[PyMOL] Exporting a selection to file

[Luca Varani]

Hello,

is it possible to generate a list of all residues within 5A of another
(or whatever you need)
and then save this list to a file/clipboard?

Thanks a lot for the help,
Luca

[annalisa bordogna]

Hi!

Try with:

select <selection name>, <name of the object to which the selection belongs>
w. 5 of <other object>
select <other selection name>, br. <selection name>
save name.pdb, <other selection name>

The first command select the atoms at 5 Angstroms from <other object>;
the second select the whole residues to which the atoms selected belong;
the third saves the complete selection.

Hope it helps!
Annalisa

------------------------------------------------
Annalisa Bordogna
PhD. Student
DISAT - Università degli Studi di Milano Bicocca
Milano
Italy
------------------------------------------------

Post by Luca Varani
Hello,
is it possible to generate a list of all residues within 5A of another (or
whatever you need)
and then save this list to a file/clipboard?
Thanks a lot for the help,
Luca
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[Nir London]

Hi, Can anyone help thierry ?
http://rosettadesigngroup.com/blog/10/pymol-scripts/#comment-3149

" I would like to ask to make a special bond in pymol. Actually in my
protein I have a real covalent bond between an Asn and a Lys..
Obviously, Pymol doesn’t know how to draw it. Can you help me ?
Thanks. "
thierry

Nir London.
Rosetta Design Group.
http://rosettadesigngroup.com/blog/

[Tsjerk Wassenaar]

Hi Nir,

Pymol just draws bonds based on distances, not based on topological
information. If atoms are within contact distance, a bond will be
drawn, whatever the atoms are. If one feels need for an additional
bond, it is possible to add them using:

bond selection1, selection2

This will draw bonds between all atoms of selection1 and all atoms of
selection2. In Thierry's case it would be something like:

bond resi X and resn asp and name CD, resi Y and resn lys and name NZ

assuming this is about a side chain - side chain amide bond.

Hope it helps,

Tsjerk

Post by Nir London
Hi, Can anyone help thierry ?
http://rosettadesigngroup.com/blog/10/pymol-scripts/#comment-3149
" I would like to ask to make a special bond in pymol. Actually in my
protein I have a real covalent bond between an Asn and a Lys.. Obviously,
Pymol doesn’t know how to draw it. Can you help me ?
Thanks. "
thierry
Nir London.
Rosetta Design Group.
http://rosettadesigngroup.com/blog/
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: [phone]
F: [phone]

[Tsjerk Wassenaar]

Obviously that should read 'resn asn' in stead of 'resn asp'. Sorry for that.

Tsjerk

Post by Tsjerk Wassenaar
Hi Nir,
Pymol just draws bonds based on distances, not based on topological
information. If atoms are within contact distance, a bond will be
drawn, whatever the atoms are. If one feels need for an additional
bond selection1, selection2
This will draw bonds between all atoms of selection1 and all atoms of
bond resi X and resn asp and name CD, resi Y and resn lys and name NZ
assuming this is about a side chain - side chain amide bond.
Hope it helps,
Tsjerk

Post by Nir London
Hi, Can anyone help thierry ?
http://rosettadesigngroup.com/blog/10/pymol-scripts/#comment-3149
" I would like to ask to make a special bond in pymol. Actually in my
protein I have a real covalent bond between an Asn and a Lys.. Obviously,
Pymol doesn’t know how to draw it. Can you help me ?
Thanks. "
thierry
Nir London.
Rosetta Design Group.
http://rosettadesigngroup.com/blog/
------------------------------------------------------------------------------
_______________________________________________
PyMOL-users mailing list
https://lists.sourceforge.net/lists/listinfo/pymol-users

--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: [phone]
F: [phone]

--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: [phone]
F: [phone]