On 01/19/2016 03:11 PM, Tsjerk Wassenaar wrote:
> Hi Pascual,
>
> The PDB file does not really have information on bonds. If atoms are closer
> than some cutoff a bond is drawn. Unbonding and saving will not change the
> distance, so the bond will be drawn again when loaded again. What is your
Hi Pascual,
The PDB file does not really have information on bonds. If atoms are closer
than some cutoff a bond is drawn. Unbonding and saving will not change the
distance, so the bond will be drawn again when loaded again. What is your
aim?
Cheers,
Tsjerk
On Tue, Jan 19, 2016 at 12:15 PM,
Well, yes, programs do use the CONECT records, including pymol
http://pymolwiki.org/index.php/Connect_mode
Removing bonds is http://pymolwiki.org/index.php/Unbond
Atoms can be translated using the command line
http://pymolwiki.org/index.php/Editing_atoms#Get_coordinates_from_Python
Or in edit
CONECT records are not used for peptide bonds for standard amino acid and
nucleic acid links. These are assumed. In addition, for these standard
chemical component, CONECT records are not used to internal bonds - they
are "known."
Non standard amino/nucleic acids used CONECT records for all
Thanks, David!
My take- Pymol is a very powerful tool for creating beautiful and insightful
figures of molecules, with myriad features for displaying aspects of interest
to structural biologists, such as different surfaces, electrostatic potential,
H-bonds and other inter-atomic interactions,
Hi Edward,
Oh, I read over the moving part. Well, what I meant to convey is that you
can use CONECT records to draw additional bonds, but for the rest
bondedness is inferred from distance. So you can only remove bonds if the
particles are further apart than the cutoff AND have a CONECT record.
Dear developer,
I had this segmentation fault problem whenever using plugin like apbs or
autodock etc. it crashes when I click button "APBS binary location" etc,
Tried both pymol 1.7.4 and 1.8.0 and gave the same error. Any help would be
greatly appreciated.
Detected OpenGL version 2.0 or
