Re: [PyMOL] Label charge sites, termini, check contrast

2021-01-29 Thread Neena Susan Eappen 
Hi Ali,

Thank you for the brief and thorough explanation! All those commands gave
exactly what I was looking for!

Many thanks,
Neena

On Fri, 29 Jan 2021 at 18:36, Ali Saad Kusay 
wrote:

> Hi Neena,
>
> A simple way to label in PyMOL is to simply select the atom you want and
> enter the following command:
> label sele, "what you want to label"
>
> I.e. for the N:
> label sele, "N"
>
> PyMOL can render the special ⨁ you are using, through unicode:
> label sele, '\u2A01'
> Visit the wiki for more info:
> https://pymolwiki.org/index.php/Label_font_id
>
> The labels may be small, to change size,
> set label_size, 30
> Change the 30 to what size you need
>
> Finally, the labels will likely be off in position, the easiest way to
> change position is by using the editing mode:
> This helpful video shows this around 3:30 (
> https://www.youtube.com/watch?v=yBFzJ3ql4qU_channel=MolecularMemory)
>
> Cheers,
>
> Ali
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> Supervised by A/Prof Thomas Balle
> The University of Sydney School of Pharmacy | Faculty of Medicine and
> Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
>
>
>
>
>
>
>
>
>
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[PyMOL] Label charge sites, termini, check contrast

2021-01-29 Thread Neena Susan Eappen 
Hello PyMOL users,

Is there a way to label charge sites and termini on PyMOL as I have shown
in the below figure instead of using Paint?
In addition, is there a way to check color contrast for this peptide
structure for making it more accessible to the readers?
[image: image.png]
Many thanks,
Neena
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Re: [PyMOL] representation of residue sidechain within a beta strand?

2021-01-29 Thread Thomas Holder 
Hi Yufeng,

The "Properties" panel can show you which settings got changed with the preset. 
The "pretty" preset indeed sets "cartoon_side_chain_helper" to "off" for the 
object. The easiest way to clear this setting is to use the "unset_deep" 
command.

unset_deep cartoon_side_chain_helper
set cartoon_side_chain_helper

https://pymolwiki.org/index.php/Unset_deep
https://pymolwiki.org/index.php/Properties_Inspector

Cheers,
  Thomas


> On Jan 29, 2021, at 6:26 AM, Yufeng Tong  wrote:
> 
> Hi Tomas,
> 
> I noticed this setting is not working when
> preset.pretty(selection='all') has been invoked, that is, whether
> cartoon_side_chain_helper is set to on or off, the side chain is
> disconnected. Do you know what is changed when preset.pretty() is
> called?
> 
> The reason I want to call preset.pretty() is that if this is not
> called, the sticks representation of an isopeptide cannot be properly
> displayed (no sticks shown for the isopeptide bond), a bit of a
> dilemma.
> 
> Thanks,
> 
> Yufeng
> 
> 
> On Mon, Jan 18, 2021 at 3:35 AM Tomas Malinauskas
>  wrote:
>> 
>> Hi Emilia,
>> 
>> You might try the following:
>> set cartoon_side_chain_helper, on
>> 
>> Hope that helps,
>> Tomas
>> 
>> On Mon, Jan 18, 2021 at 7:52 AM Emilia C. Arturo (Emily)
>>  wrote:
>>> 
>>> Hi All,
>>> 
>>> I'm wondering if anyone here knows how to represent an amino acid residue 
>>> side chain that resides within a beta strand in stick representation such 
>>> that the residue is linked in space with the backbone. This works fine when 
>>> representing as sticks a residue that is within a loop or helix, but not 
>>> within a strand; there it just sticks out into space, which looks awful if 
>>> the figure is not turned 'just so' so that the viewer cannot see the space. 
>>> I am using version 2.4.0 on my Mac.
>>> 
>>> Regards,
>>> Emilia.
>>> 
>>> --
>>> "Study as if you were going to live forever; live as if you were going to 
>>> die tomorrow." - Maria Mitchell
>>> 
>>> "I'm not afraid of storms for I'm learning to sail my ship."  - Louisa May 
>>> Alcott
>>> 
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>> 
>> 
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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