pymol-users

[PyMOL] sticks

[Ahmet y. <ahm...@gm...>]

Dear users,

I want to show the residue 15 as a stick in xxxx.pdb.
pymol-->file-->Open-->xxxx.pdb
PyMOL> hide everything, all
PyMOL> select active, resi 15
PyMOL> show sticks, resi 15

Unfortunately, pymol doesnt show it as a stick. Please see image
https://www.dropbox.com/s/24gz1kcathiu2x6/resi-15.png
Where did I mistake?

Thanks in advance

-- 
Ahmet Yıldırım

Re: [PyMOL] sticks

[Thomas H. <sp...@us...>]

Hi Ahmet,

could be a shader problem (missing support by your graphics driver). Try:

PyMOL> set cylinder_shader_ff_workaround
(see http://pymolwiki.org/index.php/Cylinder_shader_ff_workaround )

or:

PyMOL> set use_shaders, 0

Cheers,
  Thomas

On 22 Dec 2013, at 00:39, Ahmet yıldırım <ahm...@gm...> wrote:

> Dear users,
> 
> I want to show the residue 15 as a stick in xxxx.pdb.
> pymol-->file-->Open-->xxxx.pdb
> PyMOL> hide everything, all
> PyMOL> select active, resi 15
> PyMOL> show sticks, resi 15
> 
> Unfortunately, pymol doesnt show it as a stick. Please see image https://www.dropbox.com/s/24gz1kcathiu2x6/resi-15.png
> Where did I mistake?
> 
> Thanks in advance
> 
> -- 
> Ahmet Yıldırım

Re: [PyMOL] sticks

[Noinaj, N. (NIH/N. [E] <no...@ni...>]

this works for me when testing using PDB ID code 4GRV (and others).  Can you test this PDB ID with your setup to see if it works?  The unknown variable here is your pdb file, possibly something is odd about it or something might be wrong with PyMOL as Thomas has indicated.  If PDB ID code 4GRV works ok for you, then the problem is probably your pdb file.


Cheers,
Nick


________________________________________
From: Ahmet yıldırım [ahm...@gm...]
Sent: Sunday, December 22, 2013 12:39 AM
To: pym...@li...
Subject: [PyMOL] sticks

Dear users,

I want to show the residue 15 as a stick in xxxx.pdb.
pymol-->file-->Open-->xxxx.pdb
PyMOL> hide everything, all
PyMOL> select active, resi 15
PyMOL> show sticks, resi 15

Unfortunately, pymol doesnt show it as a stick. Please see image https://www.dropbox.com/s/24gz1kcathiu2x6/resi-15.png
Where did I mistake?

Thanks in advance

--
Ahmet Yıldırım

Re: [PyMOL] sticks

[Thomas H. <sp...@us...>]

Hi Ahmet,

On 22 Dec 2013, at 12:17, Ahmet yıldırım wrote:
> Pymol show them as a sticks but they are very similar. How can I color each residue with different colors?

if you have incentive PyMOL 1.6, you can use the spectrum command to color by residue type:

PyMOL> spectrum resn

With older versions or with open-source, you have to do this manually:

PyMOL> color blue, resn ALA
PyMOL> color red, resn GLY
PyMOL> color yellow, resn CYS
PyMOL> ...

There are scripts on the web for that, for example Robert Campbell has one:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Hope that helps.

Cheers,
  Thomas

On 22 Dec 2013, at 12:17, Ahmet yıldırım <ahm...@gm...> wrote:

> Dear Thomas,
> 
> I did as you said "PyMOL> set use_shaders, 0". The problem is solved. Thanks.
> But I have a small problem.
> I typed:  
> select resi resi 15-18
> show sticks, sele
> 
> Pymol show them as a sticks but they are very similar. How can I color each residue with different colors?
> 
> Thanks in advance
> 
> 2013/12/22 Thomas Holder
> Hi Ahmet,
> 
> could be a shader problem (missing support by your graphics driver). Try:
> 
> PyMOL> set cylinder_shader_ff_workaround
> (see http://pymolwiki.org/index.php/Cylinder_shader_ff_workaround )
> 
> or:
> 
> PyMOL> set use_shaders, 0
> 
> Cheers,
>   Thomas
> 
> On 22 Dec 2013, at 00:39, Ahmet yıldırım wrote:
> 
> > Dear users,
> >
> > I want to show the residue 15 as a stick in xxxx.pdb.
> > pymol-->file-->Open-->xxxx.pdb
> > PyMOL> hide everything, all
> > PyMOL> select active, resi 15
> > PyMOL> show sticks, resi 15
> >
> > Unfortunately, pymol doesnt show it as a stick. Please see image https://www.dropbox.com/s/24gz1kcathiu2x6/resi-15.png
> > Where did I mistake?
> >
> > Thanks in advance
> >
> > --
> > Ahmet Yıldırım
> -- 
> Ahmet Yıldırım