Re: [PyMOL] morph issues

[harold s. <h.a...@gm...>]

Hi Annemarie,

Thank you for the answer. Do you know the command to remove the alternative conformation?


> On Apr 26, 2016, at 4:31 AM, Honegger Annemarie <hon...@bi...> wrote:
> 
> Hi Adam
> 
> This additional letter means that you have an alternative conformation for the atom, therefore you do not have a 1:1 correspondence between the 
> atoms in the two endpoints of the morph. If you eliminate the alternative conformations  (remove (not alt “”+A)) or restrict the selection to those atoms, the morph should work.
> 
> best regards
> 
> 		Annemarie
> _______________________________
> 
> Dr. Annemarie Honegger PhD
> Department 
> of Biochemistry
> Zürich University
> Winterthurerstrasse 190
> CH-8057 Zürich
> Switzerland
> 
> e-Mail: hon...@bi...
> 
> websites
> http://www.bioc.uzh.ch/plueckthun
> http://www.bioc.uzh.ch/plueckthun/antibody
> http://www.bioc.uzh.ch/plueckthun/nanowelt
> 
> 
> 
> 
> 
>> 
>> 
>> Message: 6
>> Date: Mon, 25 Apr 2016 20:54:01 -0500
>> From: harold steinberg <h.a...@gm...>
>> Subject: [PyMOL] morph issues
>> To: pymol-users <pym...@li...>
>> Message-ID: <0E8...@gm...>
>> Content-Type: text/plain; charset="utf-8"
>> 
>> Hi all,
>> 
>> I need to generate a morph from 3J5R to 3J5Q. When I load both files and generate the morph, it?s all messed up. When I generate a morph of other structures it works just fine.
>> 
>> In the structures that do not morph correctly a sample selection is:
>> /3j5r/A/B/ILE`573/CD1
>> /3j5q/C/E/ILE`573/CD1
>> 
>> Notice that these files have an extra letter (?A? and ?C? before the chain identifier).
>> 
>> In files that the morph does work this letter is missing (it?s a blank space):
>> /3lut//D/GLY`338/CA
>> 
>> Is that what is messing up the morph?
>> 
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
>> 
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H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366