OK, after some trial and error I have found out a way that works.
The two structures have the corresponding chains in different orders and with
different chain labels:
You can copy-paste the following commands into Pymol to follow that I did:
#--------------------------------------------------------------------------------------------------------------------------------
# get the structures from the pdb:
load http://www.rcsb.org/pdb/files/3j5r.pdb
load http://www.rcsb.org/pdb/files/3j5q.pdb
hide all
show ribbon
util.cbc
# chain labels are not the same in both molecules,
# chain A in 3j5r corresponds to chain B in 3j5q, B to E, C to D, D to G
# chains A,C,F and A in 3j5q are additional small domains of unknown sequence
# the order in the pdb file is B-A-C-D for 3j5r and D-B-E-G in 3j5q
# additional "UNK" residues in 3j5q confuse the issue
remove resn UNK
# morphing a single chain, /3j5r//A to /3j5q//B
create objA, /3j5r//A
create objB, /3j5q//B
morph objC, objA, objB
# this works!!!
delete objA objB objC
#-----------------------------------
# now all 4 chains: if I do
morph objD, 3j5r, 3j5q
# the wrong chains morph into each other
delete objD
#-----------------------------------
# give corresponding chains the same chain label
alter /3j5q//B, chain="A"
alter /3j5q//E, chain="B"
alter /3j5q//D, chain="C"
alter /3j5q//G, chain="D"
util.cbc
morph objE, 3j5r, 3j5q
# to change the chain identifiers is not enough!!!
delete objE
#-----------------------------------
# is it possible to take objects apart and put them back to
extract 3j5rA, /3j5r//A
extract 3j5rB, /3j5r//B
extract 3j5rC, /3j5r//C
extract 3j5rD, /3j5r//D
delete 3j5r
extract 3j5qA, /3j5q//A
extract 3j5qB, /3j5q//B
extract 3j5qC, /3j5q//C
extract 3j5qD, /3j5q//D
delete 3j5q
create 3j5r, 3j5rA or 3j5rB or 3j5rC or 3j5rD
create 3j5q, 3j5qA or 3j5qB or 3j5qC or 3j5qD
morph objF, 3j5r, 3j5q
# still something strange happening, I am loosing atoms in chain B and D
delete objF
#-----------------------------------
morph objG, 3j5rA, 3j5qA
morph objH, 3j5rB, 3j5qB
morph objI, 3j5rC, 3j5qC
morph objJ, 3j5rD, 3j5qD
# OK, this works
#--------------------------------------------------------------------------------------------------------------------------------
although I do not understand haow you managed to get segment identifiers into
your selections
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 14:24, 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
>> <mailto: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
>> <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 <mailto:honeg...@bioc.uzh.ch>
>>
>> websites
>> http://www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun>
>> http://www.bioc.uzh.ch/plueckthun/antibody
>> <http://www.bioc.uzh.ch/plueckthun/antibody>
>> http://www.bioc.uzh.ch/plueckthun/nanowelt
>> <http://www.bioc.uzh.ch/plueckthun/nanowelt>
>>
>>
>>
>>
>>
>>
>>> On 26 Apr 2016, at 13:21, harold steinberg <h.adam.steinb...@gmail.com
>>> <mailto: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
>>>> <mailto: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
>>>>> <mailto: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 <mailto:honeg...@bioc.uzh.ch>
>>>>>
>>>>> websites
>>>>> http://www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun>
>>>>> http://www.bioc.uzh.ch/plueckthun/antibody
>>>>> <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
>>>>>>
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>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Find and fix application performance issues faster with Applications
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>>>>> Applications Manager provides deep performance insights into multiple
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>>>>
>>>> H. Adam Steinberg
>>>> 7904 Bowman Rd
>>>> Lodi, WI 53555
>>>> 608/592-2366
>>>>
>>>
>>> H. Adam Steinberg
>>> 7904 Bowman Rd
>>> Lodi, WI 53555
>>> 608/592-2366
>>>
>>
>
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366
>
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