pymol-users

[PyMOL] comments ?

[Sebastien M. <seb...@ig...>]

Hello,
I try to add comment lines in my pml scripts but I don't know how to do.
I tried #, /*, //, <!-- or <-- characters but everything fails.

I got this kind of error messages:
	color red, 1DHS #color
	Selector-Error: Invalid Selection Name.
	( 1DHS #color )<--
or
	color red, 1DHS
	<-- second essai -->
	Error: unrecognized keyword: <--

How can I use comments in PyMOL scripts ?
Thanks

I use PyMOL 0.98 on Linux OS.

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

Re: [PyMOL] comments ?

[<li...@ul...>]

On Monday 01 August 2005 11:08, Sebastien Moretti wrote:
> Hello,
> I try to add comment lines in my pml scripts but I don't know how to do.
> I tried #, /*, //, <!-- or <-- characters but everything fails.
...
> How can I use comments in PyMOL scripts ?

The hash character (#) works to include comments on separate lines, but not at 
the end of a line that contains commands. So you can do

# Create separate dimer
create dimer,(chain A,B)

but not

create dimer,(chain A,B)  # Create separate dimer

-- 
Lieven Buts
Ultrastructure Laboratory
Vrije Universiteit Brussel

Re: [PyMOL] comments ?

[Ezequiel H P. <za...@pa...>]

> I try to add comment lines in my pml scripts but I don't know how to do.
> I tried #, /*, //, <!-- or <-- characters but everything fails.

use '#' but  on a line of its own not at the end of
line containing a pymol command, like this:

# color 1DHS in red
color red, 1DHS

Re: [PyMOL] comments ?

[Sebastien M. <seb...@ig...>]

>> I try to add comment lines in my pml scripts but I don't know how to d=
o.
>> I tried #, /*, //, <!-- or <-- characters but everything fails.
>=20
> use '#' but  on a line of its own not at the end of
> line containing a pymol command, like this:
>=20
> # color 1DHS in red
> color red, 1DHS

'#' seems to be incorrect:
	#second essai
	Error: unrecognized keyword: #second
	delete AaA

The script goes on but it sends an error message

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

Re: [PyMOL] comments ?

[Ezequiel H P. <za...@pa...>]

> '#' seems to be incorrect:

It is not incorrect.

If you post your script and how you use it we might be able to help.

Also, if you have something in you $HOME/.pymolrc or $HOME/.pymolrc.py
you should try temporarily moving these files elsewhere and trying again.
Something may have gone wrong in one of those files, it happened to me before.

Zac

Re: [PyMOL] comments ?

[Sebastien M. <seb...@ig...>]

>> '#' seems to be incorrect:
>=20
> It is not incorrect.
>=20
> If you post your script and how you use it we might be able to help.
>=20
> Also, if you have something in you $HOME/.pymolrc or $HOME/.pymolrc.py
> you should try temporarily moving these files elsewhere and trying agai=
n.
> Something may have gone wrong in one of those files, it happened to me=20
> before.
>=20
> Zac

I didn't properly test the '#' character.
It works in the external GUI and in standard scripts like in pml files.

But, '#' doesn't work in p1m file.
	Error: unrecognized keyword: #second
The # line involves an error but the script goes on.

I join an example where I removed the embedded lines with the structure=20
because the e-mail size was too large for the mailist server.

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

Re: [PyMOL] comments ?

[Ezequiel H P. <za...@pa...>]

> But, '#' doesn't work in p1m file.
>     Error: unrecognized keyword: #second
> The # line involves an error but the script goes on.

I think indeed you found a bug with the parsing of p1m files.
I have the same behaviour on my Linux computer.

Nice choice of colors by the way.

Cheers,

Zac