Maybe this could be interesting to.
http://www.pymolwiki.org/index.php/Color_by_conservation
This script reads an alignment object and colors the protein objects in the
alignment by the sequence conservation found in the alignment.
I tried to update a little list with the different methods available.
http://www.pymolwiki.org/index.php/Align#SEE_ALSO
Good luck
/T
2012/1/15 QT
> Dear all,
>
> Thank you for all of the replies. I compiled pymol from svn. Current
> revision is 3975.
>
> I also switched to cealign. It seems to give better rmsd without any
> argument than align does. Also, if you mess around with align and give it
> low cutoff value, it will eventually make one of the structure you're
> trying to align disappeared completely...I don't think that is intended.
>
> Best,
> Quyen
>
>
> On Fri, Jan 13, 2012 at 10:09 AM, Jason Vertrees <
> jason.vertr...@schrodinger.com> wrote:
>
>> Hi,
>>
>> Cealign's the way to go here. If you have a massively powerful
>> computer you can continue turning off the "guide" which selects
>> special carbons to "guide" the alignment. We need to improve/extend
>> for nucleic acids. Would someone mind filing a feature request on the
>> open-source bug tracker? We also need to standardize the alignment
>> interface as more and more alignment algorithms appear.
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Fri, Jan 13, 2012 at 8:52 AM, David Hall
>> wrote:
>> > I decided to dig in and answer my own question about what the seq
>> argument does.
>> >
>> > seq:
>> > positive means use sequence and structure
>> > 0 means use only structure
>> > negative means only use sequence
>> >
>> > For super, I assume you only want to use structure, so messing with
>> > that argument is silly advice.
>> >
>> > The problem is that when you use structure, SelectorGetResidueVLA gets
>> > an argument of true for ca_only
>> >
>> > Obviously, nucleic acids don't have any c-alphas, so when
>> > SelectorGetResidueVLA searches for residues using strcmp(ai1->name,
>> > "CA") == 0 , pymol finds no residues in the selections, then complains
>> > to you about "invalid selections" because it thinks the selections are
>> > empty.
>> >
>> > -David
>> >
>> > On Fri, Jan 13, 2012 at 8:37 AM, David Hall
>> wrote:
>> >> I think super does not handle nucleic acid sequences well.
>> >>
>> >> super ec-5s, hm-5s, seq=-1
>> >>
>> >> works.
>> >>
>> >> I'll leave it to someone else to say what that does. I just noted
>> >> that align works, super doesn't, guessed it had to do with sequence
>> >> and noted that for align, the default value of seq was -1 and for
>> >> super, the default value was 0.
>> >>
>> >> -David
>> >>
>> >> On Fri, Jan 13, 2012 at 7:44 AM, QT wrote:
>> >>> Dear all,
>> >>>
>> >>> I'm having a tough time using the super command correctly. I want to
>> >>> superimpose two 5S structures.
>> >>>
>> >>> In pymol, I'll do the following
>> >>>
>> >>> load 2awb.pdb
>> >>> load 3cc2.pdb
>> >>>
>> >>> create ec-5s, 2awb and chain a
>> >>> create hm-5s, 3cc2 and chain 9
>> >>>
>> >>> If I issue super ec-5s, hm-5s then the cryptic error "ExecutiveAlign:
>> >>> invalid selections for alignment. would appear."
>> >>>
>> >>> Issuing super /ec-5s//a, /hm-5s//9 does not help either.
>> >>>
>> >>> What am I missing? align /ec-5s//a, /hm-5s//9 works just fine
>> though...
>> >>>
>> >>> Any help from the community would be very appreciated.
>> >>>
>> >>> Best,
>> >>> Quyen
>> >>>
>> --
>> >>> RSA(R) Conference 2012
>> >>> Mar 27 - Feb 2
>> >>> Save $400 by Jan. 27
>> >>> Register now!
>> >>> http://p.sf.net/sfu/rsa-sfdev2dev2
>> >>> ___
>> >>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> >>> Archives:
>> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> >
>> >
>> --
>> > RSA(R) Conference 2012
>> > Mar 27 - Feb 2
>> > Save $400 by Jan. 27
>> > Register now!
>> > http://p.sf.net/sfu/rsa-sfdev2dev2
>> > ___
>> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
>>
>>
>> --
>> RSA(R) Conference 2012
>> Mar 27 - Feb 2
>> Save $400 by Jan. 27
>> Register now!
>> http://p.sf.net/sfu/rsa-sfdev2dev2
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: