Re: [PyMOL] Color residue in cartoon mode

[harold steinberg]

I’m sorry, I thought she was trying to use two different cartoon modes and two 
different colors.


> On Aug 2, 2016, at 12:07 PM, Thomas Holder  
> wrote:
> 
> Hi Maria and Adam,
> 
> I think it's not that complicated. You need "cartoon_ring_mode" for the 
> residue selection. Example:
> 
> fetch 1rna, async=0
> as cartoon
> select firstres, chain A & resi 1
> set cartoon_ring_finder, 2
> set cartoon_ring_mode, 2, firstres
> color blue
> color red, firstres extend 1
> 
> Hope that helps.
> 
> Cheers,
>  Thomas
> 
> On 02 Aug 2016, at 12:42, harold steinberg  wrote:
> 
>> I believe that you can only apply the cartoon setting to an entire obj 
>> (object). And so you are correct in trying to duplicate the nucleotide so 
>> you can apply one setting to it, while allowing the other setting to display 
>> the rest of them. But that doesn’t work either since the program will only 
>> allow one display type at a time. There may be a complex way to override it 
>> but I do not know it.
>> 
>> The way I have gotten around this in the past is to set up the entire object 
>> the way you want it, then render it once with each setting.
>> 
>> Then open both of the resulting images in photoshop or similar program. Put 
>> them both into one file as layers.
>> 
>> Then delete most of one of the files (say the top one) so only the single 
>> nucleotide is left in the cartoon setting that you want in that layer. The 
>> rest of the image will appear from the bottom layer.
>> 
>> Then you can flatten the image and save it. It’s fast and works great.
>> 
>> 
>>> On Aug 2, 2016, at 9:41 AM, COSTA Maria  
>>> wrote:
>>> 
>>> Dear pymol-users,
>>> 
>>> I’m still learning how to use pymol to do basic things.
>>> At present, I’m working with a nucleic acid molecule that is colored by 
>>> sequence domains (each domain is a different objet). All the domains are 
>>> displayed in the cartoon mode, with backbone as dumbbell and 
>>> cartoon_ring_finder,0  (no nucleobases or riboses displayed). Now, I would 
>>> like to display only the first residue of one of the domains as 
>>> cartoon_ring_finder,2 (ring only for nucleobases) and then color it  
>>> entirely (dumbbell + ribose stick + base ring) with a different color from 
>>> the rest of the domain sequence.  The problem is that it does not work ! 
>>> 
>>> I tried to copy that nucleotide into a new objet to manipulate it 
>>> independently but all the arguments I write in the command line do not 
>>> apply to it, nothing is changing on the screen. The only thing that works 
>>> is the menu on the right, use the objet line corresponding to this residue, 
>>> display it entirely as sticks and then change the color of the sticks. But 
>>> that’s not what I need!
>>> 
>>> Do you have any ideas how to display the desired nucleotide?
>>> 
>>> Many thanks in advance,
>>> 
>>> Maria
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
> 
> -- 
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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Re: [PyMOL] Color residue in cartoon mode

[Thomas Holder]

Hi Maria and Adam,

I think it's not that complicated. You need "cartoon_ring_mode" for the residue 
selection. Example:

fetch 1rna, async=0
as cartoon
select firstres, chain A & resi 1
set cartoon_ring_finder, 2
set cartoon_ring_mode, 2, firstres
color blue
color red, firstres extend 1

Hope that helps.

Cheers,
  Thomas

On 02 Aug 2016, at 12:42, harold steinberg  wrote:

> I believe that you can only apply the cartoon setting to an entire obj 
> (object). And so you are correct in trying to duplicate the nucleotide so you 
> can apply one setting to it, while allowing the other setting to display the 
> rest of them. But that doesn’t work either since the program will only allow 
> one display type at a time. There may be a complex way to override it but I 
> do not know it.
> 
> The way I have gotten around this in the past is to set up the entire object 
> the way you want it, then render it once with each setting.
> 
> Then open both of the resulting images in photoshop or similar program. Put 
> them both into one file as layers.
> 
> Then delete most of one of the files (say the top one) so only the single 
> nucleotide is left in the cartoon setting that you want in that layer. The 
> rest of the image will appear from the bottom layer.
> 
> Then you can flatten the image and save it. It’s fast and works great.
> 
> 
>> On Aug 2, 2016, at 9:41 AM, COSTA Maria  
>> wrote:
>> 
>> Dear pymol-users,
>>  
>> I’m still learning how to use pymol to do basic things.
>> At present, I’m working with a nucleic acid molecule that is colored by 
>> sequence domains (each domain is a different objet). All the domains are 
>> displayed in the cartoon mode, with backbone as dumbbell and 
>> cartoon_ring_finder,0  (no nucleobases or riboses displayed). Now, I would 
>> like to display only the first residue of one of the domains as 
>> cartoon_ring_finder,2 (ring only for nucleobases) and then color it  
>> entirely (dumbbell + ribose stick + base ring) with a different color from 
>> the rest of the domain sequence.  The problem is that it does not work ! 
>>  
>> I tried to copy that nucleotide into a new objet to manipulate it 
>> independently but all the arguments I write in the command line do not apply 
>> to it, nothing is changing on the screen. The only thing that works is the 
>> menu on the right, use the objet line corresponding to this residue, display 
>> it entirely as sticks and then change the color of the sticks. But that’s 
>> not what I need!
>>  
>> Do you have any ideas how to display the desired nucleotide?
>>  
>> Many thanks in advance,
>>  
>> Maria
> 
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Color residue in cartoon mode

[harold steinberg]

I believe that you can only apply the cartoon setting to an entire obj 
(object). And so you are correct in trying to duplicate the nucleotide so you 
can apply one setting to it, while allowing the other setting to display the 
rest of them. But that doesn’t work either since the program will only allow 
one display type at a time. There may be a complex way to override it but I do 
not know it.

The way I have gotten around this in the past is to set up the entire object 
the way you want it, then render it once with each setting.

Then open both of the resulting images in photoshop or similar program. Put 
them both into one file as layers.

Then delete most of one of the files (say the top one) so only the single 
nucleotide is left in the cartoon setting that you want in that layer. The rest 
of the image will appear from the bottom layer.

Then you can flatten the image and save it. It’s fast and works great.


> On Aug 2, 2016, at 9:41 AM, COSTA Maria  
> wrote:
> 
> Dear pymol-users,
>  
> I’m still learning how to use pymol to do basic things.
> At present, I’m working with a nucleic acid molecule that is colored by 
> sequence domains (each domain is a different objet). All the domains are 
> displayed in the cartoon mode, with backbone as dumbbell and 
> cartoon_ring_finder,0  (no nucleobases or riboses displayed). Now, I would 
> like to display only the first residue of one of the domains as 
> cartoon_ring_finder,2 (ring only for nucleobases) and then color it  entirely 
> (dumbbell + ribose stick + base ring) with a different color from the rest of 
> the domain sequence.  The problem is that it does not work ! 
>  
> I tried to copy that nucleotide into a new objet to manipulate it 
> independently but all the arguments I write in the command line do not apply 
> to it, nothing is changing on the screen. The only thing that works is the 
> menu on the right, use the objet line corresponding to this residue, display 
> it entirely as sticks and then change the color of the sticks. But that’s not 
> what I need!
>  
> Do you have any ideas how to display the desired nucleotide?
>  
> Many thanks in advance,
>  
> Maria
> --
> ___
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> )
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> 
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net 
> 
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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[PyMOL] Color residue in cartoon mode

[COSTA Maria]

Dear pymol-users,

I'm still learning how to use pymol to do basic things.
At present, I'm working with a nucleic acid molecule that is colored by 
sequence domains (each domain is a different objet). All the domains are 
displayed in the cartoon mode, with backbone as dumbbell and 
cartoon_ring_finder,0  (no nucleobases or riboses displayed). Now, I would like 
to display only the first residue of one of the domains as 
cartoon_ring_finder,2 (ring only for nucleobases) and then color it  entirely 
(dumbbell + ribose stick + base ring) with a different color from the rest of 
the domain sequence.  The problem is that it does not work !

I tried to copy that nucleotide into a new objet to manipulate it independently 
but all the arguments I write in the command line do not apply to it, nothing 
is changing on the screen. The only thing that works is the menu on the right, 
use the objet line corresponding to this residue, display it entirely as sticks 
and then change the color of the sticks. But that's not what I need!

Do you have any ideas how to display the desired nucleotide?

Many thanks in advance,

Maria
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