Re: [ccp4bb] strict structure based alignment
Dear all, thanks a lot for all your comments and suggestions for the alignment. I tested already the pdb server, which works great and I am currently installing a few other programs mentioned (Chimera, Prosmart.) for comparison. Best Regards Christian Am Freitag 13 Juli 2012 16:30:57 schrieb Christian Roth: > Dear all, > > I want align a couple or protein structures by secondary structure matching > to one target and want get a kind of aminoacid alignment file e.g. what > residue fit the other, without adjustments due to sequence based > alignments. > I tried Strap, but as far as I understood it, it takes also the sequence > into account. I tried also Rapido, but this does only a pairwise > comparison. Superpose does align it nicely (ccp4 based or Coot based) but > there seems to be no option to print the sequence alignment in a file and > it is again just a pairwise comparison . > Is there an other program which does something similar? > > Best Regards > > Christian >
Re: [ccp4bb] strict structure based alignment
Hi - SSM algorithm at PDBeFold will do this sort of thing http://www.ebi.ac.uk/msd-srv/ssm/ I wrote a tutorial for multiple alignment to go with a Phaser story http://www.ebi.ac.uk/pdbe-apps/quips?story=Phaser&auxpage=MultiplePDBeFoldminitutorial The last page of this tells you where to get an multiple fastA alignment of the superimposed structures and explains the format. Hope that helps. Martyn Martyn Symmons EBI Cambridge From: Eric Pettersen To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, 16 July 2012, 2:17 Subject: Re: [ccp4bb] strict structure based alignment On Jul 13, 2012, at 4:00 PM, Christian Roth wrote: I want align a couple or protein structures by secondary structure matching to >one target and want get a kind of aminoacid alignment file e.g. what residue >fit >the other, without adjustments due to sequence based alignments. >I tried Strap, but as far as I understood it, it takes also the sequence into >account. I tried also Rapido, but this does only a pairwise comparison. >Superpose does align it nicely (ccp4 based or Coot based) but there seems to >be no option to print the sequence alignment in a file and it is again just a >pairwise comparison . >Is there an other program which does something similar? If you use UCSF Chimera (www.cgl.ucsf.edu/chimera), you can use the MatchMaker tool to superimpose the structures. MatchMaker allows you to adjust the weight of sequence similarity vs. secondary structure matching, so you can just make the sequence similarity 0% and the secondary structure 100%. With the structures superimposed, you can use the Match->Align tool to generate a sequence alignment based solely on the proximity of residues to one another in space. Be warned that Match->Align will be very slow for 10+ structures, but is fine for half a dozen or so. The generated alignment will be displayed in a window that will have a "File" menu where you can save the alignment to a variety of common formats. --Eric Eric Pettersen UCSF Computer Graphics Lab
Re: [ccp4bb] strict structure based alignment
Try ProSMART www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/prosmart/prosmart.html etheses.whiterose.ac.uk/2120/ Conformation-independent comparison of protein structures Nicholls, Robert Adam (2011) Conformation-independent comparison of protein structures. PhD thesis, University of York. On Jul 13, 2012 11:37 AM, "Christian Roth" < christian.r...@bbz.uni-leipzig.de> wrote: > On Jul 13, 2012, at 4:00 PM, Christian Roth wrote: > > I want align a couple or protein structures by secondary structure > matching to > one target and want get a kind of aminoacid alignment file e.g. what > residue fit > the other, without adjustments due to sequence based alignments. > I tried Strap, but as far as I understood it, it takes also the sequence > into > account. I tried also Rapido, but this does only a pairwise comparison. > Superpose does align it nicely (ccp4 based or Coot based) but there seems > to > be no option to print the sequence alignment in a file and it is again > just a > pairwise comparison . > Is there an other program which does something similar? > > > If you use UCSF Chimera (www.cgl.ucsf.edu/chimera), you can use the > MatchMaker tool to superimpose the structures. MatchMaker allows you to > adjust the weight of sequence similarity vs. secondary structure matching, > so you can just make the sequence similarity 0% and the secondary structure > 100%. With the structures superimposed, you can use the Match->Align tool > to generate a sequence alignment based solely on the proximity of residues > to one another in space. Be warned that Match->Align will be very slow for > 10+ structures, but is fine for half a dozen or so. The generated > alignment will be displayed in a window that will have a "File" menu where > you can save the alignment to a variety of common formats. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > >
Re: [ccp4bb] strict structure based alignment
On Jul 13, 2012, at 4:00 PM, Christian Roth wrote: > I want align a couple or protein structures by secondary structure matching > to > one target and want get a kind of aminoacid alignment file e.g. what residue > fit > the other, without adjustments due to sequence based alignments. > I tried Strap, but as far as I understood it, it takes also the sequence into > account. I tried also Rapido, but this does only a pairwise comparison. > Superpose does align it nicely (ccp4 based or Coot based) but there seems to > be no option to print the sequence alignment in a file and it is again just > a > pairwise comparison . > Is there an other program which does something similar? If you use UCSF Chimera (www.cgl.ucsf.edu/chimera), you can use the MatchMaker tool to superimpose the structures. MatchMaker allows you to adjust the weight of sequence similarity vs. secondary structure matching, so you can just make the sequence similarity 0% and the secondary structure 100%. With the structures superimposed, you can use the Match->Align tool to generate a sequence alignment based solely on the proximity of residues to one another in space. Be warned that Match->Align will be very slow for 10+ structures, but is fine for half a dozen or so. The generated alignment will be displayed in a window that will have a "File" menu where you can save the alignment to a variety of common formats. --Eric Eric Pettersen UCSF Computer Graphics Lab
Re: [ccp4bb] strict structure based alignment
Dear Christian, PDBefold superimposes the structures and generates the sequence alignment in fasta(??) format. You can then read this file in Multialign for example to get the sequence alignment and then add the secondary structures to the sequence alignment using ESPript for example. David On 07/13/2012 04:30 PM, Christian Roth wrote: > Dear all, > > I want align a couple or protein structures by secondary structure matching > to > one target and want get a kind of aminoacid alignment file e.g. what residue > fit > the other, without adjustments due to sequence based alignments. > I tried Strap, but as far as I understood it, it takes also the sequence into > account. I tried also Rapido, but this does only a pairwise comparison. > Superpose does align it nicely (ccp4 based or Coot based) but there seems to > be no option to print the sequence alignment in a file and it is again just > a > pairwise comparison . > Is there an other program which does something similar? > > Best Regards > > Christian > -- David Cobessi Institut de Biologie Structurale 41, Rue Jules Horowitz 38027 Grenoble Cedex-1, France Tel:33(0)438789613 33(0)608164340 Fax:33(0)438785122
Re: [ccp4bb] strict structure based alignment
On 13/07/12 15:30, Christian Roth wrote: Dear all, I want align a couple or protein structures by secondary structure matching to one target and want get a kind of aminoacid alignment file e.g. what residue fit the other, without adjustments due to sequence based alignments. I tried Strap, but as far as I understood it, it takes also the sequence into account. I tried also Rapido, but this does only a pairwise comparison. Superpose does align it nicely (ccp4 based or Coot based) but there seems to be no option to print the sequence alignment in a file and it is again just a pairwise comparison . It is not clear to me what you mean by "just" a pairwise comparison. Coot outputs the SSM residue alignment to the terminal. HTH, Paul.
Re: [ccp4bb] strict structure based alignment
Hi, SSM (via PDBefold) (http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver) will do a structure based alignment and outputs a table of rmsd but will not give you a alignment file as such. -Sujata On Fri, Jul 13, 2012 at 10:30 AM, Christian Roth < christian.r...@bbz.uni-leipzig.de> wrote: > Dear all, > > I want align a couple or protein structures by secondary structure > matching to > one target and want get a kind of aminoacid alignment file e.g. what > residue fit > the other, without adjustments due to sequence based alignments. > I tried Strap, but as far as I understood it, it takes also the sequence > into > account. I tried also Rapido, but this does only a pairwise comparison. > Superpose does align it nicely (ccp4 based or Coot based) but there seems > to > be no option to print the sequence alignment in a file and it is again > just a > pairwise comparison . > Is there an other program which does something similar? > > Best Regards > > Christian >
[ccp4bb] strict structure based alignment
Dear all, I want align a couple or protein structures by secondary structure matching to one target and want get a kind of aminoacid alignment file e.g. what residue fit the other, without adjustments due to sequence based alignments. I tried Strap, but as far as I understood it, it takes also the sequence into account. I tried also Rapido, but this does only a pairwise comparison. Superpose does align it nicely (ccp4 based or Coot based) but there seems to be no option to print the sequence alignment in a file and it is again just a pairwise comparison . Is there an other program which does something similar? Best Regards Christian
