Re: [ccp4bb] RMSD calculation for large assemblies
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 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 detecting and calculating RMSD, but I'd like to have the spread for each atom in the final graph that Coot generates. Thank you. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031
[ccp4bb] RMSD calculation for large assemblies
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 detecting and calculating RMSD, but I'd like to have the spread for each atom in the final graph that Coot generates. Thank you. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031
Re: [ccp4bb] rmsd calculation for all atoms.
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 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 using only one domain then output the rmsd values for all the atoms or at least individual residues. The structures are not completely identical as some extra residues were visible in the bound structure so I hope there is a program that can ignore those differences. If anyone knows of a program that will do this calculation I would much appreciate hearing about it. There seem to be many programs that will give an average rmsd over the whole structure or just the region used for alignment but I haven't found anything that will give me distances between atoms or residues that were not used in the alignment. Thanks, Mike.
Re: [ccp4bb] rmsd calculation for all atoms.
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 pairs until no pair exceeds: " You can play with the value and see when the residues you are interested in are no longer involved in the superposition. To see the RMSD between the atoms pairs used you need to look in the reply log (Favorites > Reply log) Stephen On 29 December 2010 14:52, Michael Swan wrote: > 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 > using only one domain then output the rmsd values for all the atoms or at > least individual residues. The structures are not completely identical as > some extra residues were visible in the bound structure so I hope there is a > program that can ignore those differences. > If anyone knows of a program that will do this calculation I would much > appreciate hearing about it. There seem to be many programs that will give > an average rmsd over the whole structure or just the region used for > alignment but I haven't found anything that will give me distances between > atoms or residues that were not used in the alignment. > Thanks, > Mike. >
Re: [ccp4bb] rmsd calculation for all atoms.
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 and name CA # select domains select dom1, resi 69-239 select dom2, resi 250-411 # superimpose on dom1 and calculate RMSD for dom2 fit (conf1 like conf2) and dom1, (conf2 like conf1) and dom1 rms_cur (conf1 like conf2) and dom2, (conf2 like conf1) and dom2 Cheers, Thomas On Wed, 2010-12-29 at 13:52 +, Michael Swan wrote: > 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 using only one domain then output the rmsd values for > all the atoms or at least individual residues. The structures are not > completely identical as some extra residues were visible in the bound > structure so I hope there is a program that can ignore those > differences. > If anyone knows of a program that will do this calculation I would > much appreciate hearing about it. There seem to be many programs that > will give an average rmsd over the whole structure or just the region > used for alignment but I haven't found anything that will give me > distances between atoms or residues that were not used in the > alignment. > Thanks, > Mike. -- Thomas Holder AG Jekely MPI for Developmental Biology Spemannstr. 35 D-72076 Tuebingen
Re: [ccp4bb] rmsd calculation for all atoms
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 protein and one is the bound structure. I would like to superimpose them using only one domain then output the rmsd values for all the atoms or at least individual residues. The structures are not completely identical as some extra residues were visible in the bound structure so I hope there is a program that can ignore those differences. If anyone knows of a program that will do this calculation I would much appreciate hearing about it. There seem to be many programs that will give an average rmsd over the whole structure or just the region used for alignment but I haven't found anything that will give me distances between atoms or residues that were not used in the alignment. Thanks, Mike. If the domain is an entire chain, you could use Chimera's MatchMaker tool to do the alignment: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/matchmaker/matchmaker.html It will report that RMSD for the atoms used for matching. To get the RMSD for all atoms in common you would have to use the 'rmsd' command and specify the parts in common: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/rmsd.html So if all of chain A and residues 12-20 of chain B were in common, then: rmsd #0:.a:12-20.b #1:.a:12-20.b If there were differences in the side chains (say some were incomplete) then you might have to restrict the RMSD measurement to the backbone (which you might want to do anyway): rmsd #0:@c,ca,n:12-2...@c,ca,n #1:@c,ca,n:12-2...@c,ca,n --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
[ccp4bb] 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 protein and one is the bound structure. I would like to superimpose them using only one domain then output the rmsd values for all the atoms or at least individual residues. The structures are not completely identical as some extra residues were visible in the bound structure so I hope there is a program that can ignore those differences. If anyone knows of a program that will do this calculation I would much appreciate hearing about it. There seem to be many programs that will give an average rmsd over the whole structure or just the region used for alignment but I haven't found anything that will give me distances between atoms or residues that were not used in the alignment. Thanks, Mike.
Re: [ccp4bb] rmsd calculation
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. Then you can look at the average structure file
that is output (_ave.pdb at the end of the filename), and the B-
factor column has the overall RMSD for each atom in there. You can
look at the full superposition (the _sup.pdb file) in rasmol or in
pymol with the 'set all_states, on' command.
However, if you really need to do the very analysis that you asked
about, the following bash script will do exactly that with theseus
(you need both awk and theseus in your executable path). It prints
out the average RMSD for the atoms you specify in the loop, after
pairwise least-squares superpositioning on all atoms other than the
loop, for all possible pairwise combinations of your pdb files. (Note
that in this script all backslashes '\' must have a carriage return
immediately after them.) You will need to change the lower and upper
values at the top of the script (inclusive for the loop you want
excluded). You invoke the script something like "karen.sh pdb1.pdb
pdb2.pdb pdb3.pdb" or "karen.sh *.pdb" to do all the .pdbs in one
directory. If you have any problems or have other specific
superpositioning issues I'm glad to help out.
Cheers,
Douglas
karen.sh
#
#!/bin/bash
# everything including and between lower and upper
# is excluded from the superposition
lower=40;
upper=60;
pdbs=($*);
for (( i = 0; i < [EMAIL PROTECTED]; ++i ))
do
for (( j = 0; j < i; ++j ))
do
name="${pdbs[i]%.*}_${pdbs[j]%.*}";
theseus -l -r ${name} -S ${lower}-${upper} ${pdbs[i]} ${pdbs[j]}\
> ${name}.log;
rmsd=$(cut -c 7-11,61-67 ${name}_ave.pdb |\
awk '{if ($1 > lo && $1 < up) {sum += $2; n++}}; END {print sum/
n}'\
lo=${lower} up=${upper});
echo "${name} rmsd = ${rmsd}";
done
done
^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`^`
Douglas L. Theobald
Department of Biochemistry
Brandeis University
Waltham, MA 02454-9110
[EMAIL PROTECTED]
^\
/` /^. / /\
/ / /`/ / . /`
/ / ' '
'
On May 11, 2007, at 1:58 PM, Olve Peersen wrote:
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 which residues you want to
superimpose. Places where the whole set of structures show
divergence are effectively down-weighted and don't contribute much
to the final solution vs. least squares where every atom position
has equal weight and the "bad" parts screw up the alignment of the
"good" parts. For this, I would do a Theseus superposition of all
the structures and then analyze the set of superimposed structures
by whatever method you want (e.g. rmsd of variances in important
sections of the structures).
- Olve
---
Olve Peersen
Associate Professor
Dept. of Biochemistry & Molecular Biology
1870 Campus Delivery
Colorado State University
Ft. Collins, CO 80523-1870
---
970.491-0433Office (MRB 279)
970.491-0271Lab (MRB 149)
970.491-0494Fax
[EMAIL PROTECTED]
---
On May 11, 2007, at 11:15 AM, Donnie Berkholz wrote:
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 match all pairs with the same RESIDUE ID and give the
RMSD
distance
There is documentation for it.
There's a nice (non-CCP4) program called ProFit that does a pretty
nice
job of superimposing with a lot of flexibility.
Thanks,
Donnie
On May 10, 2007, at 6:45 PM, Jenny wrote:
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 pair, so if
there is any script or program available to do this quickly, that
would be great.
Thanks.
Jenny
Re: [ccp4bb] rmsd calculation
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 which residues you want to superimpose. Places where the whole set of structures show divergence are effectively down-weighted and don't contribute much to the final solution vs. least squares where every atom position has equal weight and the "bad" parts screw up the alignment of the "good" parts. For this, I would do a Theseus superposition of all the structures and then analyze the set of superimposed structures by whatever method you want (e.g. rmsd of variances in important sections of the structures). - Olve --- Olve Peersen Associate Professor Dept. of Biochemistry & Molecular Biology 1870 Campus Delivery Colorado State University Ft. Collins, CO 80523-1870 --- 970.491-0433Office (MRB 279) 970.491-0271Lab (MRB 149) 970.491-0494Fax [EMAIL PROTECTED] --- On May 11, 2007, at 11:15 AM, Donnie Berkholz wrote: 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 match all pairs with the same RESIDUE ID and give the RMSD distance There is documentation for it. There's a nice (non-CCP4) program called ProFit that does a pretty nice job of superimposing with a lot of flexibility. Thanks, Donnie
Re: [ccp4bb] rmsd calculation
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 match all pairs with the same RESIDUE ID and give the RMSD > distance > > There is documentation for it. There's a nice (non-CCP4) program called ProFit that does a pretty nice job of superimposing with a lot of flexibility. Thanks, Donnie signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] rmsd calculation. .
-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 alignment. I may be wrong, but in >> these cases, I use lsqman (from DVD) or lsqkab (from ccp4) to superpose >> the proteins (using one as reference) according to a particular scheme >> (Jenny's 1-40,60-100) and then write a script to calculate the rmsds for >> the "interesting" 41-59 residues. There may be an easier way, which I'll >> be interested to learn about. > > hola miguel, > > i would use the rmsd command in lsqman, like so: > > read m1 m1.pdb > read m2 m2.pdb > expl m1 "a1-40 a60-100" m2 "a1 a60" > rmsd m1 a41-59 m2 a41 > > --gerard > > ** > Gerard J. Kleywegt > [Research Fellow of the Royal Swedish Academy of Sciences] > Dept. of Cell & Molecular Biology University of Uppsala > Biomedical Centre Box 596 > SE-751 24 Uppsala SWEDEN > > http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] > ** >The opinions in this message are fictional. Any similarity >to actual opinions, living or dead, is purely coincidental. > ** > > - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: [EMAIL PROTECTED] www: http://www.pangea.org/mol/spip.php?rubrique2 ~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.6 (GNU/Linux) iD8DBQFGRDtWF6oOrDvhbQIRAiYIAJ9Zsh5KNyqzfWhz2WaaRYlRUfKXTwCeLQOK YtSKkl+Q4N3TF8MganziUDs= =TWIp -END PGP SIGNATURE-
Re: [ccp4bb] rmsd calculation
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 same RESIDUE ID and give the RMSD distance There is documentation for it. Eleanor Jenny wrote: 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 pair, so if there is any script or program available to do this quickly, that would be great. Thanks. Jenny
Re: [ccp4bb] rmsd calculation. .
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Jenny and Iain, 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 alignment. I may be wrong, but in these cases, I use lsqman (from DVD) or lsqkab (from ccp4) to superpose the proteins (using one as reference) according to a particular scheme (Jenny's 1-40,60-100) and then write a script to calculate the rmsds for the "interesting" 41-59 residues. There may be an easier way, which I'll be interested to learn about. Cheers, M. Kerr, Iain escribió: > Hi Jenny, > > > > You can do this in LSQMAN (if I’m understanding your question correctly…) > > > > You’d first superimpose the residues in the “fixed region” to give a > superimposed core using the ‘EXplicit’ command, eg: > > > > *LSQMAN > ex m1* > > * Range 1 ? (A1-10) "a4-10 a19-23 a28-36 a44-51 a53-66 a91-97 a106-111 > a123:126"* > > * Mol 2 ? (M1) m2* > > * Range 2 ? (A1) "a4 a19 a28 a44 a53 a91 a106 a123"* > > * Explicit fit of M1 "A4-10 A19-23 A28-36 A44-51 A53-66 A91-97 A106-111 > A123:126"* > > * And M2 "A4 A19 A28 A44 A53 A91 A106 A123"* > > * Atom types | CA | N | C | O | CB |* > > * Nr of atoms to match : (295)* > > * The295 atoms have an RMS distance of0.892 A* > > * Rotation: -0.956932 0.127723 -0.260706* > > * 0.170532 -0.479456 -0.860837* > > *-0.234946 -0.868222 0.437026* > > * Translation : 13.78726.80038.541* > > > > > > Then use the “IMProve” command to iteratively improve the fit over all > CAs…this only works for two molecules at a time though…I guess choose a > fixed standard to align all the others against. Remember to write out > the coordinates for the rotated (ie. “m2”) molecules: > > > > Ø apply m1 m2 > > Ø wr m2 blah_rotated.pdb > > > > Then to calculate the RMSDs for just the loop regions compare the > superimposed molecules to the fixed standard (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 > > > > > > > > *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 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 pair, so if there is any script or program > available to do this quickly, that would be great. > > Thanks. > > Jenny > - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: [EMAIL PROTECTED] www: http://www.pangea.org/mol/spip.php?rubrique2 ~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.6 (GNU/Linux) iD8DBQFGRAwlF6oOrDvhbQIRAjmEAJ9UvAWXfIZU7bR1idcVqn8hE5zPwQCfc8Ko JkvZQL9IHdB+ENi92nVVUmI= =3HO2 -END PGP SIGNATURE-
Re: [ccp4bb] rmsd calculation. .
Hi Jenny, You can do this in LSQMAN (if I'm understanding your question correctly...) You'd first superimpose the residues in the "fixed region" to give a superimposed core using the 'EXplicit' command, eg: LSQMAN > ex m1 Range 1 ? (A1-10) "a4-10 a19-23 a28-36 a44-51 a53-66 a91-97 a106-111 a123:126" Mol 2 ? (M1) m2 Range 2 ? (A1) "a4 a19 a28 a44 a53 a91 a106 a123" Explicit fit of M1 "A4-10 A19-23 A28-36 A44-51 A53-66 A91-97 A106-111 A123:126" And M2 "A4 A19 A28 A44 A53 A91 A106 A123" Atom types | CA | N | C | O | CB | Nr of atoms to match : (295) The295 atoms have an RMS distance of0.892 A Rotation: -0.956932 0.127723 -0.260706 0.170532 -0.479456 -0.860837 -0.234946 -0.868222 0.437026 Translation : 13.78726.80038.541 Then use the "IMProve" command to iteratively improve the fit over all CAs...this only works for two molecules at a time though...I guess choose a fixed standard to align all the others against. Remember to write out the coordinates for the rotated (ie. "m2") molecules: * apply m1 m2 * wr m2 blah_rotated.pdb Then to calculate the RMSDs for just the loop regions compare the superimposed molecules to the fixed standard (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 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 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 pair, so if there is any script or program available to do this quickly, that would be great. Thanks. Jenny
[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 superimpose the fixed region ( 1-40,60-100) and then calculate the rmsd for the loop?I need to calculate for each pair, so if there is any script or program available to do this quickly, that would be great. Thanks. Jenny
