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
> <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/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
>>>>>
>>>>> -------------- next part --------------
>>>>> An HTML attachment was scrubbed...
>>>>>
>>>>> ------------------------------
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Find and fix application performance issues faster with Applications
>>>>> Manager
>>>>> Applications Manager provides deep performance insights into multiple
>>>>> tiers of
>>>>> your business applications. It resolves application problems quickly and
>>>>> reduces your MTTR. Get your free trial!
>>>>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>>>>>
>>>>> ------------------------------
>>>>>
>>>>> _______________________________________________
>>>>> PyMOL-users mailing list
>>>>> PyMOL-users@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>>
>>>>>
>>>>> End of PyMOL-users Digest, Vol 119, Issue 16
>>>>> ********************************************
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Find and fix application performance issues faster with Applications
>>>> Manager
>>>> Applications Manager provides deep performance insights into multiple
>>>> tiers of
>>>> your business applications. It resolves application problems quickly and
>>>> reduces your MTTR. Get your free trial!
>>>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>>
>>> 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
------------------------------------------------------------------------------
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
