pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Anatoliy,

add this line to your script:

set internal_feedback, 0

See also:
http://www.pymolwiki.org/index.php/Internal_feedback

Hope that helps.

Cheers,
   Thomas

Anatoliy Volkov wrote, On 03/31/12 20:36:
> Dear PyMOL users,
> 
> Is there a way to hide the lower command line?
> In ideal case, I would like to add such a command to my *.pml script.
> 
> Thank you,
> Anatoliy
> -------------------------------------
> Anatoliy Volkov, Ph.D.
> Department of Chemistry
> Middle Tennessee State University

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Dear PyMOL users,

Is there a way to hide the lower command line?
In ideal case, I would like to add such a command to my *.pml script.

Thank you,
Anatoliy
-------------------------------------
Anatoliy Volkov, Ph.D.
Department of Chemistry
Middle Tennessee State University

Hi all

My pymol session has developed a memory leak. While I can manipulate the session quite easily, it's constantly pushing 70-100% on my processor. Any ideas on how to fix this? (Closing and restarting only results in the same). 

Thanks!

F



---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

Hi James,

"connect_mode" is for loading. I think "pdb_conect_all" is what you are 
looking for:

set pdb_conect_all

http://www.pymolwiki.org/index.php/Pdb_Conect_All
http://www.pymolwiki.org/index.php/Connect_mode

Cheers,
   Thomas

James Starlight wrote, On 03/30/12 11:53:
> Hi all :)
> 
> Recently I've been needed to parametrise my short protein mollecule by 
> ATB server for futher MD simulation.
> 
> The input pdb file for that server must consist of CONNECT records at 
> the bottom of such pdb.
> 
> How I could add such missing CONNECT records for my pdb ?
> 
> I've tried
> 
> set connect_mode, 1
> 
> but saved pdb still have not contained CONNECT :(
> 
> Thanks for help
> 
> James

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tu"bingen

Hi all :)


Recently I've been needed to parametrise my short protein mollecule by ATB
server for futher MD simulation.

The input pdb file for that server must consist of CONNECT records at the
bottom of such pdb.

How I could add such missing CONNECT records for my pdb ?

I've tried

set connect_mode, 1



but saved pdb still have not contained CONNECT :(

Thanks for help

James

30 марта 2012 г. 13:52 пользователь James Starlight
<jms...@gm...>написал:

> Hi all :)
>
>
> Recently I've been needed to parametrise my short protein mollecule by ATB
> server for futher MD simulation.
>
> The input pdb file for that server must consist of CONNECT records at the
> bottom of such pdb.
>
> How I could add such missing CONNECT records for my pdb ?
>
> I've tried
>
> set connect_mode, 1
>
>
>
> but saved pdb still have not contained CONNECT :(
>
> Thanks for help
>
> James
>
> 21 марта 2012 г. 13:14 пользователь Tsjerk Wassenaar <ts...@gm...>написал:
>
> Hi James,
>>
>> Pymol adds a TER statement at the end of each continuous piece of the
>> protein.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> 2012/3/21 James Starlight <jms...@gm...>:
>> > Hi Tsjerk,
>> >
>> > I'm not quite understood if pymol adds TER enty after residues wich
>> consist
>> > of missing atoms or in the place with the missing residues  ( e.g in
>> loops
>> > of GPCRs or other flexible regions) ?
>> >
>> > James
>> >
>> > 21 марта 2012 г. 10:38 пользователь Tsjerk Wassenaar <ts...@gm...
>> >
>> > написал:
>> >
>> >> Hi James,
>> >>
>> >> Broken refers to non-continuity of a chain, i.e. missing residues.
>> Broken
>> >> does not mean wrong... But for the rest, I admitted to be wrong with my
>> >> arguments already :p
>> >>
>> >> Cheers,
>> >>
>> >> Tsjerk
>> >>
>> >> On Mar 21, 2012 6:47 AM, "James Starlight" <jms...@gm...>
>> wrote:
>> >>
>> >> Hi Tsjerk!
>> >>
>> >> It's very strange because I've obtained all same structures with the
>> same
>> >> TER statements in the body of the pdb file in the case of processing of
>> >> x-ray structures of GPCRs ( It's different membrane proteins solved by
>> the
>> >> different lab groups in the different time ). So it's strange that all
>> of
>> >> those structures were broken!
>> >>
>> >> James
>> >>
>> >> 20 марта 2012 г. 14:35 пользователь Tsjerk Wassenaar <
>> ts...@gm...>
>> >> написал:
>> >>
>> >> > > Hi James, > > In addition to Thomas' answer... What is _wrong_
>> about
>> >> > > the TER > statement? Your ...
>> >>
>> >>
>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
>>
>
>

Dear Tsjerk,
thank you very much for your help.
I apologise for this question but could not find in the WIKI help for this.
I noticed just now I have to get the width and height correct so everything fits into the frame. Then nothing is cut off in the final image.
Thank you again!
Kind regards
Gudrun 

Am 29.03.2012 um 12:19 schrieb Tsjerk Wassenaar:

> Hi Gudrun,
> 
> If you raytrace an image it is written to disk and loaded into the
> viewport. If the imge is larger than the viewport it is displayed
> smaller with the real resolution mentioned underneath. If you save the
> image, using 'png', it is saved in the large format, without the black
> padding.
> 
> Cheers,
> 
> Tsjerk
> 
> On Thu, Mar 29, 2012 at 1:12 PM, Gudrun Lotze <gud...@gm...> wrote:
>> Dear Pymol-Experts,
>> a while ago I had problems with the ray command. It always showed me a black frame with mentioning at the bottom the image size.
>> The group advised me to use viewport.
>> 
>> viewport 800, 600
>> 
>> ray 800, 600
>> 
>> 
>> This works and I don't get this black frame, however if I try different values, for example 1200, 1000 I still get the black frame. Everything fits nicely on the screen and I don't know where this black box comes really in the other cases.
>> I would like to use a higher resolution than 800, 600 without the black box.
>> 
>> Thank you very much for your help.
>> Kind regards
>> Gudrun
>> 
>> 
>> ------------------------------------------------------------------------------
>> This SF email is sponsosred by:
>> Try Windows Azure free for 90 days Click Here
>> http://p.sf.net/sfu/sfd2d-msazure
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> 
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands

Hi Gudrun,

If you raytrace an image it is written to disk and loaded into the
viewport. If the imge is larger than the viewport it is displayed
smaller with the real resolution mentioned underneath. If you save the
image, using 'png', it is saved in the large format, without the black
padding.

Cheers,

Tsjerk

On Thu, Mar 29, 2012 at 1:12 PM, Gudrun Lotze <gud...@gm...> wrote:
> Dear Pymol-Experts,
> a while ago I had problems with the ray command. It always showed me a black frame with mentioning at the bottom the image size.
> The group advised me to use viewport.
>
> viewport 800, 600
>
> ray 800, 600
>
>
> This works and I don't get this black frame, however if I try different values, for example 1200, 1000 I still get the black frame. Everything fits nicely on the screen and I don't know where this black box comes really in the other cases.
> I would like to use a higher resolution than 800, 600 without the black box.
>
> Thank you very much for your help.
> Kind regards
> Gudrun
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

Dear Pymol-Experts,
a while ago I had problems with the ray command. It always showed me a black frame with mentioning at the bottom the image size.
The group advised me to use viewport.

viewport 800, 600

ray 800, 600


This works and I don't get this black frame, however if I try different values, for example 1200, 1000 I still get the black frame. Everything fits nicely on the screen and I don't know where this black box comes really in the other cases.
I would like to use a higher resolution than 800, 600 without the black box.

Thank you very much for your help.
Kind regards
Gudrun 

Thank you very much! Really cool!
Gudrun

Am 28.03.2012 um 17:38 schrieb Jason Vertrees:

> Hi Gudrun,
> 
> The quickest way would be to center the camera on your selection/protein:
> 
> # create the axes
> 
> run axes.py
> 
> # put camera center at center of protein geometry
> 
> orient 6lys
> 
> x = cmd.get_position()
> 
> # move the axes
> 
> cmd.set_object_ttt("axes", [1, 0, 0, x[0], 0, 1, 0, x[1], 0, 0, 1,
> x[2], 0, 0, 0, 1])
> 
> Cheers,
> 
> -- Jason
> 
> On Wed, Mar 28, 2012 at 9:00 AM, Gudrun Lotze <gud...@gm...> wrote:
>> Dear all,
>> 
>> I used the second script from page http://www.pymolwiki.org/index.php/Axes to draw those axes.
>> 
>> However they are not plotted within my 6Lys.pdb file, those axes are located next to the crystal structure. I honestly don't know whee is the center of 6Lys.pdb, but is there a chance to bring 6Lys.pdb and axes.py with regard to their centers into one point, please? Basically, the axes.py sits in the center of the molecule.
>> Is there a defined way to achieve this without random try & fail translations, please?
>> 
>> Thank you for your help.
>> Kind regards
>> Gudrun
>> ------------------------------------------------------------------------------
>> This SF email is sponsosred by:
>> Try Windows Azure free for 90 days Click Here
>> http://p.sf.net/sfu/sfd2d-msazure
>> _______________________________________________
>> 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
> PyMOL Product Manager
> Schrödinger, LLC
> 
> (e) Jas...@sc...
> (o) +1 (603) 374-7120

Hi Gudrun,

The quickest way would be to center the camera on your selection/protein:

# create the axes

run axes.py

# put camera center at center of protein geometry

orient 6lys

x = cmd.get_position()

# move the axes

cmd.set_object_ttt("axes", [1, 0, 0, x[0], 0, 1, 0, x[1], 0, 0, 1,
x[2], 0, 0, 0, 1])

Cheers,

-- Jason

On Wed, Mar 28, 2012 at 9:00 AM, Gudrun Lotze <gud...@gm...> wrote:
> Dear all,
>
> I used the second script from page http://www.pymolwiki.org/index.php/Axes to draw those axes.
>
> However they are not plotted within my 6Lys.pdb file, those axes are located next to the crystal structure. I honestly don't know whee is the center of 6Lys.pdb, but is there a chance to bring 6Lys.pdb and axes.py with regard to their centers into one point, please? Basically, the axes.py sits in the center of the molecule.
> Is there a defined way to achieve this without random try & fail translations, please?
>
> Thank you for your help.
> Kind regards
> Gudrun
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> 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
PyMOL Product Manager
Schrödinger, LLC

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

Dear all,

I used the second script from page http://www.pymolwiki.org/index.php/Axes to draw those axes.

However they are not plotted within my 6Lys.pdb file, those axes are located next to the crystal structure. I honestly don't know whee is the center of 6Lys.pdb, but is there a chance to bring 6Lys.pdb and axes.py with regard to their centers into one point, please? Basically, the axes.py sits in the center of the molecule.  
Is there a defined way to achieve this without random try & fail translations, please?

Thank you for your help.
Kind regards 
Gudrun 

Greetings,

I saw this post on the CCP4 list and thought that some PyMOLers may
like to know:

> Dear All,
> I have successfully setup Toshiba Qosmio F7500 -3D gaming laptop for molecular visualization purposes. This 15" notebook computer can support 3D stereo in Coot and Pymol in glasses-free 3D mode. It works for 2D and 3D Windows7 applications in parallel.
> Details on the settings can be found on my post.
> http://nanonan.wordpress.com/2012/03/28/pymol-and-coot-3d-stereo-on-qosmio-f750-laptop/
> Best wishes,
> Duangrudee

Cheers,

-- Jason

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

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

Hi Werner,

doing *flexible* alignment of a *single* residue sounds a bit strange. 
What exactly is your goal? Do you want to superpose the rotamers? That 
would be:

align seleA and name N+C+CA+CB, seleB

Hope that helps.

Cheers,
   Thomas

On 03/27/2012 01:06 PM, werner schroedinger wrote:
> I have two PDB protein structures and would just like to do flexible
> alignment of one residue from structure A to another residue (of the
> same type) from structure B which remains fixed. I know pymol can do
> rigid alignment but wonder about tools for this purpose of flexible
> alignment.

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Hi Francis,

for ray tracing, mesh_width might be overwritten by mesh_radius. Try to 
change mesh_radius or unset it.

set mesh_radius, 0.01

unset mesh_radius

Cheers,
   Thomas

On 03/27/2012 05:53 PM, Francis E Reyes wrote:
> Hi all
>
> I'm not getting reasonable WYSIWYG behavior for setting mesh_width and then the final png.
>
> set mesh_width 0.01
> ray 600,544
> save file.png
>
> The mesh width in file.png looks thick to me and I can't seem to change it.
>
> Any ideas?
>
> Thanks!
>
> F
>
> ---------------------------------------------
> Francis E. Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Hi all

I'm not getting reasonable WYSIWYG behavior for setting mesh_width and then the final png. 

set mesh_width 0.01
ray 600,544
save file.png


The mesh width in file.png looks thick to me and I can't seem to change it. 

Any ideas?

Thanks!

F



---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

I have two PDB protein structures and would just like to do flexible
alignment of one residue from structure A to another residue (of the same
type) from structure B which remains fixed. I know pymol can do rigid
alignment but wonder about tools for this purpose of flexible alignment.

Hi Nat,

In mine its

C:\Program Files\PyMOL\PyMOL\PyMOL.exe

Hope this helps

_________________________________
Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand   
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea               +64 3 4797293
Fax / Waeawhakaahua     +64 3 4797034


-----Original Message-----
From: Nat Echols [mailto:nat...@gm...] 
Sent: Monday, 26 March 2012 5:52 a.m.
To: pym...@li...
Subject: [PyMOL] where does PyMOL install to on Windows?

I'm trying to figure out how to launch PyMOL automatically from a script on Windows.  I'm stuck with the 0.99 build for now, where the .exe is

C:\Program Files\DeLano Scientifc\PyMOL\PyMOL.exe

Is this now

C:\Program Files\Schrodinger\PyMOL\PyMOL.exe

in the newer versions, or somewhere else?

thanks,
Nat

------------------------------------------------------------------------------
This SF email is sponsosred by:
Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________
PyMOL-users mailing list (PyM...@li...)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pym...@li...

I'm trying to figure out how to launch PyMOL automatically from a
script on Windows.  I'm stuck with the 0.99 build for now, where the
.exe is

C:\Program Files\DeLano Scientifc\PyMOL\PyMOL.exe

Is this now

C:\Program Files\Schrodinger\PyMOL\PyMOL.exe

in the newer versions, or somewhere else?

thanks,
Nat

Greetings PyMOLers,

Just a quick note to welcome you to the Schrodinger booth (#503) at
the ACS meeting's exposition here in San Diego.  We'll be demoing new
PyMOL features, answering questions, and talking science.

Cheers,

-- Jason

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

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

Hi Suhaila,

Correct me if I'm wrong but you want create *new* GUI elements for
pymol to enhance your application, right?

To my knowledge, there is not a great tutorial on this, but I can give
you some pointers to plugins that do this currently and hopefully you
can backfill some knowledge.

The first point I should make though is that, as far as I know, you
*cannot* modify the existing PyMol windows, that is, you can't add an
item to the menu you get when you right click on a protein or make it
so there are additional per object menus on the right side of the
screen for your application.

Generally, for PyMol, your plugin interface is written using Tkinter,
which is widely documented across the internet (
http://wiki.python.org/moin/TkInter ).

http://www.pymolwiki.org/index.php/Plugins_Tutorial provides a simple
example of a plugin with a graphical interface. The __init__ adds your
plugin to the menu bar in PyMol and tells PyMol what to execute when
you click on the button. From there, it is just Tkinter with python
and pymol scripting.

The only pymol plugin I currently use with a graphical interface is
the Autodock plugin:
https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/plugins/autodock_plugin.py
It's a pretty complex piece of code, but it is a nice plugin that
seems highly reliable, so understanding looking at how it does things
can probably help you solve any issues you have along the way. There
are other plugins that you can find by browsing the pymolwiki that
also use graphical elements and may also be helpful.

-David




On Thu, Mar 22, 2012 at 4:39 PM, Suhaila Haji Mohd Hussin
<bel...@ho...> wrote:
> Hello everyone.
>
> Is there any useful online reference that can be shared for me to learn how
> to add GUI executed by Python script?
>
> I know PyMOL can visualize the protein just by typing in on PyMOL command
> but my supervisor will  grade my group project higher if we can make it more
> interactive where the user can just use a mouse to click button or something
> and less typing on command.
>
> Best regards,
> Suhaila
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Sorry for being rude, it was not meant in that way.

I was just puzzled by the fact, that you would be graded higher if you
don't use the command line.
That is just weird.

Back to the question.
Suhaila, you should try to explore the "action button".

First get a protein, which is good to illustrate.
Go to the menu: "Plugin"->"PDB Loader Service". Enter: "1hpu"
(Or write in command: fetch 1hpu )  :-)

Then go to the "A" (Action) button in the right menu.
Press: preset -> ligand sites -> cartoon

Try some of the presets. They are very good!

If you want to find some polar contacts.
Select your residue by clicking it:
Action -> find -> polar contacts -> Then something from the menu

I hope that helps!

Best
Troels

2012/3/23 Suhaila Haji Mohd Hussin <bel...@ho...>

>  OK. It does sound pretty weird prolly because the way I asked isn't
> precise.
>
> We plot predicted contacts that can be viewed in various ways. So it'd be
> better to create a GUI select menu or something like that for user's ease
> of interacting with our project.
>
> Suhaila.
>
> ------------------------------
> From: tl...@gm...
> Date: Thu, 22 Mar 2012 22:14:39 +0100
> CC: pym...@li...
> Subject: Re: [PyMOL] GUI to improve interaction between user and PyMOL
>
>
> That is seriously the strangest thing I ever heard about...
>
> The GUI is for the small fast thing to do.
> Why just don't press all button and see?
> It can only take a little time.
>
> Or google: pymol + "name of button"
> That should give you an answer...
>
> The command line is where the power is.
> Use that.
>
> /Troels
>
>
>
> 2012/3/22 Suhaila Haji Mohd Hussin <bel...@ho...>
>
>  Hello everyone.
>
> Is there any useful online reference that can be shared for me to learn
> how to add GUI executed by Python script?
>
> I know PyMOL can visualize the protein just by typing in on PyMOL command
> but my supervisor will  grade my group project higher if we can make it
> more interactive where the user can just use a mouse to click button or
> something and less typing on command.
>
> Best regards,
> *Suhaila*
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by: Try Windows Azure free for 90 days Click
> Here http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________ PyMOL-users mailing list (
> PyM...@li...) Info Page:
> https://lists.sourceforge.net/lists/listinfo/pymol-users Archives:
> http://www.mail-archive.com/pym...@li...
>

Jordan,

The 'hide' and 'show' commands to not take a state parameter. You
could use the "multiplex" option when loading the trajectories and
then use 'mdo' in the movie to control which states are shown/hidden.
This will slow down moviemaking and be a pain, but will get you where
you need to be.

We definitely need to add better state-level representation control. I
have filed this and we'll get to this as soon as we can.

Cheers,

-- Jason

On Thu, Mar 22, 2012 at 7:24 PM, Jordan Willis <jwi...@gm...> wrote:
> Hello,
>
> I was wondering if anyone could help me with some state mapping for movies. I have 1000 states or so that are output from a dynamics simulation automatically to pymol. I was wondering two things:
>
> 1. Can I hide the lines for state 500-1000 and show the lines for 1-500? I have all the states that map to one object because the program just appends that object with a new state.
>
> 2. Can I combine states where say states 800-1000 can be mapped with states 600-800? Essentially I want to show two parts of the simulation at once, one that maps to 800-1000 and the other that maps to 600-800. I can't think of how I would do this.
>
> Thanks so much,
> Jordan
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> 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
PyMOL Product Manager
Schrödinger, LLC

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

OK. It does sound pretty weird prolly because the way I asked isn't precise.
We plot predicted contacts that can be viewed in various ways. So it'd be better to create a GUI select menu or something like that for user's ease of interacting with our project.

Suhaila.

From: tl...@gm...
Date: Thu, 22 Mar 2012 22:14:39 +0100
CC: pym...@li...
Subject: Re: [PyMOL] GUI to improve interaction between user and PyMOL

That is seriously the strangest thing I ever heard about...
The GUI is for the small fast thing to do.Why just don't press all button and see?It can only take a little time.


Or google: pymol + "name of button"That should give you an answer...
The command line is where the power is.Use that.

/Troels




2012/3/22 Suhaila Haji Mohd Hussin <bel...@ho...>









Hello everyone.
 
Is there any useful online reference that can be shared for me to learn how to add GUI executed by Python script?
 
I know PyMOL can visualize the protein just by typing in on PyMOL command but my supervisor will  grade my group project higher if we can make it more interactive where the user can just use a mouse to click button or something and less typing on command.


 
Best regards,
Suhaila
 		 	   		  

------------------------------------------------------------------------------

This SF email is sponsosred by:

Try Windows Azure free for 90 days Click Here

http://p.sf.net/sfu/sfd2d-msazure
_______________________________________________

PyMOL-users mailing list (PyM...@li...)

Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users

Archives: http://www.mail-archive.com/pym...@li...



------------------------------------------------------------------------------
This SF email is sponsosred by:
Try Windows Azure free for 90 days Click Here 
http://p.sf.net/sfu/sfd2d-msazure
_______________________________________________
PyMOL-users mailing list (PyM...@li...)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pym...@li... 		 	   		  

Hello,

I was wondering if anyone could help me with some state mapping for movies. I have 1000 states or so that are output from a dynamics simulation automatically to pymol. I was wondering two things:

1. Can I hide the lines for state 500-1000 and show the lines for 1-500? I have all the states that map to one object because the program just appends that object with a new state.

2. Can I combine states where say states 800-1000 can be mapped with states 600-800? Essentially I want to show two parts of the simulation at once, one that maps to 800-1000 and the other that maps to 600-800. I can't think of how I would do this.

Thanks so much,
Jordan

That is seriously the strangest thing I ever heard about...

The GUI is for the small fast thing to do.
Why just don't press all button and see?
It can only take a little time.

Or google: pymol + "name of button"
That should give you an answer...

The command line is where the power is.
Use that.

/Troels



2012/3/22 Suhaila Haji Mohd Hussin <bel...@ho...>

>  Hello everyone.
>
> Is there any useful online reference that can be shared for me to learn
> how to add GUI executed by Python script?
>
> I know PyMOL can visualize the protein just by typing in on PyMOL command
> but my supervisor will  grade my group project higher if we can make it
> more interactive where the user can just use a mouse to click button or
> something and less typing on command.
>
> Best regards,
> *Suhaila*
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>