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.vertrees@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 <lists@cowsandmilk.net> 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 <lists@cowsandmilk.net> 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 <rdirective@gmail.com> 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
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120

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