By the way also I've tried use super_all script wich can do multiple
alignment via Super command
pldserver1.biochem.queensu.ca/~rlc/work/*pymol*/*super_all*.py
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.
Thanks
James
2011/11/21 James Starlight <jmsstarli...@gmail.com>
> Jason,
>
> 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)
>
>
>
> James
>
> 2011/11/21 Jason Vertrees <jason.vertr...@schrodinger.com>
>
>> Hi James,
>>
>> > set fetch_host, pdbe
>>
>> Your PyMOL looks to be outdated. This was added to the open-source in
>> v1.3r1, I think.
>>
>> > 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 :(
>>
>> You should use the 'cealign' or 'super' commands to do this. Cealign
>> 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.
>>
>> Cheers,
>>
>> -- Jason
>>
>> >
>> > James
>> >
>> > 2011/11/21 Jason Vertrees <jason.vertr...@schrodinger.com>
>> >>
>> >> James,
>> >>
>> >> > 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
>> >>
>> >> Cheers,
>> >>
>> >> -- Jason
>> >>
>> >>
>> >>
>> >> --
>> >> Jason Vertrees, PhD
>> >> PyMOL Product Manager
>> >> Schrodinger, LLC
>> >>
>> >> (e) jason.vertr...@schrodinger.com
>> >> (o) +1 (603) 374-7120
>> >
>> >
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
>>
>
>
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