[PyMOL] Problems with superposing small molecules and transformation

[German Erlenkamp]

Hi all,

I have two sets of ligands, the first are the crystal structures, the=
second
one are the same compounds, but aligned by a flexible ligand alignmen=
t, where
I used one of the crystal structures as a template. Unfortunately the
coordinates of the templates changed during the alignment.
Now I want to calculate the RMSD-values between these structures, and=
for this
I want to superpose the group of aligned ligands to the template liga=
nd.=20
I started with 'align Aligned_1, Start_1' but after this command, all=
atoms of
'Aligned_1' vanished and I can only represent this as a sphere. This =
will be
Ok for me, because the RMSD between 'Aligned_1' and 'Start_1' is 0.
But after this I want to move 'Aligned_2' the same way as I moved 'Al=
igned_1'.
I thought 'matrix_copy Alinged_1, Start_1' should do the job, but aft=
er this
all atoms of 'Aligned_2' are gone. I still have this object, but noth=
ing more.

My questions are: Am I using the correct commands for this task, or n=
ot? And, if
I am using the right commands, what is going wrong? And - for the cas=
e my way
is not correct - what would be the proper way to solve my problem?

Thanks in advance,

German
--=20
German Erlenkamp

Computational Pharmaceutical Chemistry=20
and Molecular Bioinformatics

Heinrich-Heine-Universit=E4t D=FCsseldorf
Institut f=FCr Pharmazeutische und Medizinische Chemie
Universit=E4tsstr. 1
40225 D=FCsseldorf
Germany

Tel: [phone]
E-Mail: ***@uni-duesseldorf.de
URL: http://cpclab.uni-duesseldorf.de

[Sampson, Jared]

Hi German -

I’m not sure I follow exactly what you’re asking, but `align` does its superimposition based on sequence alignment, which isn’t really meaningful for small molecule ligands. I would suggest using `fit`, `super`, or `cealign` instead, which all use just the coordinates, although it’s possible these also won’t work.

For a more sophisticated approach, maybe check out LigAlign, which comes with a tutorial: http://www.pymolwiki.org/index.php/LigAlign.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Aug 5, 2014, at 10:04 AM, German Erlenkamp <***@uni-duesseldorf.de<mailto:***@uni-duesseldorf.de>> wrote:

Hi all,

I have two sets of ligands, the first are the crystal structures, the second
one are the same compounds, but aligned by a flexible ligand alignment, where
I used one of the crystal structures as a template. Unfortunately the
coordinates of the templates changed during the alignment.
Now I want to calculate the RMSD-values between these structures, and for this
I want to superpose the group of aligned ligands to the template ligand.
I started with 'align Aligned_1, Start_1' but after this command, all atoms of
'Aligned_1' vanished and I can only represent this as a sphere. This will be
Ok for me, because the RMSD between 'Aligned_1' and 'Start_1' is 0.
But after this I want to move 'Aligned_2' the same way as I moved 'Aligned_1'.
I thought 'matrix_copy Alinged_1, Start_1' should do the job, but after this
all atoms of 'Aligned_2' are gone. I still have this object, but nothing more.

My questions are: Am I using the correct commands for this task, or not? And, if
I am using the right commands, what is going wrong? And - for the case my way
is not correct - what would be the proper way to solve my problem?

Thanks in advance,

German
--
German Erlenkamp

Computational Pharmaceutical Chemistry
and Molecular Bioinformatics

Heinrich-Heine-Universität Düsseldorf
Institut für Pharmazeutische und Medizinische Chemie
Universitätsstr. 1
40225 Düsseldorf
Germany

Tel: [phone]
E-Mail: ***@uni-duesseldorf.de<mailto:***@uni-duesseldorf.de>
URL: http://cpclab.uni-duesseldorf.de


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[German Erlenkamp]

Hi Jared,

I've also tried the 'super' command, but this gives me only this erro=
r
message:=09super aligned_1, cryst_1
=09=09=09 ExecutiveAlign: invalid selections for alignment.

And I'll have a closer look at LigAlign, but on the first sight it se=
ems, that
I'll need the binding site for this approach.

Cheers,

German

Post by Sampson, Jared
Hi German -
=20
I=E2=80=99m not sure I follow exactly what you=E2=80=99re asking, b=

ut `align` does its superimposition based on sequence alignment, whic=
h isn=E2=80=99t really meaningful for small molecule ligands. I woul=
d suggest using `fit`, `super`, or `cealign` instead, which all use j=
ust the coordinates, although it=E2=80=99s possible these also won=
=E2=80=99t work.

Post by Sampson, Jared
=20
For a more sophisticated approach, maybe check out LigAlign, which =

comes with a tutorial: http://www.pymolwiki.org/index.php/LigAlign.

Post by Sampson, Jared
=20
Cheers,
Jared
=20
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
=20
=20
=20
=20
=20
=20
=20
Hi all,
=20
I have two sets of ligands, the first are the crystal structures, t=

he second

Post by Sampson, Jared
one are the same compounds, but aligned by a flexible ligand alignm=

ent, where

Post by Sampson, Jared
I used one of the crystal structures as a template. Unfortunately t=

he

Post by Sampson, Jared
coordinates of the templates changed during the alignment.
Now I want to calculate the RMSD-values between these structures, a=

nd for this

Post by Sampson, Jared
I want to superpose the group of aligned ligands to the template li=

gand.

Post by Sampson, Jared
I started with 'align Aligned_1, Start_1' but after this command, a=

ll atoms of

Post by Sampson, Jared
'Aligned_1' vanished and I can only represent this as a sphere. Thi=

s will be

Post by Sampson, Jared
Ok for me, because the RMSD between 'Aligned_1' and 'Start_1' is 0.
But after this I want to move 'Aligned_2' the same way as I moved '=

Aligned_1'.

Post by Sampson, Jared
I thought 'matrix_copy Alinged_1, Start_1' should do the job, but a=

fter this

Post by Sampson, Jared
all atoms of 'Aligned_2' are gone. I still have this object, but no=

thing more.

Post by Sampson, Jared
=20
My questions are: Am I using the correct commands for this task, or=

not? And, if

Post by Sampson, Jared
I am using the right commands, what is going wrong? And - for the c=

ase my way

Post by Sampson, Jared
is not correct - what would be the proper way to solve my problem?
=20
Thanks in advance,
=20
German
--
German Erlenkamp
=20
Computational Pharmaceutical Chemistry
and Molecular Bioinformatics
=20
Heinrich-Heine-Universit=C3=A4t D=C3=BCsseldorf
Institut f=C3=BCr Pharmazeutische und Medizinische Chemie
Universit=C3=A4tsstr. 1
40225 D=C3=BCsseldorf
Germany
=20
Tel: [phone]

rf.de>

Post by Sampson, Jared
URL: http://cpclab.uni-duesseldorf.de
=20
=20
-------------------------------------------------------------------=

-----------

Post by Sampson, Jared
Infragistics Professional
Build stunning WinForms apps today!
Reboot your WinForms applications with our WinForms controls.
Build a bridge from your legacy apps to the future.
http://pubads.g.doubleclick.net/gampad/clk?id=3D153845071&iu=3D/414=

0/ostg.clktrk

Post by Sampson, Jared
_______________________________________________
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users

.net

Post by Sampson, Jared
=20

--=20
German Erlenkamp

Computational Pharmaceutical Chemistry=20
and Molecular Bioinformatics

Heinrich-Heine-Universit=C3=A4t D=C3=BCsseldorf
Institut f=C3=BCr Pharmazeutische und Medizinische Chemie
Universit=C3=A4tsstr. 1
40225 D=C3=BCsseldorf
Germany

Tel: [phone]
E-Mail: ***@uni-duesseldorf.de
URL: http://cpclab.uni-duesseldorf.de