Re: [PyMOL] Using super correctly

2012-01-15 Thread 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

Re: [PyMOL] Using super correctly

2012-01-15 Thread Troels Emtekær Linnet
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

[PyMOL] Using super correctly

2012-01-13 Thread QT
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

Re: [PyMOL] Using super correctly

2012-01-13 Thread David Hall
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

Re: [PyMOL] Using super correctly

2012-01-13 Thread Thomas Holder
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

Re: [PyMOL] Using super correctly

2012-01-13 Thread Thomas Holder
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

Re: [PyMOL] Using super correctly

2012-01-13 Thread David Hall
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

Re: [PyMOL] Using super correctly

2012-01-13 Thread Jason Vertrees
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