Re: [PyMOL] format problem

[Tsjerk W. <ts...@gm...>]

Hi Kanika,

> alter_state 1, 1a8y_a, 1a8y,(x,y,z)=(-0.5*x + 0.886025*y, 0.886025*x +
>  0.5*y, -z)

This doesn't work like that. It should probably be

alter_state 1, 1a8y_a,(x,y,z)=(-0.5*x + 0.886025*y, 0.886025*x + 0.5*y, -z)

> then i saved the molecule in pymol from file-->save molecule-->1a8y_a.pdb

This worked for me as expected.

> The problem is that when i open the file as text file the format is improper
> since the space distribution is different from actual pdb files.
> I am saying this because i have to use this file to convert in tleap format
> and further use in a program. Is there any other way to save the molecule in
> pymol?

Can you give an example of where the spacing is wrong, e.g., post a
section from the original file and the corresponding section from the
new file?

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands