[PyMOL] any hotkey?

2015-09-03 Thread Albert 
Hello:

I am just wondering is there any hotkey in Pymol so that we can center 
in the Ligand automatically? For instance:

If I press keyboard "L", Pymol zoom to ligand binding pocket 
automatically

Thanks a lot

Albert

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[PyMOL] How to highlight the interactions between two proteins consituting the complex?

2015-09-03 Thread sunyeping 
Dear pymol users,
I wish to highlight the interactions between two proteins consituting the 
complex. I want to make these interacting residues clear but other residues 
obscure as the background in Pymol. Which would be the skill?
Thanks a lotYeping Sun
Institute of Microbiology, Chinese Academy of Sciences--
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Re: [PyMOL] any hotkey?

2015-09-03 Thread Osvaldo Martin 
Hi Albert,

You can use Set_Key , to bind
any function (predefined or defined by you) to any “hotkey/shorcut”

Cheers,
Osvaldo.

On Thu, Sep 3, 2015 at 5:57 AM, Albert  wrote:

Hello:
>
> I am just wondering is there any hotkey in Pymol so that we can center
> in the Ligand automatically? For instance:
>
> If I press keyboard "L", Pymol zoom to ligand binding pocket
> automatically
>
> Thanks a lot
>
> Albert
>
>
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> Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
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>
​
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Re: [PyMOL] XYZ format - max size of the name field

2015-09-03 Thread Thomas Holder 
Hi Pawel,

The 4 character limit is currently a hard limit. As a workaround I suggest you 
reformat your file into PDB format and split the atom name into the name and 
segi columns for example. Your selection expression will become:

For H1:
name H1 and segi ""

For H1000:
name H100 and segi "0"

To properly handle atom names with more than 4 characters we would have to 
refactor the internal data representation, just like we did for multi-letter 
chain identifiers in PyMOL 1.7.4.

Cheers,
  Thomas

On 02 Sep 2015, at 20:03, Pawe? Gniewek  wrote:

> Hi,
> 
> I'm trying to read a large file in XYZ format.
> 
> By default the first line is the number of atoms in the file. 
> The other lines are giving the name and the coordinates for each atom:
>
> 
> I've noticed that when the name of the atom is longer than 4 characters, I 
> cannot select that atom - or it's not even read.  For example I have a file 
> like that:
> 1000
> H1 0.0 0.0 0.0
> ...
> H1000 1000.0 1000.0 1000.0
> 
> then the command:
> select H_1000, name H1000
> gives me:
> selection "H1000" defined with 0 atoms
> 
> However, at the same time if I do:
> select H_100, name H100
> I get:
> selection "H100" defined with 2 atoms
> what means that the last character has been omitted. 
> 
> Of course I can work it out by naming atoms like: HH01 instead of H1000, but 
> I wonder if there is more elegant way of doing it. Any tricks off top of your 
> heads ?
> 
> Thanks.
> Pawel

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] any hotkey?

2015-09-03 Thread Thomas Holder 
Hi Albert & Osvaldo,

This should work in PyMOL 1.7+ to bind the F1 key to zoom on the first 
"organic" residue:

set_key F1, zoom byres first organic, animate=1

Cheers,
  Thomas

On 03 Sep 2015, at 06:48, Osvaldo Martin  wrote:

> Hi Albert,
> 
> You can use Set_Key, to bind any function (predefined or defined by you) to 
> any “hotkey/shorcut”
> 
> Cheers,
> Osvaldo.
> 
> On Thu, Sep 3, 2015 at 5:57 AM, Albert  wrote:
> 
> Hello:
> 
> I am just wondering is there any hotkey in Pymol so that we can center
> in the Ligand automatically? For instance:
> 
> If I press keyboard "L", Pymol zoom to ligand binding pocket
> automatically
> 
> Thanks a lot
> 
> Albert

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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[PyMOL] Unable to import fragment

2015-09-03 Thread Pablo Garay 
The problem is solved changing the path of chempy from this file :

/usr/lib/python2.7/dist-packages/chempy/fragments/__init__.py

In that file I change the line:

path = chempy.path + 'fragments/'

for this line:

path = '/usr/share/pymol/data/chempy/fragments/'

And that works, cheers.
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