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

[Neena Susan Eappen]

Hi Jared,

Thank you for teaching me that special feature on pymol; on my pymol
version set label_position worked (instead of set label_offset).

Neena

On Sun, 31 Jan 2021 at 20:17, Jared Sampson 
wrote:

> Hi Neena -
>
> There is also a `label_offset` setting, which can be given an x,y,z vector
> in viewport coordinates. So if you want all labels to be in the foreground
> compared to their respective atom(s), you might set it via:
>
> set label_offset, [0,0,5]
>
> I believe this can also be done in an object-specific fashion, so you
> could also do:
>
> set label_offset, [0,0,5], myobject
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On Sat, Jan 30, 2021 at 2:52 AM Neena Susan Eappen <
> neenasusan...@gmail.com> wrote:
>
>> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ___
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
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Re: [PyMOL] Label charge sites, termini, check contrast

[Jon R Sayers]

Or you can use "3 button edit mode" with a combination of Control (on a
Mac) and the left mouse button. It allows you to move the label in first
2Ds, release, rotate and do it again to position exactly where you want it,
e.g. in front, behind etc.

BW Jon

On Mon, 1 Feb 2021 at 21:23, Jared Sampson 
wrote:

> Sorry, I replied from my phone earlier...the correct setting is
> `label_position`.  https://pymolwiki.org/index.php/Label_position
>
> Best,
> Jared
>
> On Sun, Jan 31, 2021 at 8:17 PM Jared Sampson 
> wrote:
>
>> Hi Neena -
>>
>> There is also a `label_offset` setting, which can be given an x,y,z
>> vector in viewport coordinates. So if you want all labels to be in the
>> foreground compared to their respective atom(s), you might set it via:
>>
>> set label_offset, [0,0,5]
>>
>> I believe this can also be done in an object-specific fashion, so you
>> could also do:
>>
>> set label_offset, [0,0,5], myobject
>>
>> Hope that helps.
>>
>> Cheers,
>> Jared
>>
>>
>> On Sat, Jan 30, 2021 at 2:52 AM Neena Susan Eappen <
>> neenasusan...@gmail.com> wrote:
>>
>>> 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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>>
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-- 
Professor Jon R Sayers, FRSB
Department of Infection, Immunity & Cardiovascular Disease
University of Sheffield Medical School
Beech Hill Rd
Sheffield
S10 2RX
United Kingdom

Tel: +44 (0)114 215 9552
Fax: +44 (0)114 271 1863
Email: j.r.say...@sheffield.ac.uk

https://www.sheffield.ac.uk/iicd/profiles/sayers

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

[Jared Sampson]

Sorry, I replied from my phone earlier...the correct setting is
`label_position`.  https://pymolwiki.org/index.php/Label_position

Best,
Jared

On Sun, Jan 31, 2021 at 8:17 PM Jared Sampson 
wrote:

> Hi Neena -
>
> There is also a `label_offset` setting, which can be given an x,y,z vector
> in viewport coordinates. So if you want all labels to be in the foreground
> compared to their respective atom(s), you might set it via:
>
> set label_offset, [0,0,5]
>
> I believe this can also be done in an object-specific fashion, so you
> could also do:
>
> set label_offset, [0,0,5], myobject
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On Sat, Jan 30, 2021 at 2:52 AM Neena Susan Eappen <
> neenasusan...@gmail.com> wrote:
>
>> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ___
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
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Re: [PyMOL] Label charge sites, termini, check contrast

[Jared Sampson]

Hi Neena -

There is also a `label_offset` setting, which can be given an x,y,z vector
in viewport coordinates. So if you want all labels to be in the foreground
compared to their respective atom(s), you might set it via:

set label_offset, [0,0,5]

I believe this can also be done in an object-specific fashion, so you could
also do:

set label_offset, [0,0,5], myobject

Hope that helps.

Cheers,
Jared


On Sat, Jan 30, 2021 at 2:52 AM Neena Susan Eappen 
wrote:

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

[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

[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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