By the way also I've tried use super_all script wich can do multiple alignment via Super command
but as the consequense the resulted sequence alignment in CGO in pair-wise manner. How could I make something like this super all but for just one reference ( similar to the align ) so I'd like to obtain multiple sequence alignment on one reference based on the multiple structure alignment.
but as I've understood super did alignment only for two structures, Is there any way to do the same operation for ensemble ? (for CE as I understood this could be done by alignto command but it lack for seq alignment iin this case)
James2011/11/21 Jason Vertrees <firstname.lastname@example.org>Hi James,
> set fetch_host, pdbe
Your PyMOL looks to be outdated. This was added to the open-source in
v1.3r1, I think.
You should use the 'cealign' or 'super' commands to do this. Cealign
> By the way could you also help me with the alignment of my structure ( I've
> posted this question today at this topic). I think that I should use the
> combination of the structure alignment ( like CEalign) with the common seq.
> alignment but I dont know exactly how :(
uses only structure, whereas 'super' uses both structure and sequence.
Please continue to post questions like this to the list for best
results: there are some very smart people on our PyMOL list.
> 2011/11/21 Jason Vertrees <email@example.com>
>> > 1) I've already tried to use it but the downloading was to slow. How I
>> > can
>> > change source for pdb downloading ? E.g set fetch_host didnt worked :(
>> set fetch_host, pdbe
>> should work. Please let me know if it doesn't.
>> > 2) How I can specify individual chain for uploading via fetch command?
>> You can't--PyMOL downloads the entire structure. To show just a given
>> chain type something like:
>> fetch 1hpv
>> # "c. A" means "chain A"
>> color blue, c. A
>> Use similar selectors, for example
>> # remove all atoms from the structure
>> # except those in chain B
>> remove not chain B
>> -- Jason
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>> (e) Jason.Vertrees@schrodinger.com
>> (o) +1 (603) 374-7120
Jason Vertrees, PhD
PyMOL Product Manager
(o) +1 (603) 374-7120