Re: [PyMOL] morph issues

[Thomas H. <tho...@sc...>]

Hi Adam and Annemarie,

There are no alt location in these files. In the slash notation, the second item is the segment identifier, which for mmCIF files in the label_asym_id field (the third item, chain, is the auth_asym_id field). For this example, the label_asym_id (segi) should be easier to match up between the two structures than the auth_asym_id (chain).

# To illustrate the arrangement of label_asym_ids:

fetch 3j5r 3j5q, async=0
as ribbon
set grid_mode
spectrum segi
label guide and resn ALA, segi
set_view (\
    -0.985940218,   -0.146149188,   -0.081017971,\
     0.152838722,   -0.984706044,   -0.083635844,\
    -0.067555539,   -0.094843410,    0.993197739,\
     0.000000000,    0.000000000, -619.393493652,\
     0.042427063,   -0.005607605,    6.552642822,\
   516.705444336,  722.081604004,  -20.000000000 )

# So I would swap segi A and C for one of the structures to bring
# the chains into the same order. The chain identifier (third item in
# slash notation) doesn't affect sorting in this case, since the segi
# has higher priority.

stored.remap = {'A': 'C', 'C': 'A'}
alter 3j5q, segi = stored.remap.get(segi, segi)
sort

# illustrate that the order is the same now:

spectrum segi
label guide and resn ALA, segi

# Now the morphing should work as expected:

morph mout, 3j5r, 3j5q, refinement=0

Hope that helps.

See also:
http://pymolwiki.org/index.php/Selection_Macros

Cheers,
  Thomas

On 26 Apr 2016, at 08:24, harold steinberg <h.a...@gm...> wrote:

> When I use the remove command it seems to be removing atoms. There is no explanation in the pymol wiki about how to specify details to the command.
> 
> Since I have multiple chains I’m not sure if I have to use it multiple times (once on each chain) and I’m also not sure if I have to specify the first letter in the chain code or the second (/A/B/ or /C/E). I also have two files open so I’m not sure if the remove command is working on both at the same time or if it only works on one and not the other.    I have tried it all the ways I can think of, I tried all possible combinations.
> 
> These are .cif files not .pdb files.
> 
> No matter how I apply the remove command the morph is still messed up. It seems to take two of the four chains and rotate them around a circle instead of morphing them, the other two chains morph okay.
> 
>> On Apr 26, 2016, at 6:29 AM, Honegger Annemarie <hon...@bi...> wrote:
>> 
>> Yes, you want to keep atoms that have no alternative conformation  (alt “”) as well as the first conformation ( alt A) for those that do contain alternative conformation,
>> therefore you specify:
>> 
>> remove not (alt “”+A) see http://www.pymolwiki.org/index.php/Property_Selectors , bottom of page
>> 
>> 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
>> 
>> 
>> 
>> 
>> 
>> 
>>> On 26 Apr 2016, at 13:21, harold steinberg <h.a...@gm...> wrote:
>>> 
>>> I ask because if I use the command "remove (not alt “”+A)” every atom is erased from the session.
>>> 
>>> 
>>>> On Apr 26, 2016, at 6:16 AM, harold steinberg <h.a...@gm...> wrote:
>>>> 
>>>> 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
>>>> 

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.