Dear all, Thanks very much to everyone who replied. A tip-off from Petr Leiman led me towards UCSF Chimera, which was able to generate a multiple alignment file from my 4 superposed PDB files. Protocol for the interested: Open up Chimera and from the menu select "Tools" -> "Structure Comparison" -> "Match->Align"
Much easier than hand-editing the alignment! Thanks again, Stephen On 3/4/08, Stephen Graham <[EMAIL PROTECTED]> wrote: > Hi all, > > I would like to generate a structure-based multiple sequence alignment > using 4 structures. I have already generated pairwise alignments for > each 'pair' of structures (6 alignments in all). Is there a program > out there that can take a number of aligned structures (or even just a > number of pairwise sequence alignments) and calculate the 'best' > multiple sequence alignment? Please note that there is absolutely no > sequence conservation between these structures, making standard > sequence-based alignment tools pretty useless. > > Thanks, > > Stephen > > -- > Dr Stephen Graham > Nuffield Medical Fellow > Division of Structural Biology > Wellcome Trust Centre for Human Genetics > Roosevelt Drive > Oxford OX3 7BN > United Kingdom > Phone: +44 1865 287 549 > -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549
