
I of course would suggest that you follow Olve's advice, and use
theseus to do a maximum likelihood, simultaneous superposition of all
your structures ( http://www.theseus3d.org ). The variable bits,
like your loop, will be naturally down-weighted in a rigorous
statistical manner.
I would highly recommend Doug Theobald's program Theseus for this -
the pictures at www.theseus3d.org say it all. Theseus does maximum
likely hood superimpositions of multiple structures (i.e. NOT
pairwise against a "master" copy), and the real beauty of it is that
you don't have to pick w
Eleanor Dodson wrote:
> It is a bit clunky - you can use siperpose molecules - fit residues to
> fit a selected range (1-40; 60-100 say) and write out a complete fitted
> pdb file. Then you could use a VERY old program
> compar xyzin1 original.pdb xyzin2 fitted.pdb (xyzin3 another.pdb)
> and it w
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Excellent!
Thank you Gerard,
Miguel
Gerard DVD Kleywegt escribió:
>> But my understanding is that Iain's procedure gives the rmsds of the
>> _aligned_ C-alphas, whereas Jenny actually seems to be more interested
>> in those that she excludes from th
It is a bit clunky - you can use siperpose molecules - fit residues to
fit a selected range (1-40; 60-100 say) and write out a complete fitted
pdb file. Then you could use a VERY old program
compar xyzin1 original.pdb xyzin2 fitted.pdb (xyzin3 another.pdb)
and it will match all pairs with the
andard (ie. “m1” is the fixed
> standard, “m2” is your blah_rotated.pdb), explicitly using just the loop
> atoms this time in “m1” and “m2” ranges.
>
>
>
> I’m sure there is an easier way to do this, but works for me.
>
>
>
> HTH,
>
> Iain
>
>
>
>
>
>
toms this time in "m1" and "m2" ranges.
I'm sure there is an easier way to do this, but works for me.
HTH,
Iain
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Jenny
Sent: Thursday, May 10, 2007 5:46 PM
To:
Hi, All,
I have a question about rmsd calculation.
I have some pdbs (100 residues ) and these pdbs differ pretty much only the
loop region 40-60. Is there any easy way that I can superimpose the fixed
region ( 1-40,60-100) and then calculate the rmsd for the loop?I need to
calculate for each pai
15 matches
Mail list logo
