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
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
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
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
Hi Quyen,
unfortunately, the super command does a selection on CA atoms
internally. Maybe this should be considered a bug. If you have the
latest svn version of PyMOL, I recommend cealign for this task (older
versions of cealign do select CA atoms as well).
Cheers,
Thomas
On 01/13/2012
On 01/13/2012 02:37 PM, 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
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
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
