Hi Brenton,
The n. or name selection operator is for atom names.
label resi 403 and name OG, "Ser403"
The absolute atom IDs are not typically useful.
Hope it helps,
Tsjerk
On Mon, Apr 6, 2015 at 10:52 PM, Brenton Horne <brentonho...@ymail.com>
wrote:
> How do I specify the specific atoms? I have tried:
>
> show sticks, r. 1w8
> label (r. 1w8) and n. 1403 and i. 10, "CFT"
> show sticks, r. ai8
> label (r. ai8) and n. 1676 and i. 7, "open-chain CFT"
> show sticks, r. mur
>
> show sticks, resi 403
> color green, resi 403
> label (resi 403) and i. 3, "Ser403"
>
> with and w/o the "n. and" part.
>
> On 7/04/2015 6:28 AM, Tsjerk Wassenaar wrote:
>
> Hi Brenton,
>
> Add a specific atom, at which you want the label, to the selection. You
> can pick one to get to know its name.
>
> Cheers,
>
> Tsjerk
>
> On Mon, Apr 6, 2015 at 10:03 PM, Brenton Horne <brentonho...@ymail.com>
> wrote:
>
>> Hi,
>>
>> I have skimmed the Label <http://pymolwiki.org/index.php/Label> page on
>> PyMOL Wiki and it only appears to give examples about how to label specific
>> atoms and not whole ligands or residues. See I'd like to label residue 403
>> as "Ser403", ceftaroline's open form (het ID AI8) as "Open CFT" and
>> ceftaroline (het ID 1W8) as "CFT" in the structure that has the PDB ID
>> 3ZG0. I presently have the PyMOL code:
>>
>> delete all
>> load 3zg0.pdb1
>> hide
>> show cartoon
>>
>> # Colouring secondary structure
>> set_color blues, [0.0196078,0.7607843,0.7607843]
>>
>> color red, ss h
>> color yellow, ss s
>> color blues, ss l+""
>>
>> show sticks, r. 1w8
>> label (r. 1w8), "CFT"
>> show sticks, r. ai8
>> label (r. ai8), "open-chain CFT"
>> show sticks, r. mur
>>
>> show sticks, resi 403
>> color green, resi 403
>> label (resi 403), "Ser403"
>> h_add
>> set valence, 0.2
>>
>>
>> set_color orange, [1, 0.5, 0]
>> set_color fluorine, [0.5625,0.875,0.3125]
>> set_color chlorine, [0.12109375,0.9375,0.12109375]
>> set_color sulfur, [1,1,0.18750]
>>
>> # Colouring elements
>> #color black, elem c and resi 69 and not name c+n+o
>> color black, elem c and organic
>>
>> #color blue, elem n and resi 69 and not name c+n+o
>> color blue, elem n and organic
>>
>> #color white, elem h and resi 69 and not name c+n+o
>> color white, elem h and organic
>>
>> #color red, elem o and resi 69 and not name c+n+o
>> color red, elem o and organic
>>
>> #color orange, elem p and resi 69 and not name c+n+o
>> color orange, elem p and organic
>>
>> #color fluorine, elem f and resi 69 and not name c+n+o
>> color fluorine, elem f and organic
>>
>> #color chlorine, elem cl and resi 69 and not name c+n+o
>> color chlorine, elem cl and organic
>>
>> color sulfur, elem s and organic
>>
>> # Colour backgrond white
>> bg_color white
>>
>> remove solvent
>>
>> With the relevant code indented. The result was
>> http://i.imgur.com/lXoZmQA.png. The problem, however, is that as you can
>> see in this image this code doesn't give just a single, individual label
>> for each of the two ligands and serine 403, rather it appears to label each
>> individual atom in each of these three molecules of interest. So my
>> question is how do I get just a single label for each molecule of interest
>> and not for every atom inside these molecules.
>>
>> Thanks for your time,
>> Brenton
>>
>>
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
>
--
Tsjerk A. Wassenaar, Ph.D.
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