Re: [PyMOL] Color starting midway between adjacent chains

2014-03-04 Thread I-Ji Jung 
Hi David,

Thanks. But what about between all chains? I mean, so between chains B and C 
and so on. I need a generic script that can be applied for any protein.

Thanks!

?? ??: David Hall
?? ??: ?2014?? ?3?? ?4??   ?2?:?57
?? ??: I-Ji Jung
??: pymol-users@lists.sourceforge.net

set_bond line_color, color_name, n. CA+CB

will color all bonds between CA and CB whatever color you put in as color_name

If you're doing sticks instead of lines, you should use

set_bond stick_color, color_name, n. CA+CB

-David




On Mon, Mar 3, 2014 at 10:01 PM, I-Ji Jung 
mailto:u5205...@anu.edu.au>> wrote:
Hi everyone,

I have just started learning Pymol and PyMol seems to use a different colour 
convention than Molmol, i.e. the colour of a side chain starts half way between 
the CA and CB atoms (instead of starting at the CA). Do you know whether there 
would there be a way to start the side chain colour at the CA without changing 
the colour of the backbone?

Any help will be greatly appreciated!

Thank you.

I-Ji

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[PyMOL] forward and backward keyboard shortcuts

2014-03-04 Thread Thomas Evangelidis 
Hi,

Is there any keyboard shortcut to move to the next or the previous state of
an object, namely something equivalent to "forward" and "backward" commands?


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==

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tev...@pharm.uoa.gr

  teva...@gmail.com


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Re: [PyMOL] forward and backward keyboard shortcuts

2014-03-04 Thread Jason Vertrees 
Thomas,

Right and left arrow keys.

Cheers,

Jason

On Tuesday, March 4, 2014, Thomas Evangelidis  wrote:

>
> Hi,
>
> Is there any keyboard shortcut to move to the next or the previous state
> of an object, namely something equivalent to "forward" and "backward"
> commands?
>
>
> --
>
> ==
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: 
> tev...@pharm.uoa.gr
>
>   teva...@gmail.com
>
>
> website: 
> thomasevangelidishomepage
>
>
>

-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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[PyMOL] command to deactivate/hide an object

2014-03-04 Thread Thomas Evangelidis 
Hi,

Is there some command that deactivates an object, namely something
equivalent to clicking on an object name at the object panel? I am loading
multiple files and render them as sticks but the memory overflows. If there
was a command to keep the stick representation but deactivate the object
(hide it) then I could visualize the structures one by one once they are
all loaded -which is actually what I want.

thanks,
Thomas

-- 

==

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tev...@pharm.uoa.gr

  teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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Re: [PyMOL] command to deactivate/hide an object

2014-03-04 Thread Thomas Holder 
Hi Thomas,

sure, it's "enable" and "disable".

http://pymolwiki.org/index.php/Enable
http://pymolwiki.org/index.php/Disable

Cheers,
  Thomas

On 04 Mar 2014, at 13:25, Thomas Evangelidis  wrote:

> Hi,
> 
> Is there some command that deactivates an object, namely something equivalent 
> to clicking on an object name at the object panel? I am loading multiple 
> files and render them as sticks but the memory overflows. If there was a 
> command to keep the stick representation but deactivate the object (hide it) 
> then I could visualize the structures one by one once they are all loaded 
> -which is actually what I want.
> 
> thanks,
> Thomas
> 
> -- 
> ==
> Thomas Evangelidis
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
> email: tev...@pharm.uoa.gr
>   teva...@gmail.com
> 
> website: https://sites.google.com/site/thomasevangelidishomepage/


-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


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Re: [PyMOL] command to deactivate/hide an object

2014-03-04 Thread Jordan Willis 
A super hack way is this:

hide all
python
my_list = cmd.get_object_list()  # gets all objects loaded

index = 0


def next_thing():
global index
cmd.show('sticks', my_list[index])
cmd.hide('sticks', my_list[index - 1])
index += 1


def last_thing():
global index
index -= 1
cmd.show('sticks', my_list[index - 1])
cmd.hide('sticks', my_list[index])

cmd.extend('next_thing', next_thing)
cmd.extend('last_thing', last_thing)
python end

Then you can type “next_thing” or “last_thing” to cycle through your objects. 

Jordan

On Mar 4, 2014, at 4:03 PM, Thomas Holder  wrote:

> Hi Thomas,
> 
> sure, it's "enable" and "disable".
> 
> http://pymolwiki.org/index.php/Enable
> http://pymolwiki.org/index.php/Disable
> 
> Cheers,
>  Thomas
> 
> On 04 Mar 2014, at 13:25, Thomas Evangelidis  wrote:
> 
>> Hi,
>> 
>> Is there some command that deactivates an object, namely something 
>> equivalent to clicking on an object name at the object panel? I am loading 
>> multiple files and render them as sticks but the memory overflows. If there 
>> was a command to keep the stick representation but deactivate the object 
>> (hide it) then I could visualize the structures one by one once they are all 
>> loaded -which is actually what I want.
>> 
>> thanks,
>> Thomas
>> 
>> -- 
>> ==
>> Thomas Evangelidis
>> PhD student
>> University of Athens
>> Faculty of Pharmacy
>> Department of Pharmaceutical Chemistry
>> Panepistimioupoli-Zografou
>> 157 71 Athens
>> GREECE
>> email: tev...@pharm.uoa.gr
>>  teva...@gmail.com
>> 
>> website: https://sites.google.com/site/thomasevangelidishomepage/
> 
> 
> -- 
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.
> 
> 
> --
> Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce.
> With Perforce, you get hassle-free workflows. Merge that actually works. 
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[PyMOL] Pseudo AxPyMol

2014-03-04 Thread Jordan Willis 
I’m using powerpoint for mac, so I don’t have the luxury of Axpymol (any plans 
for OSX?)

I wanted to make a movie that iterates through scenes of a PyMol session and 
pauses there until I hit the “next” button on powerpoint. My workaround was to 
simply make a movie that went trough all scenes and break them up into separate 
movies. When I hit “next” on the clicker for powerpoint, it would make that 
movie appear on the slide and it would be appear to be a continuation of the 
last movie.

I was wondering if there is a way to render movies by frame. For instance only 
tell PyMol to render frames 1-30. Then in another movie 31-60 etc. Perhaps the 
simplest way would be to dump every frame as a separate .png, and reconstruct 
manually.

Any thoughts on this? How to make it easier, or does this seem like the easiest 
way.

Jordan
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Re: [PyMOL] Pseudo AxPyMol

2014-03-04 Thread Folmer Fredslund 
Hi Jordan,

I don't know if this helps you, but you can start pymol in "presentation
mode" (by saving a session with scenes and then edit the name to "psw"
instead of "pse"). Then you will immediately go full-screen and hitting
space (or the clicker I presume) will let you move to the next scene.
This might not be "fancy" enough, but I thought I'd mention it.

One other thing you could do is to save the files in the movie (instead of
making a movie directly) and then make small movies from the output png's.

Hope this helps,
Folmer



2014-03-04 23:41 GMT+01:00 Jordan Willis :

> I'm using powerpoint for mac, so I don't have the luxury of Axpymol (any
> plans for OSX?)
>
> I wanted to make a movie that iterates through scenes of a PyMol session
> and pauses there until I hit the "next" button on powerpoint. My workaround
> was to simply make a movie that went trough all scenes and break them up
> into separate movies. When I hit "next" on the clicker for powerpoint, it
> would make that movie appear on the slide and it would be appear to be a
> continuation of the last movie.
>
> I was wondering if there is a way to render movies by frame. For instance
> only tell PyMol to render frames 1-30. Then in another movie 31-60 etc.
> Perhaps the simplest way would be to dump every frame as a separate .png,
> and reconstruct manually.
>
> Any thoughts on this? How to make it easier, or does this seem like the
> easiest way.
>
> Jordan
>
> --
> Subversion Kills Productivity. Get off Subversion & Make the Move to
> Perforce.
> With Perforce, you get hassle-free workflows. Merge that actually works.
> Faster operations. Version large binaries.  Built-in WAN optimization and
> the
> freedom to use Git, Perforce or both. Make the move to Perforce.
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>



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