how about mean square deviation of the rmsd of each c alpha？
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Smith Liu
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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
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
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
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
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
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
*Sent:* Thursday, May 10, 2007 5:46 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] rmsd calculation. .
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
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
-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 the
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 will
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
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
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
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Jenny
Sent: Thursday, May 10, 2007 5:46 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] rmsd calculation. .
Hi, All,
I have a question about rmsd calculation.
I have some pdbs (100 residues ) and these pdbs
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