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)
> 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Your PyMOL looks to be outdated.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