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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ___
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>> 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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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
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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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ___
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>> 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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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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[PyMOL] label color

[Oganesyan, Vaheh]

Hello PyMOLers,

In version 2.2.3 under Win upon ray-tracing label color changes. Is there a way 
to prevent that from happening?

Thank you.

Regards,

Vaheh Oganesyan, Ph.D.
Scientist, Biologic Therapeutics

AstraZeneca
R | Antibody Discovery and Protein Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-4640  M:  240-398-0046
vaheh.oganes...@astrazeneca.com

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Re: [PyMOL] Label volume

[Pedro Lacerda]

Hi Thomas,

Cool, I did something like that, copied the selection "%obj and index 1"
then labeled it. So I got an independent label.

Multi-line labels was somewhat hackish:

cmd.label(
label_obj_name,
'"' + "\\n".join([
f'ID {i}',
f'Class {ensemble.klass}',
f'S {ensemble.strength}',
]) + '"'
)


I give up of volumes right now because I didn't figured out how to align
them. The behaviour I wanted was achieved with an "pseudo" atom.

Cheers,

Em qui, 15 de ago de 2019 às 05:49, Thomas Holder <
thomas.hol...@schrodinger.com> escreveu:

> Hi Pedro,
>
> it's only possible to label atoms. If you need an independent label,
> create a pseudo atom:
>
> pseudoatom label="Hello World"
>
> You can move the atom (or the label) in 3-Button Editing mouse mode while
> holding CTRL and dragging with the left mouse button.
>
> Cheers,
>   Thomas
>
> > On Aug 12, 2019, at 7:01 PM, Pedro Lacerda  wrote:
> >
> > And how to place a single arbitrary label on the object or segment?
> >
> > Em seg, 12 de ago de 2019 às 13:55, Pedro Lacerda 
> escreveu:
> > Hi PyMOL list,
> >
> > Is possible toshow  a label independent of the associated object be
> enabled?
> >
> > Or is possible to label a volume or map?
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular
> > Faculdade de Farmácia / UFBA
> >
> > @pslacerda
> > +55 71 9 9981-1856
> >
> >
> > --
> > Pedro Sousa Lacerda
> >
> > Laboratório de Bioinformática e Modelagem Molecular
> > Faculdade de Farmácia / UFBA
> >
> > @pslacerda
> > +55 71 9 9981-1856
> > ___
> > 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
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*
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Re: [PyMOL] Label volume

[Thomas Holder]

Hi Pedro,

it's only possible to label atoms. If you need an independent label, create a 
pseudo atom:

pseudoatom label="Hello World"

You can move the atom (or the label) in 3-Button Editing mouse mode while 
holding CTRL and dragging with the left mouse button.

Cheers,
  Thomas

> On Aug 12, 2019, at 7:01 PM, Pedro Lacerda  wrote:
> 
> And how to place a single arbitrary label on the object or segment?
> 
> Em seg, 12 de ago de 2019 às 13:55, Pedro Lacerda  
> escreveu:
> Hi PyMOL list,
> 
> Is possible toshow  a label independent of the associated object be enabled?
> 
> Or is possible to label a volume or map?
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
> 
> 
> -- 
> Pedro Sousa Lacerda
> 
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
> 
> @pslacerda
> +55 71 9 9981-1856
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Re: [PyMOL] Label volume

[Pedro Lacerda]

And how to place a single arbitrary label on the object or segment?

Em seg, 12 de ago de 2019 às 13:55, Pedro Lacerda 
escreveu:

> Hi PyMOL list,
>
> Is possible toshow  a label independent of the associated object be
> enabled?
>
> Or is possible to label a volume or map?
> --
> Pedro Sousa Lacerda
>
>
> *Laboratório de Bioinformática e Modelagem Molecular*
> *Faculdade de Farmácia / UFBA*
>
> *@pslacerda*
>
> *+55 71 9 9981-1856*
>


-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*
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[PyMOL] Label volume

[Pedro Lacerda]

Hi PyMOL list,

Is possible toshow  a label independent of the associated object be
enabled?

Or is possible to label a volume or map?
-- 
Pedro Sousa Lacerda


*Laboratório de Bioinformática e Modelagem Molecular*
*Faculdade de Farmácia / UFBA*

*@pslacerda*

*+55 71 9 9981-1856*
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Re: [PyMOL] label

[Thomas Holder]

Hi Albert,

Incentive PyMOL can do that, simply type:

label all, stereo

This feature is provided by a proprietary library and thus not available in 
Open-Source PyMOL.

Cheers,
  Thomas

On 16 Sep 2015, at 03:15, Albert  wrote:

> Hello:
> 
> Does anybody have any idea whether pymol could label the absolute 
> configuration (R/S) for a chiarity atom?
> 
> Thank you very much.
> 
> Albert

-- 
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Schrödinger, Inc.


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[PyMOL] label

[Albert]

Hello:

Does anybody have any idea whether pymol could label the absolute 
configuration (R/S) for a chiarity atom?

Thank you very much.

Albert

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[PyMOL] Label problems (PyMOL ver. 1.6)

[Yoshitaka MORIWAKI]

Dear Pymol Users,

I have installed PyMOL 1.6 built from source code on Ubuntu and Windows on June 
23, 2013.
I've noticed that the label of distance (or angle) is not shown properly.

I describe the steps to reproduce:
1. load a PDB file.
2. select two atoms by clicking the middle button on the PyMOL Viewer (pushing 
a wheel of a computer mouse).
3. type dist to create a distance object (dist01).

Then, a yellow broken line was produced between the selected atoms.
However, the label of distance (i.e. 2.2 Å) was not shown though the older 
versions (including v1.6-beta2) correctly showed.
Label of angle is the same.
It is also ineffective to select Show - label of object dist01 from PyMOL 
Viewer.

Please help me.

Thanks,
Yoshitaka

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Yoshitaka Moriwaki
Dept. of Biotechnology, Grad. Sch. of Agri. and Life Sci.,
The Univ. of Tokyo
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Re: [PyMOL] Label by selection identifier

[Thomas Holder]

Hi Jordan,

use the first operator:

PyMOL label first foo, foo

or for the first CA atom in foo:

PyMOL label first (foo and guide), foo

Cheers,
  Thomas

Jordan Willis wrote, On 05/21/13 11:07:
 Yes thank you!
 
 I meant to post that as my solution considering it works pretty good.
 It preserves depth and position.
 
 Jordan
 
 On May 21, 2013, at 3:45 AM, Folmer Fredslund wrote:
 
 Hi Jordan,

 As a workaround you can label just the CA's (so this doesn't answer
 your question exactly, but might be usefull):

 label foo and n. CA, foo

 Hope this helps,
 Folmer

 2013/5/21 Jordan Willis

 Hello,

 This should be straightforward,

 Is it possible to label selections by their name?

 If I have a selection named foo and I say label foo, foo, it
 of course labels all the atoms. Is it possible to get one label
 for the entire selection without using pseudoatoms?

 Jordan
-- 
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Schrödinger Contractor

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[PyMOL] Label on top of molecules?

[Boris Kheyfets]

Hello PyMOL users,

When I print atom names with

label all, name

the labels are often behind the spheres (I use balls and sticks
representation).

I tried moving labels around, but my system is very dence -- and labels
generally get under one or another sphere.

Is there a way I can print labels on top of everything?

With great respect,
Boris.
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Re: [PyMOL] Label on top of molecules?

[Takanori Nakane]

Hi Boris,

set float_labels, on

will do the job.
But it doesn't seem to affect ray-traced images.

Then you might want to manually adjust
label_position.
See http://www.pymolwiki.org/index.php/Label_position

For example,
 set label_position, (0, 0, 20)

will bring labels 20 angstroms in front of its original position.

Best regards,

Takanori Nakane

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Re: [PyMOL] Label on top of molecules?

[Jason Vertrees]

Hi Boris,

Takanori had some good ideas to try. I just wanted to let you know
that you uncovered some bugs that we've taken note of and will fix in
both on-screen rendering and in ray traced mode.

Cheers,

-- Jason

On Wed, Oct 17, 2012 at 7:47 AM, Boris Kheyfets kheyfbo...@gmail.com wrote:
 Hello PyMOL users,

 When I print atom names with

 label all, name

 the labels are often behind the spheres (I use balls and sticks
 representation).

 I tried moving labels around, but my system is very dence -- and labels
 generally get under one or another sphere.

 Is there a way I can print labels on top of everything?

 With great respect,
 Boris.

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Re: [PyMOL] Label entire movie

[Rasbach, Anke]

Hi Thomas,

thank you very much! This is exactly what I was looking for. Is it also 
possible to change font and box color?

Cheers,
Anke



-Ursprüngliche Nachricht-
Von: Thomas Holder [mailto:ad...@thomas-holder.de] Im Auftrag von Thomas Holder
Gesendet: Freitag, 21. September 2012 20:49
An: Rasbach, Anke
Cc: pymol-users@lists.sourceforge.net
Betreff: Re: [PyMOL] Label entire movie

Hi Anke,

you can use the message wizard to place a text box to the upper left corner 
of the viewport.

PyMOL wizard message, Some free text

Cheers,
   Thomas

Rasbach, Anke wrote, On 09/21/12 13:35:
 Hi everyone,
 
 we have generated a quite complex pymol movie and would like to 
 include a label that is always located in the lower right corner 
 throughout the entire movie. We have already labeled a pseudoatom 
 positioned at the lower right corner but due to camera motions the 
 text is flying around as well. Is there the possibility of adding a 
 global text box not specified to a x,y,z position? Or an easy way to 
 move the pseudoatom accordingly?
 
 Thanks
 
 Anke

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Re: [PyMOL] Label entire movie

[Thomas Holder]

Hi Anke,

Rasbach, Anke wrote, On 09/24/12 13:08:
 [...] Is it also possible to change font and box color?

no, that's not possible. The colors are hard-coded.

Cheers,
   Thomas

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Re: [PyMOL] Label entire movie

[Jason Vertrees]

Hi Thomas,

On Mon, Sep 24, 2012 at 11:11 AM, Thomas Holder
spel...@users.sourceforge.net wrote:

 [...] Is it also possible to change font and box color?

 no, that's not possible. The colors are hard-coded.


That's not quite right. You can change the text color with some
trickery. The syntax to change the text color is:
\RGB
where R, G, B are red, green, and blue intensities from 0-9,
respectively. So, to make a red colored message just type,

wizard message, \900This is a red message.

You can change color more than once,

wizard message, \900This \550is a \255multicolor \059message.

Cheers,

-- Jason

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[PyMOL] Label entire movie

[Rasbach, Anke]

Hi everyone,

we have generated a quite complex pymol movie and would like to include a label 
that is always located in the lower right corner throughout the entire movie. 
We have already labeled a pseudoatom positioned at the lower right corner but 
due to camera motions the text is flying around as well. Is there the 
possibility of adding a global text box not specified to a x,y,z position? Or 
an easy way to move the pseudoatom accordingly?

Thanks
Anke
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Re: [PyMOL] Label entire movie

[Thomas Holder]

Hi Anke,

you can use the message wizard to place a text box to the upper left 
corner of the viewport.

PyMOL wizard message, Some free text

Cheers,
   Thomas

Rasbach, Anke wrote, On 09/21/12 13:35:
 Hi everyone,
 
 we have generated a quite complex pymol movie and would like to include 
 a label that is always located in the lower right corner throughout the 
 entire movie. We have already labeled a pseudoatom positioned at the 
 lower right corner but due to camera motions the text is flying around 
 as well. Is there the possibility of adding a global text box not 
 specified to a x,y,z position? Or an easy way to move the pseudoatom 
 accordingly? 
 
 Thanks
 
 Anke

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Re: [PyMOL] Label using API

[Thomas Holder]

Hi Ritu,

when using the API, you need to quote the text label twice:

cmd.label(chain d and name C1, 'whatever')

It's a string in a string :)

Cheers,
   Thomas

Rituparna Sengupta wrote, On 05/30/12 22:42:
 Hi,
 
 Can anyone tell me how to label something using the API. I'm having
 trouble with it and the API usage is not listed in PyMol wiki.
 I use
 
 label chain d, whatever
 
 from the command line and it works fine. But I want to use it in a
 script. I tried using
 
 cmd.label(chain d, whatever)
 
 but it generates an error; name 'whatever' not defined. Does anyone
 know what I should do? The command I want to use is
 
 label chain d and name C1, whatever
 
 what is the equivalent of this in API?
 
 Thanks,
 Ritu

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[PyMOL] Label using API

[Rituparna Sengupta]

Hi,

Can anyone tell me how to label something using the API. I'm having trouble 
with it and the API usage is not listed in PyMol wiki.
I use


label chain d, whatever


from the command line and it works fine. But I want to use it in a script. I 
tried using


cmd.label(chain d, whatever)


but it generates an error; name 'whatever' not defined. Does anyone know what I 
should do? The command I want to use is


label chain d and name C1, whatever


what is the equivalent of this in API?


Thanks,
Ritu

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[PyMOL] label position

[Christian Roth]

Dear all,

I want label a few distances independently with my own labels. I set a label 
in the form 
label  /wt//A/THR`254/CA, 10.0+ u\u00c5.encode('utf-8')
which I can move independently using the set label positio command.
If I incorporate a second label and try to change the position with the set 
label command both labels ar affected.
With mouse clicks one could independently move every label. So I guess somehow 
this must be possible using a script. So far I could not find something useful 
for me in the Wiki. 
Could anyone help me out here with the correct command or syntax for such 
positionings.

Thank you very much in advance 

Best Regards

Christian

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Re: [PyMOL] label position

[Jason Vertrees]

Christian,

 I want label a few distances independently with my own labels. I set a label
 in the form
 label  /wt//A/THR`254/CA, 10.0+ u\u00c5.encode('utf-8')
 which I can move independently using the set label positio command.
 If I incorporate a second label and try to change the position with the set
 label command both labels ar affected.
 With mouse clicks one could independently move every label. So I guess somehow
 this must be possible using a script. So far I could not find something useful
 for me in the Wiki.
 Could anyone help me out here with the correct command or syntax for such
 positionings.

Currently this it is only possible using the mouse. Please file and
RFE (http://sourceforge.net/tracker/?group_id=4546atid=354546) and
we'll get to it. Labels should be capable of being programmatically
repositioned. Here's how I see it happening:

# for the selected atom(s) set their label offsets:

set label_position, [ -0.5, 1.2, -0.5 ], (sele)


Cheers,

-- Jason

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Re: [PyMOL] Label N-Glycosilation with Pymol

[Jovine Luca]

On Jul 19, 2010, at 12:29 PM, José Ignacio Sánchez Gallego wrote:

 Hi everybody, 
 I have to make a 3D structure of my protein, I mutated some aminoacids in 
 order to add some N-linked glycans, does anyone know is it possible to show 
 the glycosilation on the surface of the 3D structure?? It would be a nice 
 picture.
 Thanks in advance,
 Greetings

Hi José,

You can use GlyProt to *model* your glycan chains:

http://www.glycosciences.de/modeling/glyprot/php/main.php

HTH,

Luca


Luca Jovine, Ph.D.
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Karolinska Institutet
Department of Biosciences and Nutrition  Center for Biosciences
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Re: [PyMOL] label bond type and molecule name

[Jason Vertrees]

Sebastian,

Here's some help on labeling:

# label all atoms with the object name (file name minus extension)
label *, model

# label by residue name
label *, resn

Your command,

label C10, resn

was a good guess, but that asks PyMOL to label the atoms in the
object called 'C10' by their residue name.  What you want is, label
residue 10's carbon atom with the name of the residue which would be
slightly different syntax:

# label residue 10's carbon atom with the residue name
label 10/C, resn

I suggest you check out the label command and syntax on the PyMOLWiki
(http://pymolwiki.org/index.php/Label) and the concomitant Labeling
category (http://pymolwiki.org/index.php/Category:Labeling).  Also
type help label into PyMOL.

In a multi-mol2 file theres the object name (determined from the file)
and the molecule name determined from the title field in the mol2
file.  Each object is loaded into a new state.  Try hitting pink
forward button in the lower right hand corner of PyMOL to switch to
the 2nd conformation.  If you want each molecule in its own object
instead of its own state load the file with:

load example.mol2, multiplex=1

Now the label command will work as expected:

label *, model

Cheers,

-- Jason


2010/6/4 Sebastian Kruggel krug...@chemie.uni-hamburg.de:
 hi,

 thanks for the answers jason and michael.

   set valence

 is what i was actually looking for. as i forgot to attach my example last
 time, my second question wasn't quite clear i guess: the filename which i
 used to load my molecules (all included in one mol2 file) is not the one of
 the different molecules - and this name, which is ATU_flexx_047/8_sis in the
 attached example, i want to display because it would be useful to see it
 cycling over the molecules in the different frames.

 i tried eg

   label C10, resn

 to put the name of each molecule on the C3 (i guess it will be no problem to
 place the label elsewhere) but i only get the beginning of the name (ATU_f)
 - which isn't very useful, because it is the same in all the different
 molecules...

 is 'resn' the right idea or do anybody have another idea how i can get the
 full name?
 thanks in advance,

 sebastian


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[PyMOL] label bond type and molecule name

[Sebastian Kruggel]

dear all,

i am quite new to pymol and even if i looked up the 
documentation i still have two -probably *very* stupid- 
questions:

i can't find a way to label the bond type (single, double, 
triple, aromatic) in a multimol2, i didn't even find a way 
to select bonds at all... also i don't manage to label the 
molecule by name (in these case ATU_flexx_047/8_sis).

would be great to get a hint,
thanks in advance,

sebastian


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Re: [PyMOL] label

[Jason Vertrees]

Gauri,

Are you looking for a script that will locate contiguous stretches of
a alpha-helical residues and then label one of the atoms in that helix
with the helix's ordinal number?  If so, nothing like this exists yet,
but it would be a cool little script to write.

Cheers,

-- Jason

On Thu, May 6, 2010 at 11:53 PM, gauri misra kamga...@gmail.com wrote:

 Dear All,
 Is there an option to label the alpha helices in a sequential manner, domain
 wise in a pdb file using pymol?
 Thanks

 Cheers
 Gauri
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[PyMOL] label

[gauri misra]

Dear All,
Is there an option to label the alpha helices in a sequential manner, domain
wise in a pdb file using pymol?
Thanks

Cheers
Gauri
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Re: [PyMOL] Label size in different scenes

[Jason Vertrees]

Vitaly,

What you want is the mdo command.  Check it out:
http://www.pymolwiki.org/index.php/Mdo.

We are planning to add features like frame-based settings in a future release.

Cheers,

-- Jason

On Tue, Apr 20, 2010 at 1:09 AM, Vitaly Vostrikov vvos...@uark.edu wrote:
 After playing around for several days, I have a related question about 
 settings and selections.

 I have a surface representation of a protein: whole structure in scene 1 and 
 a zoomed segment in scene 2. I would like to decrease the quality for the 
 first scene, but boost it up for the second one. I have tried scripting this 
 with set surface_quality, 0, all in the first scene and set 
 surface_quality, 1, all in the second one, but this does not seem to work: 
 when the script is executed, the latter setting takes effect.

 So, I guess my question is, is it possible to store the quality settings in a 
 Pymol scene?

 Thank you.

 Vitaly

 - Original Message -
 From: Jason Vertrees jason.vertr...@schrodinger.com
 Date: Tuesday, April 13, 2010 4:47 pm
 Subject: Re: [PyMOL] Label size in different scenes
 To: Vitaly Vostrikov vvos...@uark.edu
 Cc: pymol-users@lists.sourceforge.net

 Vitaly,

 Great, glad to hear it.  Most PyMOL settings now work on a per
 object basis.  For example,

  set color, red, objectName

  set sphere_scale, 0.71, solvent

  set state, 4, objectName

 Cheers,

 -- Jason

 On Tue, Apr 13, 2010 at 4:00 PM, Vitaly Vostrikov
 vvos...@uark.edu wrote:
  Jason,
 
  Thank you very much - it worked perfectly! I did not realize it
 is possible to apply that for individual objects.
 
  Vitaly
 
 
  - Original Message -
  From: Jason Vertrees jason.vertr...@schrodinger.com
  Date: Tuesday, April 13, 2010 1:58 pm
  Subject: Re: [PyMOL] Label size in different scenes
  To: Vitaly Vostrikov vvos...@uark.edu
  Cc: pymol-users@lists.sourceforge.net
 
  Vitaly,
 
  You can set label_size per object:
 
  set label_size, -0.35, pseudo1
  set label_size, -0.50, pseudo2
 
  I recently ran into similar issues.  My solution was to make use of
  the mdo command.  Try help mdo and check out the PyMOLWiki page
  http://www.pymolwiki.org/index.php/Mdo.
 
  Cheers,
 
  -- Jason
 
  On Tue, Apr 13, 2010 at 12:42 PM, Vitaly Vostrikov
  vvos...@uark.edu wrote:
   Hello,
  
   I am learning movie-making in Pymol, and I have a question about
  label size.
  
   I have a script with one state and several scenes, and I would
  like to introduce titles for each scene. I create pseudoatoms for
  each scene and label them, but because of the different length of
  text, I would like to have different font size. I thought I could
  do this just by moving pseudoatom further away, but the font size
  in the labels seems to be the final size that you see on the
  screen, no matter where a pseudoatom is located. Also, if I
  understand correctly, it is not possible to use the set
  label_size command for every scene, as the latest executed one
  will override the previous ones.
  
   Is there a workaround for this one?
  
   Thank you,
   Vitaly
  
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 Schrodinger, LLC

 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120





-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
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Re: [PyMOL] Label size in different scenes

[Vitaly Vostrikov]

Thank you, Jason.

I guess I need to dig in the mailing list archive to find a bit more 
information on the usage of mdo, since at this time I am rather confused at 
the proper application of mview and mdo for the scene transitions (aka 
movies).

Vitaly

- Original Message -
From: Jason Vertrees jason.vertr...@schrodinger.com
Date: Tuesday, April 20, 2010 9:57 am
Subject: Re: [PyMOL] Label size in different scenes
To: Vitaly Vostrikov vvos...@uark.edu
Cc: pymol-users@lists.sourceforge.net

 Vitaly,
 
 What you want is the mdo command.  Check it out:
 http://www.pymolwiki.org/index.php/Mdo.
 
 We are planning to add features like frame-based settings in a 
 future release.
 
 Cheers,
 
 -- Jason
 
 On Tue, Apr 20, 2010 at 1:09 AM, Vitaly Vostrikov 
 vvos...@uark.edu wrote:
  After playing around for several days, I have a related question 
 about settings and selections.
 
  I have a surface representation of a protein: whole structure in 
 scene 1 and a zoomed segment in scene 2. I would like to decrease 
 the quality for the first scene, but boost it up for the second 
 one. I have tried scripting this with set surface_quality, 0, all 
 in the first scene and set surface_quality, 1, all in the second 
 one, but this does not seem to work: when the script is executed, 
 the latter setting takes effect.
 
  So, I guess my question is, is it possible to store the quality 
 settings in a Pymol scene?
 
  Thank you.
 
  Vitaly
 
  - Original Message -
  From: Jason Vertrees jason.vertr...@schrodinger.com
  Date: Tuesday, April 13, 2010 4:47 pm
  Subject: Re: [PyMOL] Label size in different scenes
  To: Vitaly Vostrikov vvos...@uark.edu
  Cc: pymol-users@lists.sourceforge.net
 
  Vitaly,
 
  Great, glad to hear it.  Most PyMOL settings now work on a per
  object basis.  For example,
 
   set color, red, objectName
 
   set sphere_scale, 0.71, solvent
 
   set state, 4, objectName
 
  Cheers,
 
  -- Jason
 
  On Tue, Apr 13, 2010 at 4:00 PM, Vitaly Vostrikov
  vvos...@uark.edu wrote:
   Jason,
  
   Thank you very much - it worked perfectly! I did not realize it
  is possible to apply that for individual objects.
  
   Vitaly
  
  
   - Original Message -
   From: Jason Vertrees jason.vertr...@schrodinger.com
   Date: Tuesday, April 13, 2010 1:58 pm
   Subject: Re: [PyMOL] Label size in different scenes
   To: Vitaly Vostrikov vvos...@uark.edu
   Cc: pymol-users@lists.sourceforge.net
  
   Vitaly,
  
   You can set label_size per object:
  
   set label_size, -0.35, pseudo1
   set label_size, -0.50, pseudo2
  
   I recently ran into similar issues.  My solution was to make 
 use of
   the mdo command.  Try help mdo and check out the PyMOLWiki 
 page  http://www.pymolwiki.org/index.php/Mdo.
  
   Cheers,
  
   -- Jason
  
   On Tue, Apr 13, 2010 at 12:42 PM, Vitaly Vostrikov
   vvos...@uark.edu wrote:
Hello,
   
I am learning movie-making in Pymol, and I have a question 
 about  label size.
   
I have a script with one state and several scenes, and I would
   like to introduce titles for each scene. I create pseudoatoms 
 for  each scene and label them, but because of the different 
 length of
   text, I would like to have different font size. I thought I 
 could  do this just by moving pseudoatom further away, but the 
 font size
   in the labels seems to be the final size that you see on the
   screen, no matter where a pseudoatom is located. Also, if I
   understand correctly, it is not possible to use the set
   label_size command for every scene, as the latest executed one
   will override the previous ones.
   
Is there a workaround for this one?
   
Thank you,
Vitaly
   

 ---
  ---
   
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find
  bugs  proactively, and fine-tune applications for parallel
  performance.  See why Intel Parallel Studio got high marks
  during beta.
http://p.sf.net/sfu/intel-sw-dev
___
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Info Page: 
 https://lists.sourceforge.net/lists/listinfo/pymol-
  users  Archives: http://www.mail-archive.com/pymol-
   us...@lists.sourceforge.net
  
  
  
   --
   Jason Vertrees, PhD
   PyMOL Product Manager
   Schrodinger, LLC
  
   (e) jason.vertr...@schrodinger.com
   (o) +1 (603) 374-7120
  
  
 
 
 
  --
  Jason Vertrees, PhD
  PyMOL Product Manager
  Schrodinger, LLC
 
  (e) jason.vertr...@schrodinger.com
  (o) +1 (603) 374-7120
 
 
 
 
 
 -- 
 Jason Vertrees, PhD
 PyMOL Product Manager
 Schrodinger, LLC
 
 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120
 

--
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Re: [PyMOL] Label size in different scenes

[Jason Vertrees]

Vitaly,

mview just handles the position of the camera and clipping planes.

mdo repeats given command(s) before the rendering of a given frame.

The PyMOLWiki, the list archives and Google should offer more help.

-- Jason

On 4/20/10, Vitaly Vostrikov vvos...@uark.edu wrote:
 Thank you, Jason.

 I guess I need to dig in the mailing list archive to find a bit more
 information on the usage of mdo, since at this time I am rather confused
 at the proper application of mview and mdo for the scene transitions
 (aka movies).

 Vitaly

 - Original Message -
 From: Jason Vertrees jason.vertr...@schrodinger.com
 Date: Tuesday, April 20, 2010 9:57 am
 Subject: Re: [PyMOL] Label size in different scenes
 To: Vitaly Vostrikov vvos...@uark.edu
 Cc: pymol-users@lists.sourceforge.net

 Vitaly,

 What you want is the mdo command.  Check it out:
 http://www.pymolwiki.org/index.php/Mdo.

 We are planning to add features like frame-based settings in a
 future release.

 Cheers,

 -- Jason

 On Tue, Apr 20, 2010 at 1:09 AM, Vitaly Vostrikov
 vvos...@uark.edu wrote:
  After playing around for several days, I have a related question
 about settings and selections.
 
  I have a surface representation of a protein: whole structure in
 scene 1 and a zoomed segment in scene 2. I would like to decrease
 the quality for the first scene, but boost it up for the second
 one. I have tried scripting this with set surface_quality, 0, all
 in the first scene and set surface_quality, 1, all in the second
 one, but this does not seem to work: when the script is executed,
 the latter setting takes effect.
 
  So, I guess my question is, is it possible to store the quality
 settings in a Pymol scene?
 
  Thank you.
 
  Vitaly
 
  - Original Message -
  From: Jason Vertrees jason.vertr...@schrodinger.com
  Date: Tuesday, April 13, 2010 4:47 pm
  Subject: Re: [PyMOL] Label size in different scenes
  To: Vitaly Vostrikov vvos...@uark.edu
  Cc: pymol-users@lists.sourceforge.net
 
  Vitaly,
 
  Great, glad to hear it.  Most PyMOL settings now work on a per
  object basis.  For example,
 
   set color, red, objectName
 
   set sphere_scale, 0.71, solvent
 
   set state, 4, objectName
 
  Cheers,
 
  -- Jason
 
  On Tue, Apr 13, 2010 at 4:00 PM, Vitaly Vostrikov
  vvos...@uark.edu wrote:
   Jason,
  
   Thank you very much - it worked perfectly! I did not realize it
  is possible to apply that for individual objects.
  
   Vitaly
  
  
   - Original Message -
   From: Jason Vertrees jason.vertr...@schrodinger.com
   Date: Tuesday, April 13, 2010 1:58 pm
   Subject: Re: [PyMOL] Label size in different scenes
   To: Vitaly Vostrikov vvos...@uark.edu
   Cc: pymol-users@lists.sourceforge.net
  
   Vitaly,
  
   You can set label_size per object:
  
   set label_size, -0.35, pseudo1
   set label_size, -0.50, pseudo2
  
   I recently ran into similar issues.  My solution was to make
 use of
   the mdo command.  Try help mdo and check out the PyMOLWiki
 page  http://www.pymolwiki.org/index.php/Mdo.
  
   Cheers,
  
   -- Jason
  
   On Tue, Apr 13, 2010 at 12:42 PM, Vitaly Vostrikov
   vvos...@uark.edu wrote:
Hello,
   
I am learning movie-making in Pymol, and I have a question
 about  label size.
   
I have a script with one state and several scenes, and I would
   like to introduce titles for each scene. I create pseudoatoms
 for  each scene and label them, but because of the different
 length of
   text, I would like to have different font size. I thought I
 could  do this just by moving pseudoatom further away, but the
 font size
   in the labels seems to be the final size that you see on the
   screen, no matter where a pseudoatom is located. Also, if I
   understand correctly, it is not possible to use the set
   label_size command for every scene, as the latest executed one
   will override the previous ones.
   
Is there a workaround for this one?
   
Thank you,
Vitaly
   

 ---
  ---
   
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find
  bugs  proactively, and fine-tune applications for parallel
  performance.  See why Intel Parallel Studio got high marks
  during beta.
http://p.sf.net/sfu/intel-sw-dev
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page:
 https://lists.sourceforge.net/lists/listinfo/pymol-
  users  Archives: http://www.mail-archive.com/pymol-
   us...@lists.sourceforge.net
  
  
  
   --
   Jason Vertrees, PhD
   PyMOL Product Manager
   Schrodinger, LLC
  
   (e) jason.vertr...@schrodinger.com
   (o) +1 (603) 374-7120
  
  
 
 
 
  --
  Jason Vertrees, PhD
  PyMOL Product Manager
  Schrodinger, LLC
 
  (e) jason.vertr...@schrodinger.com
  (o) +1 (603) 374-7120
 
 



 --
 Jason Vertrees, PhD
 PyMOL Product Manager
 Schrodinger, LLC

 (e) jason.vertr

Re: [PyMOL] Label size in different scenes

[Vitaly Vostrikov]

After playing around for several days, I have a related question about settings 
and selections.

I have a surface representation of a protein: whole structure in scene 1 and a 
zoomed segment in scene 2. I would like to decrease the quality for the first 
scene, but boost it up for the second one. I have tried scripting this with 
set surface_quality, 0, all in the first scene and set surface_quality, 1, 
all in the second one, but this does not seem to work: when the script is 
executed, the latter setting takes effect.

So, I guess my question is, is it possible to store the quality settings in a 
Pymol scene?

Thank you.

Vitaly

- Original Message -
From: Jason Vertrees jason.vertr...@schrodinger.com
Date: Tuesday, April 13, 2010 4:47 pm
Subject: Re: [PyMOL] Label size in different scenes
To: Vitaly Vostrikov vvos...@uark.edu
Cc: pymol-users@lists.sourceforge.net

 Vitaly,
 
 Great, glad to hear it.  Most PyMOL settings now work on a per
 object basis.  For example,
 
  set color, red, objectName
 
  set sphere_scale, 0.71, solvent
 
  set state, 4, objectName
 
 Cheers,
 
 -- Jason
 
 On Tue, Apr 13, 2010 at 4:00 PM, Vitaly Vostrikov 
 vvos...@uark.edu wrote:
  Jason,
 
  Thank you very much - it worked perfectly! I did not realize it 
 is possible to apply that for individual objects.
 
  Vitaly
 
 
  - Original Message -
  From: Jason Vertrees jason.vertr...@schrodinger.com
  Date: Tuesday, April 13, 2010 1:58 pm
  Subject: Re: [PyMOL] Label size in different scenes
  To: Vitaly Vostrikov vvos...@uark.edu
  Cc: pymol-users@lists.sourceforge.net
 
  Vitaly,
 
  You can set label_size per object:
 
  set label_size, -0.35, pseudo1
  set label_size, -0.50, pseudo2
 
  I recently ran into similar issues.  My solution was to make use of
  the mdo command.  Try help mdo and check out the PyMOLWiki page
  http://www.pymolwiki.org/index.php/Mdo.
 
  Cheers,
 
  -- Jason
 
  On Tue, Apr 13, 2010 at 12:42 PM, Vitaly Vostrikov
  vvos...@uark.edu wrote:
   Hello,
  
   I am learning movie-making in Pymol, and I have a question about
  label size.
  
   I have a script with one state and several scenes, and I would
  like to introduce titles for each scene. I create pseudoatoms for
  each scene and label them, but because of the different length of
  text, I would like to have different font size. I thought I could
  do this just by moving pseudoatom further away, but the font size
  in the labels seems to be the final size that you see on the
  screen, no matter where a pseudoatom is located. Also, if I
  understand correctly, it is not possible to use the set
  label_size command for every scene, as the latest executed one
  will override the previous ones.
  
   Is there a workaround for this one?
  
   Thank you,
   Vitaly
  
   ---
 ---
  
   Download Intel#174; Parallel Studio Eval
   Try the new software tools for yourself. Speed compiling, find 
 bugs  proactively, and fine-tune applications for parallel 
 performance.  See why Intel Parallel Studio got high marks 
 during beta.
   http://p.sf.net/sfu/intel-sw-dev
   ___
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   Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-
 users  Archives: http://www.mail-archive.com/pymol-
  us...@lists.sourceforge.net
 
 
 
  --
  Jason Vertrees, PhD
  PyMOL Product Manager
  Schrodinger, LLC
 
  (e) jason.vertr...@schrodinger.com
  (o) +1 (603) 374-7120
 
 
 
 
 
 -- 
 Jason Vertrees, PhD
 PyMOL Product Manager
 Schrodinger, LLC
 
 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120
 

--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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[PyMOL] Label size in different scenes

[Vitaly Vostrikov]

Hello,

I am learning movie-making in Pymol, and I have a question about label size.

I have a script with one state and several scenes, and I would like to 
introduce titles for each scene. I create pseudoatoms for each scene and label 
them, but because of the different length of text, I would like to have 
different font size. I thought I could do this just by moving pseudoatom 
further away, but the font size in the labels seems to be the final size that 
you see on the screen, no matter where a pseudoatom is located. Also, if I 
understand correctly, it is not possible to use the set label_size command 
for every scene, as the latest executed one will override the previous ones.

Is there a workaround for this one?

Thank you,
Vitaly

--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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Re: [PyMOL] Label size in different scenes

[Jason Vertrees]

Vitaly,

You can set label_size per object:

set label_size, -0.35, pseudo1
set label_size, -0.50, pseudo2

I recently ran into similar issues.  My solution was to make use of
the mdo command.  Try help mdo and check out the PyMOLWiki page
http://www.pymolwiki.org/index.php/Mdo.

Cheers,

-- Jason

On Tue, Apr 13, 2010 at 12:42 PM, Vitaly Vostrikov vvos...@uark.edu wrote:
 Hello,

 I am learning movie-making in Pymol, and I have a question about label size.

 I have a script with one state and several scenes, and I would like to 
 introduce titles for each scene. I create pseudoatoms for each scene and 
 label them, but because of the different length of text, I would like to have 
 different font size. I thought I could do this just by moving pseudoatom 
 further away, but the font size in the labels seems to be the final size 
 that you see on the screen, no matter where a pseudoatom is located. Also, if 
 I understand correctly, it is not possible to use the set label_size 
 command for every scene, as the latest executed one will override the 
 previous ones.

 Is there a workaround for this one?

 Thank you,
 Vitaly

 --
 Download Intel#174; Parallel Studio Eval
 Try the new software tools for yourself. Speed compiling, find bugs
 proactively, and fine-tune applications for parallel performance.
 See why Intel Parallel Studio got high marks during beta.
 http://p.sf.net/sfu/intel-sw-dev
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net




-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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Re: [PyMOL] Label size in different scenes

[Vitaly Vostrikov]

Jason,

Thank you very much - it worked perfectly! I did not realize it is possible to 
apply that for individual objects.

Vitaly


- Original Message -
From: Jason Vertrees jason.vertr...@schrodinger.com
Date: Tuesday, April 13, 2010 1:58 pm
Subject: Re: [PyMOL] Label size in different scenes
To: Vitaly Vostrikov vvos...@uark.edu
Cc: pymol-users@lists.sourceforge.net

 Vitaly,
 
 You can set label_size per object:
 
 set label_size, -0.35, pseudo1
 set label_size, -0.50, pseudo2
 
 I recently ran into similar issues.  My solution was to make use of
 the mdo command.  Try help mdo and check out the PyMOLWiki page
 http://www.pymolwiki.org/index.php/Mdo.
 
 Cheers,
 
 -- Jason
 
 On Tue, Apr 13, 2010 at 12:42 PM, Vitaly Vostrikov 
 vvos...@uark.edu wrote:
  Hello,
 
  I am learning movie-making in Pymol, and I have a question about 
 label size.
 
  I have a script with one state and several scenes, and I would 
 like to introduce titles for each scene. I create pseudoatoms for 
 each scene and label them, but because of the different length of 
 text, I would like to have different font size. I thought I could 
 do this just by moving pseudoatom further away, but the font size 
 in the labels seems to be the final size that you see on the 
 screen, no matter where a pseudoatom is located. Also, if I 
 understand correctly, it is not possible to use the set 
 label_size command for every scene, as the latest executed one 
 will override the previous ones.
 
  Is there a workaround for this one?
 
  Thank you,
  Vitaly
 
  --
 
  Download Intel#174; Parallel Studio Eval
  Try the new software tools for yourself. Speed compiling, find bugs
  proactively, and fine-tune applications for parallel performance.
  See why Intel Parallel Studio got high marks during beta.
  http://p.sf.net/sfu/intel-sw-dev
  ___
  PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
  Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
  Archives: http://www.mail-archive.com/pymol-
 us...@lists.sourceforge.net
 
 
 
 -- 
 Jason Vertrees, PhD
 PyMOL Product Manager
 Schrodinger, LLC
 
 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120
 

--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Label size in different scenes

[Jason Vertrees]

Vitaly,

Great, glad to hear it.  Most PyMOL settings now work on a per
object basis.  For example,

  set color, red, objectName

  set sphere_scale, 0.71, solvent

  set state, 4, objectName

Cheers,

-- Jason

On Tue, Apr 13, 2010 at 4:00 PM, Vitaly Vostrikov vvos...@uark.edu wrote:
 Jason,

 Thank you very much - it worked perfectly! I did not realize it is possible 
 to apply that for individual objects.

 Vitaly


 - Original Message -
 From: Jason Vertrees jason.vertr...@schrodinger.com
 Date: Tuesday, April 13, 2010 1:58 pm
 Subject: Re: [PyMOL] Label size in different scenes
 To: Vitaly Vostrikov vvos...@uark.edu
 Cc: pymol-users@lists.sourceforge.net

 Vitaly,

 You can set label_size per object:

 set label_size, -0.35, pseudo1
 set label_size, -0.50, pseudo2

 I recently ran into similar issues.  My solution was to make use of
 the mdo command.  Try help mdo and check out the PyMOLWiki page
 http://www.pymolwiki.org/index.php/Mdo.

 Cheers,

 -- Jason

 On Tue, Apr 13, 2010 at 12:42 PM, Vitaly Vostrikov
 vvos...@uark.edu wrote:
  Hello,
 
  I am learning movie-making in Pymol, and I have a question about
 label size.
 
  I have a script with one state and several scenes, and I would
 like to introduce titles for each scene. I create pseudoatoms for
 each scene and label them, but because of the different length of
 text, I would like to have different font size. I thought I could
 do this just by moving pseudoatom further away, but the font size
 in the labels seems to be the final size that you see on the
 screen, no matter where a pseudoatom is located. Also, if I
 understand correctly, it is not possible to use the set
 label_size command for every scene, as the latest executed one
 will override the previous ones.
 
  Is there a workaround for this one?
 
  Thank you,
  Vitaly
 
  --
 
  Download Intel#174; Parallel Studio Eval
  Try the new software tools for yourself. Speed compiling, find bugs
  proactively, and fine-tune applications for parallel performance.
  See why Intel Parallel Studio got high marks during beta.
  http://p.sf.net/sfu/intel-sw-dev
  ___
  PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
  Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
  Archives: http://www.mail-archive.com/pymol-
 us...@lists.sourceforge.net



 --
 Jason Vertrees, PhD
 PyMOL Product Manager
 Schrodinger, LLC

 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120





-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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[PyMOL] label a stereo .png image in pymol

[peter hudson]

Hello all

I have made  a stereo image in pymol and photoadobeshop. But, i would like
to label the image file which should like a stereo image label. how that can
be done in the pymol. I can do it in photoadobeshop .problem lies her that i
am not sure is the labels are really stereo or not?

can anyone suggest solutions. I would appreciate that.


Thanks in advance

peter
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Re: [PyMOL] label a stereo .png image in pymol

[Schubert, Carsten [PRDUS]]

Peter, 

 

here are some general considerations for stereo images

 

A.  The images should be ~63mm apart with respect to a point which you 
consider to be neutral, i.e. neither lies in front or in the back of the 
zero-plane

B.  The distance of the images also put restrictions on their size, which 
is something you need to consider. Usually it is 1 ½ columns in a journal, if I 
am not mistaken.

C.  For labels I use a program like photoshop or canvas, just because one 
has a wider selection of fonts and they produce antialiased renderings. I 
usually attach labels to landmarks, with which they share the same depth. For 
example if you want to label residue 234 and have the residue drawn in stick, 
you could place both upper left corners of the labels on the CA position, group 
them and move them out of the way so as they do not interfere with the rest of 
the graphic. Using this trick ensures that the labels appear in the correct 
depth.

 

HTH

 

Carsten

 

From: peter hudson [mailto:peter.hudson.pe...@gmail.com] 
Sent: Monday, September 07, 2009 12:30 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] label a stereo .png image in pymol

 

Hello all

I have made  a stereo image in pymol and photoadobeshop. But, i would like to 
label the image file which should like a stereo image label. how that can be 
done in the pymol. I can do it in photoadobeshop .problem lies her that i am 
not sure is the labels are really stereo or not?

can anyone suggest solutions. I would appreciate that.


Thanks in advance 

peter

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Re: [PyMOL] Label coordinates

[Folmer Fredslund]

Dear Warran,

Thanks for the swift reply.

In the meantime I will workaround it by creating a new molecule with
the labeled atoms and move the atoms. This works more or less the way
I entended.


Best regards,
Folmer



2009/7/9 Warren DeLano war...@delsci.com:
 Folmer,

 Sorry no, this is still a to do item.

 Cheers,
 Warren

 -Original Message-
 From: Folmer Fredslund [mailto:folm...@gmail.com]
 Sent: Thursday, July 09, 2009 6:33 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Label coordinates

 Dear all,

 Is there a way to get the coordinates for manually shifted labels?
 What I want to do is to include the label positions in my script
 instead of moving the labels each time I update my figure.

 Thanks in advance,

 Folmer Fredslund


 
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[PyMOL] Label coordinates

[Folmer Fredslund]

Dear all,

Is there a way to get the coordinates for manually shifted labels?
What I want to do is to include the label positions in my script
instead of moving the labels each time I update my figure.

Thanks in advance,

Folmer Fredslund

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[PyMOL] label transparency

[Neil Ranson]

Dear All,
Does anyone now if it's possible to alter the transparency level of a  
label?
I have an object that is scripted to fade in and out, and I would like  
to bring the labels in and out at the same speed, but can't seem to  
find a setting that works.


Thanks in advance,
Neil.


Neil Ranson PhD
Level 2 Biochemistry Tutor
University Research Fellow
Astbury Centre for Structural Molecular Biology
IMCB
University of Leeds, Leeds, LS2 9JT, UK.

EM Image Processing Suite - Miall 6.02
Tel: 44 (0) 113 343 7065
email: n.a.ran...@leeds.ac.uk

Re: [PyMOL] label transparency

[Warren DeLano]

Neil,
 
Unfortunately, transparency is not supported for labels (at present).
 
Cheers,
Warren



From: Neil Ranson [mailto:n.a.ran...@leeds.ac.uk] 
Sent: Tuesday, March 10, 2009 8:31 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] label transparency


Dear All, 
Does anyone now if it's possible to alter the transparency level
of a label?
I have an object that is scripted to fade in and out, and I
would like to bring the labels in and out at the same speed, but can't
seem to find a setting that works.

Thanks in advance,
Neil.





Neil Ranson PhD
Level 2 Biochemistry Tutor
University Research Fellow
Astbury Centre for Structural Molecular Biology
IMCB
University of Leeds, Leeds, LS2 9JT, UK.

EM Image Processing Suite - Miall 6.02
Tel: 44 (0) 113 343 7065
email: n.a.ran...@leeds.ac.uk

Re: [PyMOL] label with arbitrary string

[Chavas Leo]

Dear Tsjerk, Marius, and all --

Thanks for your answers. Both methods worked perfectly. I personally  
like the one from Tsjerk, as I can play a little bit more with the font.


Kind regards.

-- Leo --

Chavas Leonard, Ph.D. @ home
Research Associate
Marie Curie Actions Fellow

Faculty of Life Sciences
The University of Manchester
The Michael Smith Building
Oxford Road
Manchester Lancashire
M13 9PT

Tel: +44(0)161-275-1586
e-mail: leonard.cha...@manchester.ac.uk
http://personalpages.manchester.ac.uk/staff/leonard.chavas/

Re: [PyMOL] label with arbitrary string

[Chavas Leo]

Dear all --

On 30 Jul 2008, at 01:03, DeLano Scientific wrote:

Richard,


label (residue 200 and name ca), My favorite C_alpha


The command you provided works as written, so what are you asking  
exactly?


Is is that you want us to add a GUI way of doing this?


Related to labeling, I was wondering how to insert symbol labels such  
as angstrom, or alpha etc., even the copyright symbol?
I've tried in the past, without much success. I know it will be  
easier to do it via an external program such as Gimp, but I'm asking  
in the idea to generate a line at the bottom of the picture for  
copyright purpose, when I'm generating hundreds of pictures for  
building a movie... Do I have to link the font library to the library  
I've got on my computer?


Kind regards.

-- Leo --

Chavas Leonard, Ph.D. @ home
Research Associate

Faculty of Life Sciences
The University of Manchester
The Michael Smith Building
Oxford Road
Manchester Lancashire
M13 9PT

Tel: +44(0)161-275-1586
e-mail: leonard.cha...@manchester.ac.uk
http://personalpages.manchester.ac.uk/staff/leonard.chavas/

Re: [PyMOL] label with arbitrary string

[Tsjerk Wassenaar]

Hi Leo,

AFAIK you can't do it with Pymol, as it would require additional
fonts. Also, it seems tough to me to position to label properly with
respect to the camera. But you have plenty control with
convert/imagemagick (see
http://www.imagemagick.org/Usage/annotating/). That will allow you to
process your images script-wise, I think even using whatever font you
want (although copyright 2008 or (c)2008 will probably also do ;) see
the examples).

Hope it helps,

Tsjerk

On Wed, Jul 30, 2008 at 10:27 AM, Chavas Leo pymolhnaa...@gmail.com wrote:
 Dear all --
 On 30 Jul 2008, at 01:03, DeLano Scientific wrote:

 Richard,

 label (residue 200 and name ca), My favorite C_alpha

 The command you provided works as written, so what are you asking exactly?

 Is is that you want us to add a GUI way of doing this?

 Related to labeling, I was wondering how to insert symbol labels such as
 angstrom, or alpha etc., even the copyright symbol?
 I've tried in the past, without much success. I know it will be easier to do
 it via an external program such as Gimp, but I'm asking in the idea to
 generate a line at the bottom of the picture for copyright purpose, when I'm
 generating hundreds of pictures for building a movie... Do I have to link
 the font library to the library I've got on my computer?
 Kind regards.
 -- Leo --
 
 Chavas Leonard, Ph.D. @ home
 Research Associate
 
 Faculty of Life Sciences
 The University of Manchester
 The Michael Smith Building
 Oxford Road
 Manchester Lancashire
 M13 9PT
 
 Tel: +44(0)161-275-1586
 e-mail: leonard.cha...@manchester.ac.uk
 http://personalpages.manchester.ac.uk/staff/leonard.chavas/



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-- 
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Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Re: [PyMOL] label with arbitrary string

[Marius Retegan]

Hello Leo,

You could use Unicode to get the special characters you were taking about.

angstrom = u\u00C5
angstrom_utf8 = angstrom.encode ('utf-8')
label (residue 200 and name ca), Distance: 8+angstrom_utf8

To see the label bigger use set label_size, 20
You can get the unicode charts from here http://www.unicode.org/charts


On Wed, Jul 30, 2008 at 11:18 AM, Tsjerk Wassenaar tsje...@gmail.comwrote:

 Hi Leo,

 AFAIK you can't do it with Pymol, as it would require additional
 fonts. Also, it seems tough to me to position to label properly with
 respect to the camera. But you have plenty control with
 convert/imagemagick (see
 http://www.imagemagick.org/Usage/annotating/). That will allow you to
 process your images script-wise, I think even using whatever font you
 want (although copyright 2008 or (c)2008 will probably also do ;) see
 the examples).

 Hope it helps,

 Tsjerk

 On Wed, Jul 30, 2008 at 10:27 AM, Chavas Leo pymolhnaa...@gmail.com
 wrote:
  Dear all --
  On 30 Jul 2008, at 01:03, DeLano Scientific wrote:
 
  Richard,
 
  label (residue 200 and name ca), My favorite C_alpha
 
  The command you provided works as written, so what are you asking
 exactly?
 
  Is is that you want us to add a GUI way of doing this?
 
  Related to labeling, I was wondering how to insert symbol labels such as
  angstrom, or alpha etc., even the copyright symbol?
  I've tried in the past, without much success. I know it will be easier to
 do
  it via an external program such as Gimp, but I'm asking in the idea to
  generate a line at the bottom of the picture for copyright purpose, when
 I'm
  generating hundreds of pictures for building a movie... Do I have to link
  the font library to the library I've got on my computer?
  Kind regards.
  -- Leo --
  
  Chavas Leonard, Ph.D. @ home
  Research Associate
  
  Faculty of Life Sciences
  The University of Manchester
  The Michael Smith Building
  Oxford Road
  Manchester Lancashire
  M13 9PT
  
  Tel: +44(0)161-275-1586
  e-mail: leonard.cha...@manchester.ac.uk
  http://personalpages.manchester.ac.uk/staff/leonard.chavas/
 
 
 
  -
  This SF.Net email is sponsored by the Moblin Your Move Developer's
 challenge
  Build the coolest Linux based applications with Moblin SDK  win great
  prizes
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 --
 Tsjerk A. Wassenaar, Ph.D.
 Junior UD (post-doc)
 Biomolecular NMR, Bijvoet Center
 Utrecht University
 Padualaan 8
 3584 CH Utrecht
 The Netherlands
 P: +31-30-2539931
 F: +31-30-2537623

 -
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Re: [PyMOL] label with arbitrary string

[Richard Baxter]

Dear All,

Can someone advise me how to insert a label with an arbitrary string, e.g.

label (residue 200 and name ca), My favorite C_alpha

Thanks for your help,

Richard Baxter

Re: [PyMOL] label with arbitrary string

[DeLano Scientific]

Richard,

 label (residue 200 and name ca), My favorite C_alpha

The command you provided works as written, so what are you asking exactly?  

Is is that you want us to add a GUI way of doing this?

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com


-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Richard
Baxter
Sent: Tuesday, July 29, 2008 4:31 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] label with arbitrary string

Dear All,

Can someone advise me how to insert a label with an arbitrary string, e.g.

label (residue 200 and name ca), My favorite C_alpha

Thanks for your help,

Richard Baxter

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[PyMOL] label in Greek letters

[Takatoshi Arakawa]

Hi All users,
I am a PyMOL ver.0.99rc6 (Win and Linux) user.
Now I want to label with chain ID ( A, B, G,... for alpha, beta,
gamma,...) in Greek letters.
I have tried it following
http://www.pymolwiki.org/index.php/Label#UTF8_Fonts , but the output
corresponds to \316\261 has not been printed.
Please give me some advice about this and tell me any other ways to do.

Thank you,

Arakawa

[PyMOL] label positions, centered, left, or right

[Seth Harris]

Hi all,

Minor thing, but thought I'd ask...

Labels now appear to be centered on whatever atom they are labeling.
Previously, the left-hand side of the label was on the atom (left-anchored).
Is there a way to choose whether the label is left-anchored, centered, or
right-anchored?

I find that it's hard to offset the label sufficiently with commands like:

label myprot and name ca, %s%s % (resn,resi)

which used to get the label to float nicely just to the right of the atom.
Now that the label is centered the spaces don't help push the labels over as
much as they used to, and the obvious route of adding twice as many spaces
somehow isn't getting me there. I thought there might be an anchor, align,
or justification flag on the labels.

I did also notice that in editing mode you can drag the labels to whatever
position you wanted in recent betas.  Very nice!

Cheers,
Seth

RE: [PyMOL] label positions, centered, left, or right

[Warren DeLano]

Seth,

Yes, via the label_position setting which specifies x,y, and z
alignment of labels.

Values in the range [-1,1] imply alignment.  Beyond that, it is a
translation along camera axes in model-space dimensions.  

# for left alignment 0.75 A in front of atom

set label_position, [-1,0,1.75]

# for right alignment directly on atom

set label_position, [1,0,0]

# for left alignment 1 A to right of atom

set label_position, [2,0,0]

# for center alignment 2 A below atom

set label_position, [0,-3,0]

# centered 3 A in front of atom

set label_position, [0,0,4]

etc.

Cheers,
Waren


--
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Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213   
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834 
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:war...@delsci.com  
 

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 Seth Harris
 Sent: Thursday, February 23, 2006 10:45 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] label positions, centered, left, or right
 
 Hi all,
 
 Minor thing, but thought I'd ask...
 
 Labels now appear to be centered on whatever atom they are 
 labeling. Previously, the left-hand side of the label was on 
 the atom (left-anchored). Is there a way to choose whether 
 the label is left-anchored, centered, or right-anchored? 
 
 I find that it's hard to offset the label sufficiently with 
 commands like:
 
 label myprot and name ca, %s%s % (resn,resi)
 
 which used to get the label to float nicely just to the right 
 of the atom. 
 Now that the label is centered the spaces don't help push the 
 labels over as much as they used to, and the obvious route of 
 adding twice as many spaces somehow isn't getting me there. I 
 thought there might be an anchor, align, or justification 
 flag on the labels. 
 
 I did also notice that in editing mode you can drag the 
 labels to whatever position you wanted in recent betas.  Very nice!
 
 Cheers,
 Seth
 
 

[PyMOL] label alternate conformations

[Seth Harris]

Hi,

I'm writing a small script to visit alternate conformations, stepping
through each as a frame in a movie with the cursor keys. I'd like to label
them to distinguish the alternates so I can see which I'd like to keep or
not, but:

label alternates, name

only displays the atom name without the pertinent `A or `B that the right
mouse click menu includes.

Is there a way to show this information with the label command or other
means?

Thanks,
Seth

p.s. Those extra 3D and other superfluous characters show up for me as
well receiving the pymol list as a digest on gmail based web. I don't know
if it's a result of the digestion process, but it seems like = signs and
other non-alpha characters are associated with these burps of indigestion,
invariably followed by 2D or 3D or such. I've kind of learned to ignore
them, but obviously they can cause some confusion and are at least minorly
amusing when they reappear like some who's on first miscommunication as
warren's advice mention there should be no 3D just the number 10 like
this, and then it proceeded to again display the 3D!! Perhaps the Digest is
the culprit and could be treated? It also displays HTML as full text with
tags and all that garbage, by the way.

quote:
I'm not sure where that 3D10 is coming from -- it should simply be the
number 10:

alter all, b=3D10

(!)
map_new can take a selection as its fourth argument, so you could

Re: [PyMOL] label alternate conformations

[Robert Immormino]

This series of commands seems to do the job although a little sloppy.

label alt a+, A%s-%s % (resn, resi)
label alt b+, B%s-%s % (resn, resi)
hide labels, alt 

Cheers,

-bob

On 12/7/05, Seth Harris set...@gmail.com wrote:

 Hi,

 I'm writing a small script to visit alternate conformations, stepping
 through each as a frame in a movie with the cursor keys. I'd like to label
 them to distinguish the alternates so I can see which I'd like to keep or
 not, but:

 label alternates, name

 only displays the atom name without the pertinent `A or `B that the right
 mouse click menu includes.

 Is there a way to show this information with the label command or other
 means?

 Thanks,
 Seth

 p.s. Those extra 3D and other superfluous characters show up for me as
 well receiving the pymol list as a digest on gmail based web. I don't know
 if it's a result of the digestion process, but it seems like = signs and
 other non-alpha characters are associated with these burps of indigestion,
 invariably followed by 2D or 3D or such. I've kind of learned to ignore
 them, but obviously they can cause some confusion and are at least minorly
 amusing when they reappear like some who's on first miscommunication as
 warren's advice mention there should be no 3D just the number 10 like
 this, and then it proceeded to again display the 3D!! Perhaps the Digest is
 the culprit and could be treated? It also displays HTML as full text with
 tags and all that garbage, by the way.

 quote:
 I'm not sure where that 3D10 is coming from -- it should simply be
 the
 number 10:

 alter all, b=3D10
 
 (!)
 map_new can take a selection as its fourth argument, so you could

Re: [PyMOL] label alternate conformations

[Seth Harris]

Hi Bob,
Good to hear from you.

I didn't know about alt as a selection, so in the end that gave the
answer... Your example, which I find quite clever, didn't exactly match my
goal, though, so just to clarify:  Rather than distinguishing residues with
alternate conformations from those normal ones without, I wanted to have
the labels distinguish alternate conformer A from B and so on within a given
residue. Since there was this backtick A or B at the end of the atom name in
the right-click drop down menu I expected it would be somehow accessible via
command line in the label command. But name didn't do it. But of course,
using your alt selection I could do:
label alt a, A
label alt b, B
or indeed color all B conformations pink with:
color pink, alt b

And after realizing this, I just tried:

label myprotein, alt

which by its simplicity is obviously something I might have tried earlier.
Elegantly, as most residues don't have any alt conformation, it has the
nice side effect that labels only show up for those with alternate
conformations as well!

Thanks for the tip!
Seth

(By the way, neither the pymol help nor the wiki include alt as symbols
defined in the name space which currently includes things like name, resn,
resi, b, q, segi, type, formal_charge, partial_charge, numeric_type,
text_type).  I guess that means I should learn to wiki it up.

On 12/7/05, Robert Immormino immorm...@gmail.com wrote:

 This series of commands seems to do the job although a little sloppy.

 label alt a+, A%s-%s % (resn, resi)
 label alt b+, B%s-%s % (resn, resi)
 hide labels, alt 

 Cheers,

 -bob

 On 12/7/05, Seth Harris set...@gmail.com wrote:
 
  Hi,
 
  I'm writing a small script to visit alternate conformations, stepping
  through each as a frame in a movie with the cursor keys. I'd like to label
  them to distinguish the alternates so I can see which I'd like to keep or
  not, but:
 
  label alternates, name
 
  only displays the atom name without the pertinent `A or `B that the
  right mouse click menu includes.
 
  Is there a way to show this information with the label command or other
  means?
 
  Thanks,
  Seth
 
  p.s. Those extra 3D and other superfluous characters show up for me as
  well receiving the pymol list as a digest on gmail based web. I don't know
  if it's a result of the digestion process, but it seems like = signs and
  other non-alpha characters are associated with these burps of indigestion,
  invariably followed by 2D or 3D or such. I've kind of learned to ignore
  them, but obviously they can cause some confusion and are at least minorly
  amusing when they reappear like some who's on first miscommunication as
  warren's advice mention there should be no 3D just the number 10 like
  this, and then it proceeded to again display the 3D!! Perhaps the Digest is
  the culprit and could be treated? It also displays HTML as full text with
  tags and all that garbage, by the way.
 
  quote:
  I'm not sure where that 3D10 is coming from -- it should simply be
  the
  number 10:
 
  alter all, b=3D10
  
  (!)
  map_new can take a selection as its fourth argument, so you could
 

[PyMOL] label

[surendra negi]

Hi, I am back with a small prob! may be i am missing
something in command line

Q: How to label residue in cartoon selection using
command line. 

Sincerely
sn





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[PyMOL] label is not displayed after raying

[eric hu]

Hi, I wonder if anyone has had the similar problem. I
can see both the label and dash at normal window.
After raytracing there is only a yellow dotted line
between two atoms without the distance. How can I make
the distance shown on the raytracing picture? Thanks!

Happy new year!

Eric

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[PyMOL] label wizard

[Ezequiel Panepucci]

Hello people,

This is a labeling wizard. It allows you to click
atoms and have a label show up near the atom position.

If the atom is a C-alpha the label is slighly
different. More info is shown in the prompt area.

To use it, put the attached file in
/pymol/modules/pymol/wizard/label.py

and from within pymol type wizard label

Comments?

Have fun,
Zac


 file: label.py

#
# Author: Ezequiel Panepucci
# Last revision: 2001-11-14
#
from pymol.wizard import Wizard
from pymol import cmd
import pymol

class Label(Wizard):

   atom=None
   messages=1
   labeling=1
   obj_name=None

   def get_prompt(self):
  self.prompt = []
  if (not self.messages):
 return ['']

  if (self.atom == None):
 self.prompt = ['Click atoms...']
  else:
 if self.atom.chain == '':
self.prompt.append( '%s %s %s %s B = %.2f  XYZ = %.3f %.3f %.3f' %
(self.obj_name,
 self.atom.resn,
 self.atom.resi,
 self.atom.name,
 self.atom.b,
 self.atom.coord[0],
 self.atom.coord[1],
 self.atom.coord[2]) )
 else:
self.prompt.append('%s %s %s%s %s B = %.2f  XYZ = %.3f %.3f %.3f' %
(self.obj_name,
 self.atom.resn,
 self.atom.chain,
 self.atom.resi,
 self.atom.name,
 self.atom.b,
 self.atom.coord[0],
 self.atom.coord[1],
 self.atom.coord[2]) )

  return self.prompt

   def toggle_messages(self):
  self.messages = not self.messages

   def toggle_labeling(self):
  self.labeling = not self.labeling

   def get_panel(self):
  return [
 [ 1, 'Labeling',''],
 [ 2, 'Toggle add/erase','cmd.get_wizard().toggle_labeling()'],
 [ 2, 'Toggle messages','cmd.get_wizard().toggle_messages()'],
 [ 2, 'Clear All','cmd.label()'],
 [ 2, 'Done','cmd.set_wizard()'],
 ]

   def do_pick(self,bondFlag):
  self.obj_name = None

#  if 'pk1' in cmd.get_names('selections'):
  if cmd.count_atoms('pk1',1):
 self.obj_name = cmd.identify('pk1',1)[0][0]

  model = cmd.get_model((pk1))
  self.atom = model.atom.pop()
  if not self.labeling:
 cmd.label((pk1), '')
  elif self.atom.name == 'CA':
 cmd.label((pk1), ' %s %s % (resn,resi)')
  else:
 cmd.label((pk1), ' %s %s % (name,resi)')
  cmd.unpick()
  cmd.refresh_wizard()