Thank you both for taking the time to work this out, and explain how and why it
works!
> On Apr 26, 2016, at 8:14 AM, Thomas Holder <thomas.hol...@schrodinger.com>
> wrote:
>
> 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.
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366
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