pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Adam and Nat,

a few clarifying remarks on this topic:

 - The leading dot is optional, so everything that starts with
   .pymolrc or pymolrc will be found by PyMOL. Files with dot
   take precedence over files without dot.

 - Files ending on .py (or .pym) will be parsed as python scripts,
   files ending on .pml (or .p1m) or without suffix will be parsed as
   PyMOL command syntax.

 - Several directories are searched, in order:
   - $HOME
   - $HOMEPATH + $HOMEDRIVE (on Windows)
   - $PYMOL_PATH

 - PyMOL will even load multiple pymolrc files, however only either
   with dot or without dot, and only from the same directory.

I'll update the PyMOLWiki with that information.

A handy script for saving the current set of changed settings to a
pymolrc file is available here:
http://pymolwiki.org/index.php/Save_settings

Cheers,
  Thomas

H. Adam Steinberg wrote, On 01/30/13 20:37:
> 1st, thank you for your patience and help.
> 2nd, for those who end up trying to also do this… Apple now hides all files in the user folder that start with a period. Therefore, the minute you hit enter after changing the name to .pymolrc, the file disappears. You have to run a third party app that allows you to see the hidden files. I used TinkerTool.
> 
> This works and solved the problem! Thanks!
> 
> On Jan 30, 2013, at 12:59 PM, Nat Echols <nat...@gm...> wrote:
>> On Wed, Jan 30, 2013 at 10:56 AM, H. Adam Steinberg <ad...@st...> wrote:
>>> You are correct, if I put the pymolrc.pym file in the user folder, MacPyMol does try to read it when it starts up.
>>>
>>> However, it errors every time.
>>>
>>> If I put just this one command in the file and start up PyMol, it comes back with:
>>>
>>> File "/Users/adam/pymolrc.pym", line 1
>>>    set auto_zoom = 0
>>>                ^
>>> SyntaxError: invalid syntax
>>
>> That's because you're using the wrong file name:
>>
>>>> "On a linux-type system, this file will be located in /path/to/home/.pymolrc."
>>
>> -Nat

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

1st, thank you for your patience and help.
2nd, for those who end up trying to also do this… Apple now hides all files in the user folder that start with a period. Therefore, the minute you hit enter after changing the name to .pymolrc, the file disappears. You have to run a third party app that allows you to see the hidden files. I used TinkerTool.

This works and solved the problem! Thanks!


On Jan 30, 2013, at 12:59 PM, Nat Echols <nat...@gm...> wrote:

> On Wed, Jan 30, 2013 at 10:56 AM, H. Adam Steinberg <ad...@st...> wrote:
>> You are correct, if I put the pymolrc.pym file in the user folder, MacPyMol does try to read it when it starts up.
>> 
>> However, it errors every time.
>> 
>> If I put just this one command in the file and start up PyMol, it comes back with:
>> 
>> File "/Users/adam/pymolrc.pym", line 1
>>    set auto_zoom = 0
>>                ^
>> SyntaxError: invalid syntax
> 
> That's because you're using the wrong file name:
> 
>>> "On a linux-type system, this file will be located in /path/to/home/.pymolrc."
> 
> 
> -Nat

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

On Wed, Jan 30, 2013 at 10:56 AM, H. Adam Steinberg <ad...@st...> wrote:
> You are correct, if I put the pymolrc.pym file in the user folder, MacPyMol does try to read it when it starts up.
>
> However, it errors every time.
>
> If I put just this one command in the file and start up PyMol, it comes back with:
>
>  File "/Users/adam/pymolrc.pym", line 1
>     set auto_zoom = 0
>                 ^
> SyntaxError: invalid syntax

That's because you're using the wrong file name:

>> "On a linux-type system, this file will be located in /path/to/home/.pymolrc."


-Nat

You are correct, if I put the pymolrc.pym file in the user folder, MacPyMol does try to read it when it starts up.

However, it errors every time.

If I put just this one command in the file and start up PyMol, it comes back with:

 File "/Users/adam/pymolrc.pym", line 1
    set auto_zoom = 0
                ^
SyntaxError: invalid syntax

On Jan 30, 2013, at 12:46 PM, Nat Echols <nat...@gm...> wrote:

> On Wed, Jan 30, 2013 at 10:43 AM, H. Adam Steinberg <ad...@st...> wrote:
>> This is great, but looks like it's only for Windows? Where would one put this pymolrc.pym file on a Mac?
>> 
>> <" rel="nofollow">http://www.pymolwiki.org/index.php/Pymolrc>
> 
> Quoting the wiki:
> 
> "On a linux-type system, this file will be located in /path/to/home/.pymolrc."
> 
> This should probably be edited to "Unix-type system", since Mac and
> Linux behave identically in this case.
> 
> -Nat

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

On Wed, Jan 30, 2013 at 10:43 AM, H. Adam Steinberg <ad...@st...> wrote:
> This is great, but looks like it's only for Windows? Where would one put this pymolrc.pym file on a Mac?
>
> <" rel="nofollow">http://www.pymolwiki.org/index.php/Pymolrc>

Quoting the wiki:

"On a linux-type system, this file will be located in /path/to/home/.pymolrc."

This should probably be edited to "Unix-type system", since Mac and
Linux behave identically in this case.

-Nat

This is great, but looks like it's only for Windows? Where would one put this pymolrc.pym file on a Mac?

<" rel="nofollow">http://www.pymolwiki.org/index.php/Pymolrc>

On Jan 30, 2013, at 12:12 PM, Nat Echols <nat...@gm...> wrote:

> On Wed, Jan 30, 2013 at 8:33 AM, H. Adam Steinberg <ad...@st...> wrote:
>> Is there anyway to change the default settings in PyMol so that when I open
>> the program, it is using my specified defaults? or perhaps there is a way a
>> script can automatically be run at startup? Or automatically run when I
>> fetch in a new pdb? I'm running MacPyMol on 10.8.
> 
> Yes, just create a file ~/.pymolrc and add whatever settings you want
> - for instance, this is mine:
> 
> set auto_zoom = 0
> set cartoon_oval_length = 0.8
> set cartoon_oval_width = 0.15
> set cartoon_rect_length = 0.8
> set cartoon_rect_width = 0.15
> set ray_shadows = 0
> set ray_opaque_background = 0
> 
> -Nat

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

Hi Pascal,

hide nonbonded

Cheers,

Jason

Sent from my Android. Please excuse the concision and any typos.
On Jan 30, 2013 1:10 PM, "Pascal Auffinger" <
p.a...@ib...> wrote:

> Hi,
>
> Just wondering how to remove the cross hair that is shown for each
> non-bonded atom
> (for example water molecules).
>
> Thanks,
>
> Pascal
>
>
> -----
> Pascal Auffinger
> IBMC/CNRS
> 15 rue René Descartes
> 67084 Strasbourg Cedex
>
> p.a...@ib...
> -----
>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
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> _______________________________________________
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

On Wed, Jan 30, 2013 at 8:33 AM, H. Adam Steinberg <ad...@st...> wrote:
> Is there anyway to change the default settings in PyMol so that when I open
> the program, it is using my specified defaults? or perhaps there is a way a
> script can automatically be run at startup? Or automatically run when I
> fetch in a new pdb? I'm running MacPyMol on 10.8.

Yes, just create a file ~/.pymolrc and add whatever settings you want
- for instance, this is mine:

set auto_zoom = 0
set cartoon_oval_length = 0.8
set cartoon_oval_width = 0.15
set cartoon_rect_length = 0.8
set cartoon_rect_width = 0.15
set ray_shadows = 0
set ray_opaque_background = 0

-Nat

Hi,

Just wondering how to remove the cross hair that is shown for each non-bonded atom
(for example water molecules).

Thanks,

Pascal


-----
Pascal Auffinger
IBMC/CNRS
15 rue René Descartes
67084 Strasbourg Cedex

p.a...@ib...
-----

Hi All,

PyMol has it's own default settings, many of them are the historically accepted ways to view structures, universally accepted colors, etc. and that is great, because when someone uses the program they have to start with something! :)

And I realize most users probably open a pdb, work on, close the program, and then don't use it again for days or weeks. However, once someone uses the program all day long, day after day after day, once someone moves beyond the basics, develops a unique color set, develops a new style, develops a better style, or is working on a project that requires dozens, or even hundreds of renderings that all need to based on defaults that are different from the original defaults the program has built in, it gets to be quite a pain to have to run a default script every time one loads another pdb to a working open window, or when one opens another running window of PyMol.

Is there anyway to change the default settings in PyMol so that when I open the program, it is using my specified defaults? or perhaps there is a way a script can automatically be run at startup? Or automatically run when I fetch in a new pdb? I'm running MacPyMol on 10.8.

Thanks

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

Hi James,

In particular I wounder to know how I could decrease width of contour

> black line (appeared in set ray_trace_mode) ?
>

Please modulate the ray_trace_gain setting to adjust the thickness of the
outline. Please do not rely upon 3rd party software until you've tried this
easier solution.

For other neat rendering tricks, please see the PyMOLWiki's Gallery (
http://www.pymolwiki.org/index.php/Gallery).

Cheers,

-- Jason

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

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi James,

PyMOL itself does not install a .pymolrc file, but you can create your own and put it in your home directory. On startup, PyMOL will search a couple of places for the .pymolrc file (current directory, home directory, PYMOL_PATH) and take the first that is found.

Hope that helps.

Cheers,
  Thomas

On Jan 26, 2013, at 7:14 AM, James Starlight <jms...@gm...> wrote:

> Recently I've tried to find pymolrc but couldn't do it ( I have pymol
> 1.5 installed from binarries package manager )
> 
> own@starlight ~/Desktop $ locate pymolrc
> own@starlight ~/Desktop $ locate .pymolrc
> own@starlight ~/Desktop $ locate *.pymolrc
> 
> How I could locate it ?
> Akso I'm looking for detailed options of the possible settings in that
> file ( e.g I didnt find how to set maximum quality of images as the
> default option )
> 
> Thanks for help
> 
> James

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi James,

to decrease the width of the contour line, render the image with a larger size and then eventually scale it down again with some image manipulation tool (photoshop, imagemagick, ...).

ray 1600, 1200

Cheers,
  Thomas

On Jan 26, 2013, at 8:03 AM, James Starlight <jms...@gm...> wrote:
> Dear PyMol users!
> 
> I wounder to know about all possible options of high-quality image's
> visualisation by means of Ray command. Below you can see list of
> commands which I've already tried
> 
> set ray_trace_mode, 3;
> #set ray_trace_fog,0
> #set ray_shadows,0
> set antialias, 2
> ray 800, 600
> 
> In particular I wounder to know how I could decrease width of contour
> black line (appeared in set ray_trace_mode) ?
> Also I'd like to show more examples besides those which I found here
> http://www.pymolwiki.org/index.php/Ray_trace_mode#Modes
> 
> James

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Dear PyMol users!

I wounder to know about all possible options of high-quality image's
visualisation by means of Ray command. Below you can see list of
commands which I've already tried

set ray_trace_mode, 3;
#set ray_trace_fog,0
#set ray_shadows,0
set antialias, 2
ray 800, 600

In particular I wounder to know how I could decrease width of contour
black line (appeared in set ray_trace_mode) ?
Also I'd like to show more examples besides those which I found here
http://www.pymolwiki.org/index.php/Ray_trace_mode#Modes


James

Recently I've tried to find pymolrc but couldn't do it ( I have pymol
1.5 installed from binarries package manager )

own@starlight ~/Desktop $ locate pymolrc
own@starlight ~/Desktop $ locate .pymolrc
own@starlight ~/Desktop $ locate *.pymolrc

How I could locate it ?
Akso I'm looking for detailed options of the possible settings in that
file ( e.g I didnt find how to set maximum quality of images as the
default option )

Thanks for help

James

2013/1/26 James Starlight <jms...@gm...>:
> Recently I've tried to find pymolrc but couldn't do it ( I have pymol
> 1.5 installed from binarries package manager )
>
> own@starlight ~/Desktop $ locate pymolrc
> own@starlight ~/Desktop $ locate .pymolrc
> own@starlight ~/Desktop $ locate *.pymolrc
>
> How I could locate it ?
> Akso I'm looking for detailed options of the possible settings in that
> file ( e.g I didnt find how to set maximum quality of images as the
> default option )
>
> Thanks for help
>
> James
>
> 2012/8/16 Folmer Fredslund <fo...@gm...>:
>> Hi James
>>
>> Check out the information about how to load custom settings and functions:
>> http://www.pymolwiki.org/index.php/Pymolrc
>>
>> Hope this helps,
>> Folmer
>>
>>
>> 2012/8/16 James Starlight <jms...@gm...>:
>>> Dear PyMol users!
>>>
>>>
>>> I wounder to know about possible way to save settings of the PyMol
>>> after LogOut from it.
>>>
>>> E.g I've defined some basic settings like fetch_host and fetch_patch
>>> for uploading of new pdb files as well as set new background colour.
>>> Also I've changed some advanced settings - e.g I defined to unchange
>>> atom order in the processed pdb by the below commands
>>> set retain_order,1  set pdb_retain_ids,1
>>>
>>>
>>> After exiting from PyMol and starting of the new session I must to
>>> define this settings each time again. Is there any way to save this
>>> parameters for each new pymol session ?
>>>
>>> JAmes
>>>
>>> ------------------------------------------------------------------------------
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond. Discussions
>>> will include endpoint security, mobile security and the latest in malware
>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>
>>
>>
>> --
>> Folmer Fredslund

Hi Ahmet,

If your PDB is named "1foo" and has one chain this should work:

iterate first 1foo and poly, resn

iterate last 1foo and poly, resn

Otherwise you'll need to specify the selection more carefully, but first
and last should still be appropriate.

Cheers,

-- Jason



On Fri, Jan 25, 2013 at 4:16 PM, Ahmet yıldırım <ahm...@gm...> wrote:

> Dear users,
>
> How can I learn the names of the residues that make up the N- and C-
> terminals of a structure using Pymol?
>
> Thanks in advance
> --
> Ahmet Yıldırım
>
>
> ------------------------------------------------------------------------------
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
> MVPs and experts. ON SALE this month only -- learn more at:
> http://p.sf.net/sfu/learnnow-d2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



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

(e) Jas...@sc...
(o) +1 (603) 374-7120

Dear users,

How can I learn the names of the residues that make up the N- and C-
terminals of a structure using Pymol?

Thanks in advance
-- 
Ahmet Yıldırım

Hi Alex,

We'll look into making this faster/smarter. To let you know, whenever you
move an atom, it deforms the surface and causes a recalculation. The bigger
your structure and higher quality the surface the longer this takes.

Cheers,

-- Jason


On Tue, Jan 22, 2013 at 10:34 AM, Alex Truong <at...@bu...> wrote:

> Hi All,
>
> This isn't really a problem per se, I'm just wondering. Is there any way
> to more efficiently code the rotation protocol when the items being viewed
> are in surface view? Maybe my computer isn't fast/strong enough or
> something, but it seems whenever I try tweaking the position of one
> subunits in relation to other subunits while everything is in surface view,
> two redraws occur, and it's difficult for me to adjust with precision
> because there's so much latency between positionings. Just a thought.
> again, it's not really much of an issue, because I can just retoggle a new
> view or something as a workaround, but it seems like manipulations while in
> surface view can get a little GPU/CPU intensive. Are the redraws necessary?
>
> Alex
>
>
> ------------------------------------------------------------------------------
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
> MVPs and experts. ON SALE this month only -- learn more at:
> http://p.sf.net/sfu/learnnow-d2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



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

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Joachim,

To my knowledge Apple does not support stereoscopic 3D. This has been a
longstanding issue they still refuse to address.

Cheers,

-- Jason


On Fri, Jan 25, 2013 at 11:34 AM, Joachim Reichelt <
Joa...@he...> wrote:

> Dear Mac-User
>
> is it possible to use active stereo, e.g. NVIDIA shutter glasses + ASUS
> 3D Monitor on the latest iMac?
> The GT 640M/650M are on the list under
> http://www.nvidia.de/object/3d-vision-requirements-de.html
>
> --
> Joachim Reichelt
>
>
> ------------------------------------------------------------------------------
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
> MVPs and experts. ON SALE this month only -- learn more at:
> http://p.sf.net/sfu/learnnow-d2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...




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

(e) Jas...@sc...
(o) +1 (603) 374-7120

Dear Mac-User

is it possible to use active stereo, e.g. NVIDIA shutter glasses + ASUS 
3D Monitor on the latest iMac?
The GT 640M/650M are on the list under 
http://www.nvidia.de/object/3d-vision-requirements-de.html

-- 
Joachim Reichelt

Hi Abhinav,

It's currently not feasible. Please see the previous discussion on this:
http://www.mail-archive.com/pym...@li.../msg08942.html.

Cheers,

-- Jason


On Thu, Jan 24, 2013 at 11:04 AM, Abhinav Kumar
<abh...@sl...>wrote:

>  Hi,
> I want to create a label that has a line break inside it. For example
> "Asn\n102".
> Is there a way to do it?
> The command 'label selection "Asn\n102"' does not work.
> --
>  Thanks,
> Abhinav
>
>  JCSG@SSRL, SLAC
> (650) 926-2992
>
>
> ------------------------------------------------------------------------------
> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
> MVPs and experts. ON SALE this month only -- learn more at:
> http://p.sf.net/sfu/learnnow-d2d
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



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

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi,
I want to create a label that has a line break inside it. For example 
"Asn\n102".
Is there a way to do it?
The command 'label selection "Asn\n102"' does not work.
-- 
Thanks,
Abhinav

JCSG@SSRL, SLAC
(650) 926-2992

Thanks Thomas,

seems to work.

-----Original Message-----
From: Thomas Holder [mailto:tho...@sc...] 
Sent: Wednesday, 23 January 2013 10:47 p.m.
To: pym...@li...
Subject: Re: [PyMOL] echo colour

Hi Joel,

the color is stored as a numeric atom property, you can use iterate to get it.

PyMOL> iterate (first objX), print color

If you need the name of the color, get the index to name mapping as a dictionary from PyMOL like this:

PyMOL> stored.cn = dict((i,c) for (c,i) in cmd.get_color_indices()) 
PyMOL> iterate (first objX), print stored.cn[color]

Last but not least, there is the psico.querying.get_color function in the PSICO module :)

Cheers,
  Thomas

Joel Tyndall wrote, On 01/23/13 02:04:
> Hi list,
> 
> With the myriad of colours in Pymol, I tend to forget which shade of 
> what I have used. Is there a way/command to print the colour I have 
> used to colour object X?
> 
> Cheers
> 
> Joel
> _________________________________
> 
> Joel Tyndall, PhD
> 
> Senior Lecturer in Medicinal Chemistry National School of Pharmacy 
> University of Otago PO Box 56 Dunedin 9054 New Zealand
> 
> Skype: jtyndall
> 
> Ph: +64 3 479 7293

--
Thomas Holder
PyMOL Developer
Schrödinger Contractor

------------------------------------------------------------------------------
Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at:
http://p.sf.net/sfu/learnnow-d2d
_______________________________________________
PyMOL-users mailing list (PyM...@li...)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pym...@li...

http://docs.python.org/2/library/tempfile.html#tempfile.NamedTemporaryFile

Quote: "If delete is true (the default), the file is deleted as soon as
it is closed."

Cheers,
  Thomas

Boris Kheyfets wrote, On 01/23/13 14:47:
> It prints the selection all right. Why then save wouldn't save it:
> 
> 
> def bk_saves_unique_pdb(Selection = None):
>     """Takes current selection (or "all" -- if nothing selected) and saves it as a uniquetly named pdb file (Frame_Selection_RandomString.pdb) in the current working directory."""
>     if not Selection:
>         Selection = cmd.get_names('selections', 1)
>         if Selection:
>             Selection = Selection[0] # it was a list
>         else:
>             Selection = 'all'
>     tempFile = tempfile.NamedTemporaryFile(dir=os.curdir, prefix="{frame:03d}_{sel}_".format(frame=cmd.get_frame(), sel=Selection) , suffix=".pdb")
>     print tempFile.name, Selection # prints righteous file name and selection name (though not in quotes)
>     cmd.save(tempFile.name, Selection) # but still saves nothing
> cmd.extend("bk_saves_unique_pdb", bk_saves_unique_pdb)

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

It prints the selection all right. Why then save wouldn't save it:

def bk_saves_unique_pdb(Selection = None):
    """Takes current selection (or "all" -- if nothing selected) and
saves it as a uniquetly named pdb file
(Frame_Selection_RandomString.pdb) in the current working
directory."""
    if not Selection:
        Selection = cmd.get_names('selections', 1)
        if Selection:
            Selection = Selection[0] # it was a list
        else:
            Selection = 'all'
    tempFile = tempfile.NamedTemporaryFile(dir=os.curdir,
prefix="{frame:03d}_{sel}_".format(frame=cmd.get_frame(),
sel=Selection) , suffix=".pdb")
    print tempFile.name, Selection # prints righteous file name and
selection name (though not in quotes)
    cmd.save(tempFile.name, Selection) # but still saves nothing
cmd.extend("bk_saves_unique_pdb", bk_saves_unique_pdb)



On Tue, Jan 22, 2013 at 10:49 PM, Thomas Holder <
tho...@sc...> wrote:

> Hi Boris,
>
> this will give you the list of active selections, which has by default
> only one entry (or zero, if no selection is enabled).
>
> active_selections = cmd.get_names('selections', 1)
>
> Hope that helps.
>
> Cheers,
>   Thomas
>
> On Jan 22, 2013, at 2:08 PM, Boris Kheyfets <khe...@gm...> wrote:
> > I want to save current selection as a uniquetly-named pdb file. So I
> need tempfile of python.
> >
> > So I write def, and I want it have current selection as default one (not
> the '(all)'). How do I do that?
> >
> > I think it will be somewhere under
> >  cmd.get_session()
> >
> > I read the sources, but couldn't find a single instance where current
> selection would be a default one.
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
>
>