Re: [PyMOL] morph issues
ote: >>>>>> >>>>>> 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 -- 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
Re: [PyMOL] morph issues
hun/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 >>>>>> >>>>>> -- next part -- >>>>>> An HTML attachment was scrubbed... >>>>>> >>>>>> -- >>>>>> >>>>>> -- >>>>>> Find and fix application performance issues faster with Applications >>>>>> Manager >>>>>> Applications Manager provides deep performance insights into multi
Re: [PyMOL] morph issues
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,\
-0.06739, -0.094843410,0.993197739,\
0.0,0.0, -619.393493652,\
0.042427063, -0.005607605,6.552642822,\
516.705444336, 722.081604004, -20.0 )
# 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 Honegge
Re: [PyMOL] morph issues
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. >&
Re: [PyMOL] morph issues
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 >>> >>> -- 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 -- 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
Re: [PyMOL] morph issues
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 > > -- 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
[PyMOL] morph issues
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 -- 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
