Re: [PyMOL] how to show PBC box?

2016-12-07 Thread Albert 

Dear Tsjerk:

Thanks a lot for such prompt reply.

It works very well.

Cheers.

Albert


On 12/07/2016 08:46 PM, Tsjerk Wassenaar wrote:

Hi Albert,

You can do:

show cell

Cheers,

Tsjerk



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Re: [PyMOL] how to show PBC box?

2016-12-07 Thread Tsjerk Wassenaar 
Hi Albert,

You can do:

show cell

Cheers,

Tsjerk

On Dec 7, 2016 8:44 PM, "Albert"  wrote:

> Hello:
>
> I am visualizing a MD simulation system in PyMOL. It contains the PBC
> information. I am just wondering how can we show the PBC box in PyMOL?
> As far as I know the PBC box can be shown in VMD using the following
> command line:
>
>  >pbc box
>
> Is there any similar command line in PyMOL?
>
> Thank you very much.
>
> Albert
>
>
> 
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[PyMOL] how to show PBC box?

2016-12-07 Thread Albert 
Hello:

I am visualizing a MD simulation system in PyMOL. It contains the PBC 
information. I am just wondering how can we show the PBC box in PyMOL? 
As far as I know the PBC box can be shown in VMD using the following 
command line:

 >pbc box

Is there any similar command line in PyMOL?

Thank you very much.

Albert


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Re: [PyMOL] Get dihedral angle of multiple objects

2016-12-07 Thread Rui Sousa 

Hi,

I am assuming it is because, when you pass the arguments on the 
cmd.dihedral() command, the "obj" is being read as a string, instead of 
the variable obj. I think your problem will be solved if you use 
something like, for your first example:

"/"+obj+"///655/CA"
Note the quotation marks placement. This is not the cleanest solution 
but should help.


Rui

Le 07/12/2016 07:09, Val Yu a écrit :

Hi,

I'm trying to use this script to get a specific dihedral angle from 
all the objects and write into a file:


PyMOL>f = open('dih.txt','w')
PyMOL>for obj in cmd.get_object_list():\
PyMOL>dih = 
cmd.dihedral('dih','/obj///655/CA','/obj///655/CB','/obj///655/CG','/obj///655/CD1')\

PyMOL>f.write(str(dih))

The software shows following complains:
Selector-Error: Invalid selection name "obj".
( ( ( % obj ) & i; 655 & n; CA ) )<--
Selector-Error: Invalid selection name "obj".
( ( ( % obj ) & i; 655 & n; CB ) )<--
Selector-Error: Invalid selection name "obj".
( ( ( % obj ) & i; 655 & n; CG ) )<--
Selector-Error: Invalid selection name "obj".
( ( ( % obj ) & i; 655 & n; CD1 ) )<--
...

What's wrong with my script?

--
Val Yu


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[PyMOL] Get dihedral angle of multiple objects

2016-12-07 Thread Val Yu 
Hi,

I'm trying to use this script to get a specific dihedral angle from all the
objects and write into a file:

PyMOL>f = open('dih.txt','w')
PyMOL>for obj in cmd.get_object_list():\
PyMOL>dih =
cmd.dihedral('dih','/obj///655/CA','/obj///655/CB','/obj///655/CG','/obj///655/CD1')\
PyMOL>f.write(str(dih))

The software shows following complains:
Selector-Error: Invalid selection name "obj".
( ( ( % obj ) & i; 655 & n; CA ) )<--
Selector-Error: Invalid selection name "obj".
( ( ( % obj ) & i; 655 & n; CB ) )<--
Selector-Error: Invalid selection name "obj".
( ( ( % obj ) & i; 655 & n; CG ) )<--
Selector-Error: Invalid selection name "obj".
( ( ( % obj ) & i; 655 & n; CD1 ) )<--
...

What's wrong with my script?

-- 
Val Yu
--
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