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.adam.steinb...@gmail.com> 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 <honeg...@bioc.uzh.ch> 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: honeg...@bioc.uzh.ch
>>
>> 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.adam.steinb...@gmail.com>
>>> 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.adam.steinb...@gmail.com>
>>>> 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 <honeg...@bioc.uzh.ch>
>>>>> 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: honeg...@bioc.uzh.ch
>>>>>
>>>>> 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.adam.steinb...@gmail.com>
>>>>>> Subject: [PyMOL] morph issues
>>>>>> To: pymol-users <pymol-users@lists.sourceforge.net>
>>>>>> Message-ID: <0e82e310-1d03-40cd-838d-50616a246...@gmail.com>
>>>>>> 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.
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