pymol-users — Collaborative support and tips for PyMOL users

RE: [PyMOL] importing pymol modules in a python script

[Warren D. <wa...@de...>]

Alan,

The only sure way to get this to work is to build into a local Python =
interpreter from PyMOL source code using distutils.  Otherwise, you're =
likely better off with "pymol -qc"

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of Alan
> Sent: Thursday, April 20, 2006 5:37 AM
> To: Pymol
> Subject: [PyMOL] importing pymol modules in a python script
>=20
> Hello List!
>=20
> I want a python script likewise:
>=20
> #!/usr/bin/python -O
> import sys, tempfile
> from pymol import editor
> from pymol import cmd
> ....
> ....
>=20
> However, even defining 'export PYTHONPATH=3D/usr/local/pymol/modules'
>=20
> I got this error:
>     from pymol import editor
>   File "/usr/local/pymol/modules/pymol/__init__.py", line 353, in ?
>     import _cmd
> ImportError: No module named _cmd
>=20
> Is there a way to run the python script with pymol stuff=20
> imported or only via 'pymol -c'?
>=20
> Many thanks in advance.
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - Research Associate=20
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>=20
>=20
> -------------------------------------------------------
> Using Tomcat but need to do more? Need to support web=20
> services, security?
> Get stuff done quickly with pre-integrated technology to make=20
> your job easier Download IBM WebSphere Application Server=20
> v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=3Dk&kid=120709&bid&3057&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] ..and rotate

[Noinaj <no...@uk...>]

orla,

If in fact you actually have to move molecules independently using the =
'dirty' method that I have suggested, you will probably need the rotate =
command too, for more flexibility in setting things up. =20

--------------------------------------------
rotate
DESCRIPTION

   "rotate" can be used to rotate the atomic coordinates of a
   molecular object.  Behavior differs depending on whether or not the
   "object" parameter is specified.

   If object is None, then rotate rotates the atomic coordinates
   according to the axes and angle for the selection and state
   provided.  All representation geometries will need to be
   regenerated to reflect the new atomic coordinates.

   If object is set to an object name, then selection and state are
   ignored and instead of translating the atomic coordinates, the
   object's representation display matrix is modified.  This option
   is for use in animations only.

USAGE

   rotate axis, angle [,selection [,state [,camera [,object =
[,origin]]]]]

PYMOL API

   cmd.rotate(list-or-string axis, string selection =3D "all", int state =
=3D 0,
              int camera =3D 1, string object =3D None)

EXAMPLES

   rotate x, 45, pept

NOTES

   if state =3D 0, then only visible state(s) are affected.
   if state =3D -1, then all states are affected.
---------------------------------Cheers,Nickreference:http://pymol.source=
forge.net/newman/ref/S1000comref.html

  ----- Original Message -----=20
  From: Orla O'Sullivan=20
  To: pym...@li...=20
  Sent: Thursday, April 20, 2006 6:56 AM
  Subject: [PyMOL] (no subject)


  =20

  Hi  all

  This probably a very stupid question but its driving me mad. I have =
produced two Raster 3D scences using molscript and have loaded them into =
pymol.=20

  What I want to do is to be able to move them on screen independent of =
each other. Is this possible?

  =20

  Regards

  Orla

  =20

  Dr.Orla O'Sullivan

  Research Officer

  Biotechnology

  =20

  =20

  Moorepark Food Research Centre
  Teagasc

  Moorepark
  Fermoy, Co. Cork
  Ireland

  =20

  Tel:       +353 - (0)25 - 42344

  =20

[PyMOL] pymol transitions recorded as movie?

[Eva V. <eva...@ms...>]

I regularly use the F function keys in PyMol to store
conformations and call them back in a presentation.
I really like the transition effects. Is it possible to record those
transitions as a movie and use them in a Powerpoint presentation?
Thanks in advance,
 - Eva

Fw: [PyMOL] translation

[Noinaj <no...@uk...>]

orla,

not actually had to do this, but I think you can try the translate =
command.

----------------------------------------------
translate
DESCRIPTION

   "translate" can be used to translate the atomic coordinates of a
   molecular object.  Behavior differs depending on whether or not the
   "object" parameter is specified.

   If object is None, then translate translates atomic coordinates
   according to the vector provided for the selection and in the state
   provided.  All representation geometries will need to be
   regenerated to reflect the new atomic coordinates.

   If object is set to an object name, then selection and state are
   ignored and instead of translating the atomic coordinates, the
   object's overall representation display matrix is modified.  This
   option is for use in animations only.

   The "camera" option controls whether the camera or the model's
   axes are used to interpret the translation vector.

USAGE

   translate vector [,selection [,state [,camera [,object ]]]]

PYMOL API

   cmd.translate(list vector, string selection =3D "all", int state =3D =
0,
                 int camera =3D 1, string object =3D None)

EXAMPLES

   translate [1,0,0], name ca

NOTES

   if state =3D 0, then only visible state(s) are affected.
   if state =3D -1, then all states are affected.
------------------------------------------------- This seems like a =
pain, probably a better option somewhere, not sure?  Hope this hopes.  =
Cheers,Nick

  ----- Original Message -----=20
  From: Orla O'Sullivan=20
  To: pym...@li...=20
  Sent: Thursday, April 20, 2006 6:56 AM
  Subject: [PyMOL] (no subject)


  =20

  Hi  all

  This probably a very stupid question but its driving me mad. I have =
produced two Raster 3D scences using molscript and have loaded them into =
pymol.=20

  What I want to do is to be able to move them on screen independent of =
each other. Is this possible?

  =20

  Regards

  Orla

  =20

  Dr.Orla O'Sullivan

  Research Officer

  Biotechnology

  =20

  =20

  Moorepark Food Research Centre
  Teagasc

  Moorepark
  Fermoy, Co. Cork
  Ireland

  =20

  Tel:       +353 - (0)25 - 42344

  =20

Re: [PyMOL] mutations

[Andrew C. <aco...@gm...>]

I follow the method outlined by Nick with one additional step, after
selecting the new residue you can run through a sidechain rotamer
library using the forward arrows at the bottom of the window.  You
also have a choice to use backbone dependant or backbone independant
rotamers.

Andrew

On 4/18/06, Noinaj <no...@uk...> wrote:
>
> Orla,
>
> This is simply, for the most part.  Here is what I do.
>
> Load your *.pdb file.  Then under WIZARD in the menu bar, select
> MUTAGENESIS.  Then pretty much, follow directions.  In the PyMOL VIEWER
> window, it will ask you to ' pick a residue.'  Once you pick a residue,
> select the type of residue you want to mutate to by left clicking on [No
> Mutation] button and holding down (under Mutagenesis).  This brings up a
> list of residues that you can then select from.  Once you select the resi=
due
> you want, hit APPLY, then DONE.  If everything was done correctly, you
> should see your mutated residue.
>
> There are probably other ways to do this, but I hope this helps.  If you
> would like screenshots of the steps, just let me know.
>
>
>
> Cheers,
> Nick
>
>
>
>
> ----- Original Message -----
> From: Orla O'Sullivan
> To: pym...@li...
> Sent: Tuesday, April 18, 2006 11:31 AM
> Subject: [PyMOL] mutations
>
>
>
>
> Hi all
>
> I'm a newbie to Pymol and so far have been very impressed. However I have
> tried to mutate some residues in my structure and have hit a brick wall.
>
> Has anyone done this with pymol and let me know how to do it?
>
>
>
> Regards
>
>
>
> Orla
>
>
>
> Dr.Orla O'Sullivan
>
> Research Officer
>
> Biotechnology
>
>
>
>
>
> Moorepark Food Research Centre
> Teagasc
>
> Moorepark
> Fermoy, Co. Cork
> Ireland
>
>
>
>
> Tel:       +353 - (0)25 - 42344
>
>

[PyMOL] importing pymol modules in a python script

[Alan <ala...@gm...>]

Hello List!

I want a python script likewise:

#!/usr/bin/python -O
import sys, tempfile
from pymol import editor
from pymol import cmd
....
....

However, even defining 'export PYTHONPATH=3D/usr/local/pymol/modules'

I got this error:
    from pymol import editor
  File "/usr/local/pymol/modules/pymol/__init__.py", line 353, in ?
    import _cmd
ImportError: No module named _cmd

Is there a way to run the python script with pymol stuff imported or
only via 'pymol -c'?

Many thanks in advance.
Alan
--
Alan Wilter S. da Silva, D.Sc. - Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.

[PyMOL] (no subject)

[Orla O'S. <Orl...@te...>]

=20

Hi  all

This probably a very stupid question but its driving me mad. I have
produced two Raster 3D scences using molscript and have loaded them into
pymol.=20

What I want to do is to be able to move them on screen independent of
each other. Is this possible?

=20

Regards

Orla

=20

Dr.Orla O'Sullivan

Research Officer

Biotechnology

=20

=20

Moorepark Food Research Centre
Teagasc

Moorepark
Fermoy, Co. Cork
Ireland

=20

Tel:       +353 - (0)25 - 42344

=20

Re: [PyMOL] (small) Pymol feature request--filter for edit settings window

[Jerome P. <j.p...@pa...>]

Hello Michelle,

You can also edit the SetEditor.py file. The file is in the=20
'/usr/lib/python2.3/site-packages/pmg_tk' directory on linux and add the=20
feature. It can be done by adding to small portion of add-on code to the=20
file. If you do so:

Keep a copy of the original file in a safe place !

Here is a part of the modified file:
#######################################
class SetEditor:

   def __init__(self,app):

      self.app =3D app
      self.list =3D []
      for a in  pymol.setting.get_index_list():
         self.list.append("%-30s %s"%(pymol.setting._get_name(a),
                    cmd.get_setting_text(a,'',-1)))

      self.index =3D {}
      c =3D 0
      for a in pymol.setting.get_name_list():
         self.index[a] =3D c
         c =3D c + 1
        =20
      self.dialog =3D Pmw.SelectionDialog(self.app.root,title=3D"Settings",
                          buttons =3D ('Edit', 'Done'),
                                   defaultbutton=3D'Edit',
                          scrolledlist_labelpos=3DN,
                          label_text=3D'Double click to edit',
                          scrolledlist_items =3D self.list,
                          command =3D self.command)
      self.dialog.geometry("500x400")

     # start of the add-on
      interior =3D self.dialog.interior()
      self.filter =3D Pmw.EntryField(interior,
                              labelpos =3D 'w',
                              label_text=3D 'Filter:',
                              validate =3D None,
                              command =3D self.filter_list)
      self.filter.pack()
      # end of the add-on

      self.listbox =3D self.dialog.component('scrolledlist')
      self.listbox.component('listbox').configure(font=3Dapp.my_fw_font)
      self.dialog.protocol('WM_DELETE_WINDOW',self.cancel)
      app.my_show(self.dialog)

  # start of the add-on
   def filter_list(self):
      self.list =3D []
      for a in pymol.setting.get_index_list():
          if self.filter.getvalue() in pymol.setting._get_name(a):
              self.list.append("%-30s %s"%(pymol.setting._get_name(a),
                               cmd.get_setting_text(a,'',-1)))
      self.dialog.setlist(self.list)
      self.dialog.update()
   # end of the add-on

   def cancel(self,event=3DNone):
      self.command(result=3D'Done')
#######################################

This code works fine on my linux box. If you have some problem, don't hesit=
ate=20
to ask me !

Cheers,

Jerome Pansanel

Le Mardi 18 Avril 2006 18:02, Michelle Gill a =E9crit=A0:
> While we're discussing ways to make our favorite program a little
> better, I had an idea I thought I'd throw out there...
>
> While making some figures the other day, I found myself scrolling
> endlessly through the edit settings menu (under Setting --> Edit All) a
> number of times, mostly to locate a relatively small number of settings
> related to ray tracing. This got me thinking about a way to improve
> access to the many wonderful features that have been added to PyMOL.
>
> The solution I came up with is a filter line which could be placed
> directly above the window listing all the settings. Users could then
> type a word, say "ray" or "cartoon", and only the settings containing
> this word would be shown.
>
> The best example of a program containing this feature is the
> "about:config" window in Firefox. When you open a browser and type
> "about:config" instead of an address, a window containing hundreds of
> settings appears. At the top is a filter bar which you can use to pare
> down the number of settings listed below.
>
> I think this would be a great addition to PyMOL and would help users
> familiarize themselves with the many new settings which have been (and
> will be) implemented. :)
>
> Perhaps others have even better solutions to this problem. The use of a
> filter is just the first idea which came to my mind. I think it would be
> relatively easy to implement, although my python programming skills are
> somewhat limited.
>
> Thanks,
> Michelle Gill
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting langua=
ge
> that extends applications into web and mobile media. Attend the live
> webcast and join the prime developer group breaking into this new coding
> territory!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=
=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] (small) Pymol feature request--filter for edit settings window

[Jerome P. <j.p...@pa...>]

Hello Michelle,

You can also edit the SetEditor.py file. The file is in the=20
'/usr/lib/python2.3/site-packages/pmg_tk' directory on linux and add the=20
feature. It can be done by adding to small portion of add-on code to the=20
file. If you do so:

Keep a copy of the original file in a safe place !

Here is a part of the modified file:
#######################################
class SetEditor:

   def __init__(self,app):

      self.app =3D app
      self.list =3D []
      for a in  pymol.setting.get_index_list():
         self.list.append("%-30s %s"%(pymol.setting._get_name(a),
                    cmd.get_setting_text(a,'',-1)))

      self.index =3D {}
      c =3D 0
      for a in pymol.setting.get_name_list():
         self.index[a] =3D c
         c =3D c + 1
        =20
      self.dialog =3D Pmw.SelectionDialog(self.app.root,title=3D"Settings",
                          buttons =3D ('Edit', 'Done'),
                                   defaultbutton=3D'Edit',
                          scrolledlist_labelpos=3DN,
                          label_text=3D'Double click to edit',
                          scrolledlist_items =3D self.list,
                          command =3D self.command)
      self.dialog.geometry("500x400")

     # start of the add-on
      interior =3D self.dialog.interior()
      self.filter =3D Pmw.EntryField(interior,
                              labelpos =3D 'w',
                              label_text=3D 'Filter:',
                              validate =3D None,
                              command =3D self.filter_list)
      self.filter.pack()
      # end of the add-on

      self.listbox =3D self.dialog.component('scrolledlist')
      self.listbox.component('listbox').configure(font=3Dapp.my_fw_font)
      self.dialog.protocol('WM_DELETE_WINDOW',self.cancel)
      app.my_show(self.dialog)

  # start of the add-on
   def filter_list(self):
      self.list =3D []
      for a in pymol.setting.get_index_list():
          if self.filter.getvalue() in pymol.setting._get_name(a):
              self.list.append("%-30s %s"%(pymol.setting._get_name(a),
                               cmd.get_setting_text(a,'',-1)))
      self.dialog.setlist(self.list)
      self.dialog.update()
   # end of the add-on

   def cancel(self,event=3DNone):
      self.command(result=3D'Done')
#######################################

This code works fine on my linux box. If you have some problem, don't hesit=
ate=20
to ask me !

Cheers,

Jerome Pansanel

Le Mardi 18 Avril 2006 18:02, Michelle Gill a =E9crit=A0:
> While we're discussing ways to make our favorite program a little
> better, I had an idea I thought I'd throw out there...
>
> While making some figures the other day, I found myself scrolling
> endlessly through the edit settings menu (under Setting --> Edit All) a
> number of times, mostly to locate a relatively small number of settings
> related to ray tracing. This got me thinking about a way to improve
> access to the many wonderful features that have been added to PyMOL.
>
> The solution I came up with is a filter line which could be placed
> directly above the window listing all the settings. Users could then
> type a word, say "ray" or "cartoon", and only the settings containing
> this word would be shown.
>
> The best example of a program containing this feature is the
> "about:config" window in Firefox. When you open a browser and type
> "about:config" instead of an address, a window containing hundreds of
> settings appears. At the top is a filter bar which you can use to pare
> down the number of settings listed below.
>
> I think this would be a great addition to PyMOL and would help users
> familiarize themselves with the many new settings which have been (and
> will be) implemented. :)
>
> Perhaps others have even better solutions to this problem. The use of a
> filter is just the first idea which came to my mind. I think it would be
> relatively easy to implement, although my python programming skills are
> somewhat limited.
>
> Thanks,
> Michelle Gill
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting langua=
ge
> that extends applications into web and mobile media. Attend the live
> webcast and join the prime developer group breaking into this new coding
> territory!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=
=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] (small) Pymol feature request--filter for edit settings window

[<an...@bi...>]

Hey Michelle,

Ezequiel Panepucci wrote grepset, a little script that allows you to do=20
exactly what you want and even more.  No need even to open the edit=20
settings menu, just type 'grepset ray', and you're cruising.

Get grepset from http://www.pymolwiki.org/index.php/Grepset and put it=20
into your .pymolrc file as 'run /path/to/grepset.py'.  Life is good.


Andreas


Michelle Gill wrote:
> While we're discussing ways to make our favorite program a little=20
> better, I had an idea I thought I'd throw out there...
>=20
> While making some figures the other day, I found myself scrolling=20
> endlessly through the edit settings menu (under Setting --> Edit All) a=
=20
> number of times, mostly to locate a relatively small number of settings=
=20
> related to ray tracing. This got me thinking about a way to improve=20
> access to the many wonderful features that have been added to PyMOL.
>=20
> The solution I came up with is a filter line which could be placed=20
> directly above the window listing all the settings. Users could then=20
> type a word, say "ray" or "cartoon", and only the settings containing=20
> this word would be shown.
>=20
> The best example of a program containing this feature is the=20
> "about:config" window in Firefox. When you open a browser and type=20
> "about:config" instead of an address, a window containing hundreds of=20
> settings appears. At the top is a filter bar which you can use to pare=20
> down the number of settings listed below.
>=20
> I think this would be a great addition to PyMOL and would help users=20
> familiarize themselves with the many new settings which have been (and=20
> will be) implemented. :)
>=20
> Perhaps others have even better solutions to this problem. The use of a=
=20
> filter is just the first idea which came to my mind. I think it would b=
e=20
> relatively easy to implement, although my python programming skills are=
=20
> somewhat limited.
>=20
> Thanks,
> Michelle Gill
>=20

--=20
    -->       Andreas F=F6rster       <--
  8 rue Doudart de Lagr=E9e, 38000 Grenoble
++33.(0)438.866201 and ++33.(0)456.452000
       www.biochem.utah.edu/~andreas
          docandreas.blogspot.com

RE: [PyMOL] align and iterate residues

[Warren D. <wa...@de...>]

Andrea,

This feature will be present with alignment visualization, but that is =
not quite ready yet...

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Andrea Spitaleri
> Sent: Wednesday, April 19, 2006 5:04 AM
> To: pymol-users
> Subject: [PyMOL] align and iterate residues
>=20
> Hi all,
> I found very nice the align command in order to align domains=20
> within huge complex. However, I was wondering whether is it=20
> possible to iterate on the superimposed structure in order to=20
> know "which with wich" residues. Creating the object, I=20
> cannot iterate on it.
> Thanks for any suggestion
>=20
> Regards
>=20
> andrea
> --
> "La conoscenza libera il genere umano dalla superstizione"
> J. Watson
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking=20
> scripting language that extends applications into web and=20
> mobile media. Attend the live webcast and join the prime=20
> developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=3Dk&kid=110944&bid$1720&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] a scaling question

[Peter A. M. <pa...@co...>]

Fei,

The easiest way would be to use get_view/set_view.
1. Move your first frame pdb around until you're happy with the view
2. type get_view (pymol viewer window, or pymol gui window), and save the
output in a new text file (I'd call it view.pml, but that's just me)
3. Load all of your frames in a script (which you're probably doing
already), change "load frame2.pdb" to load frame2.pdb ; @view.pml" for all
of your frames (or change whatever loop structure you're using).

This way all of your frames will be in the same scale, as well as
orientation (which may not be what you're looking for).  If you only want
to control scale (not orientation), then you could probably work something
up that only takes the scale parameters out of the orientation matrix.

Hope this helps,

Pete

> Hi!:
> I met a scaling problem.
> I created many pdb files along one trajectory of DNA movement. I loaded
each pdb file in pymol to create a picture, that is, one frame of the
trajectory. Pymol shows each molecule in an optimal size automatically
according the general shape of the molecular. The shape of the molecule
along trajectory kept changing so that the size of the molecule also
kept
> changing. When I connected all the time frames together, I saw the funny
effect that the molecule was jumping back and forth.
> How can I put the molecule in the different time frames in exactly the
same size?
> Thanks!
> Fei
>
>
>
>
>
> -------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services,
security?
> Get stuff done quickly with pre-integrated technology to make your job
easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache
Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
_______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

[PyMOL] Pymol / C

[<cmm...@ya...>]

Hi!

I must develop a program in language C, in which I
have to execute “Pymol”
and to invocate functions as “select…” or “translate…”
inside my program.

I am writing to enquire how can I do it, 
how can I invocate the Pymol’s functions.


Thanks!


		
______________________________________________ 
LLama Gratis a cualquier PC del Mundo. 
Llamadas a fijos y móviles desde 1 céntimo por minuto. 
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[PyMOL] a scaling question

[Fei Xu <fe...@ru...>]

Hi!:
I met a scaling problem.
I created many pdb files along one trajectory of DNA movement. I loaded
each pdb file in pymol to create a picture, that is, one frame of the
trajectory. Pymol shows each molecule in an optimal size automatically
according the general shape of the molecular. The shape of the molecule
along trajectory kept changing so that the size of the molecule also kept
changing. When I connected all the time frames together, I saw the funny
effect that the molecule was jumping back and forth.
How can I put the molecule in the different time frames in exactly the
same size?
Thanks!
Fei

[PyMOL] align and iterate residues

[Andrea S. <and...@gm...>]

Hi all,
I found very nice the align command in order to align domains within
huge complex. However, I was wondering whether is it possible to
iterate on the superimposed structure in order to know "which with
wich" residues. Creating the object, I cannot iterate on it.
Thanks for any suggestion

Regards

andrea
--
"La conoscenza libera il genere umano dalla superstizione"
J. Watson

Re: [PyMOL] RE: povray image mapping and default pigments

[Tsjerk W. <ts...@gm...>]

Hi,

Actually, one of the first of these images I made was of conotoxin floating
above a see. Will that do? I'd still have to add the sunset though ;) O, an=
d
the checkered beach...

In regards the problem of Seth, it's good you've solved it. It is possible
though to remove all statements about textures from a mesh2 object. You hav=
e
to remove both the texture_list as well as the references to the textures.
If you don't know what I'm talking about, you can check out the povray
manual on mesh2. Besides, you may be better off using statements like

union { #include "moleculedef.inc" pigment {image_map{ " mypicturehere.gif"
}} }

rather than changing the #default for that. Especially handy if you can fin=
d
a snowboarder object you want to merge with your kinase piste...

By the way, I may try to write a script to process the mesh2 file from Pymo=
l
to strip out texture statements (and add them as #declares) if I can find
some time. Also, it would be so nice to have a tidied up mesh2 file, rather
than an endless set of triangles. mesh2 can be so much better (smaller, mor=
e
efficient, easier to handle).

Cheers,

Tsjerk

On 4/19/06, Thomas Stout <ts...@ex...> wrote:
>
>
>
> I'm glad you solved your problem, but more importantly when are we going
> to get to see this picture of an easter bunny on some wood-textured
> rendition of a half-submerged albumin glowing softly in the warm lights o=
f a
> double sunset over an infinite lake lapping at the shores of a checkered
> beach???
>
> :)
>
> -Tom
>
>
> -----Original Message-----
> From: pym...@li... on behalf of Seth Harris
> Sent: Tue 4/18/2006 2:45 PM
> To: pym...@li...
> Subject: [PyMOL] RE: povray image mapping and default pigments
>
> To answer my own question...instead of entirely taking out the
> pigment{blah
> blah blah} statements from the texture_lists in the povray input as used
> to
> work, I found that in this case replacing them with "pigment {}"
> statements
> was still a permissible syntax and also allowed a #default pigment
> declaration in the header file to override the molecular scene
> descriptions.
>
> If you have no idea what I'm talking about, it's probably for the best.
>
> Funny how often just describing your problem to someone else allows you t=
o
> lay it out logically enough to lead you to a solution...thanks for
> listening!
>
> -Seth
>
> ---------- Forwarded message ----------
> From: Seth Harris <se...@gm...>
> Date: Apr 18, 2006 2:18 PM
> Subject: povray image mapping and default pigments
> To: pym...@li...
>
>
>  This is for the povray gurus out there...
>
> Occasionally I muck around with the time-consuming practice of trying to
> map
> pictures onto molecular surfaces with povray.
>
> I had this working to some extent, but something has changed (I think wit=
h
> the povray file format produced by pymol & make_pov where now there are
> fancy texture_list texture and pigment statements, rather than simple
> "pigment" ones.)
>
> In the past, I set it up so that the povray file has a header (cameras,
> lights, etc.) separate from the molecular scene description. Then I would
> usually edit the header to apply some #default texture or pigment to use
> the
> povray parlance. So the approach I used to use was to strip out all the
> pigment {} statements from the molecular scene descriptor povray input
> with
> a perl script, and then use the #default pigment {image_map{ "
> mypicturehere.gif" }} syntax in the header to map the image on to the
> surface...the practical uses of having a picture of someone, say,
> snowboarding down a mountain mapped onto the surface of some kinase are
> just
> endless. But that aside, the problem now is that these newer texture_list
> statements aren't so amenable to this global pigment removal thing, and I
> haven't quite figured out how best to get around this. (Couldn't remove
> them
> entirely and putting in the image_map pigment thing didn't seem to work,
> although maybe I just didn't get the right combination of open and closed
> brackets {?}}})
>
> Anyone have any experiences along these lines? As near as I can tell,
> there
> was some switch in smooth triangle definitions with Povray 3.5 which was
> capitalized on by some pymol 0.98 edition. Perhaps I have to go back to a=
n
> old archived version of pymol? Or, more sensibly, perhaps I should
> recognize
> that pictures of easter bunnies or whatever don't belong on some
> wood-textured rendition of a half-submerged albumin, glowing softly in th=
e
> warm light(s) of a double sunset over an infinite lake lapping at the
> shores
> of a checkered beach. But for some reason journal editors seem to enjoy
> this.
>
> Thanks,
>  Seth
>
>  This email (including any attachments) may contain material
> that is confidential and privileged and is for the sole use of
> the intended recipient. Any review, reliance or distribution by
> others or forwarding without express permission is strictly
> prohibited. If you are not the intended recipient, please
> contact the sender and delete all copies.
>
>
> Exelixis, Inc. reserves the right, to the extent and under
> circumstances permitted by applicable law, to retain, monitor
> and intercept e-mail messages to and from its systems.
>
>


--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

RE: [PyMOL] RE: povray image mapping and default pigments

[Thomas S. <ts...@ex...>]

I'm glad you solved your problem, but more importantly when are we going =
to get to see this picture of an easter bunny on some wood-textured =
rendition of a half-submerged albumin glowing softly in the warm lights =
of a double sunset over an infinite lake lapping at the shores of a =
checkered beach???

:)

-Tom

-----Original Message-----
From: pym...@li... on behalf of Seth Harris
Sent: Tue 4/18/2006 2:45 PM
To: pym...@li...
Subject: [PyMOL] RE: povray image mapping and default pigments
=20
To answer my own question...instead of entirely taking out the =
pigment{blah
blah blah} statements from the texture_lists in the povray input as used =
to
work, I found that in this case replacing them with "pigment {}" =
statements
was still a permissible syntax and also allowed a #default pigment
declaration in the header file to override the molecular scene =
descriptions.

If you have no idea what I'm talking about, it's probably for the best.

Funny how often just describing your problem to someone else allows you =
to
lay it out logically enough to lead you to a solution...thanks for
listening!

-Seth

---------- Forwarded message ----------
From: Seth Harris <se...@gm...>
Date: Apr 18, 2006 2:18 PM
Subject: povray image mapping and default pigments
To: pym...@li...


 This is for the povray gurus out there...

Occasionally I muck around with the time-consuming practice of trying to =
map
pictures onto molecular surfaces with povray.

I had this working to some extent, but something has changed (I think =
with
the povray file format produced by pymol & make_pov where now there are
fancy texture_list texture and pigment statements, rather than simple
"pigment" ones.)

In the past, I set it up so that the povray file has a header (cameras,
lights, etc.) separate from the molecular scene description. Then I =
would
usually edit the header to apply some #default texture or pigment to use =
the
povray parlance. So the approach I used to use was to strip out all the
pigment {} statements from the molecular scene descriptor povray input =
with
a perl script, and then use the #default pigment {image_map{ "
mypicturehere.gif" }} syntax in the header to map the image on to the
surface...the practical uses of having a picture of someone, say,
snowboarding down a mountain mapped onto the surface of some kinase are =
just
endless. But that aside, the problem now is that these newer =
texture_list
statements aren't so amenable to this global pigment removal thing, and =
I
haven't quite figured out how best to get around this. (Couldn't remove =
them
entirely and putting in the image_map pigment thing didn't seem to work,
although maybe I just didn't get the right combination of open and =
closed
brackets {?}}})

Anyone have any experiences along these lines? As near as I can tell, =
there
was some switch in smooth triangle definitions with Povray 3.5 which was
capitalized on by some pymol 0.98 edition. Perhaps I have to go back to =
an
old archived version of pymol? Or, more sensibly, perhaps I should =
recognize
that pictures of easter bunnies or whatever don't belong on some
wood-textured rendition of a half-submerged albumin, glowing softly in =
the
warm light(s) of a double sunset over an infinite lake lapping at the =
shores
of a checkered beach. But for some reason journal editors seem to enjoy
this.

Thanks,
 Seth



This email (including any attachments) may contain material
that is confidential and privileged and is for the sole use of
the intended recipient. Any review, reliance or distribution by
others or forwarding without express permission is strictly
prohibited. If you are not the intended recipient, please
contact the sender and delete all copies.


Exelixis, Inc. reserves the right, to the extent and under
circumstances permitted by applicable law, to retain, monitor
and intercept e-mail messages to and from its systems.

[PyMOL] RE: povray image mapping and default pigments

[Seth H. <se...@gm...>]

To answer my own question...instead of entirely taking out the pigment{blah
blah blah} statements from the texture_lists in the povray input as used to
work, I found that in this case replacing them with "pigment {}" statements
was still a permissible syntax and also allowed a #default pigment
declaration in the header file to override the molecular scene descriptions=
.

If you have no idea what I'm talking about, it's probably for the best.

Funny how often just describing your problem to someone else allows you to
lay it out logically enough to lead you to a solution...thanks for
listening!

-Seth

---------- Forwarded message ----------
From: Seth Harris <se...@gm...>
Date: Apr 18, 2006 2:18 PM
Subject: povray image mapping and default pigments
To: pym...@li...


 This is for the povray gurus out there...

Occasionally I muck around with the time-consuming practice of trying to ma=
p
pictures onto molecular surfaces with povray.

I had this working to some extent, but something has changed (I think with
the povray file format produced by pymol & make_pov where now there are
fancy texture_list texture and pigment statements, rather than simple
"pigment" ones.)

In the past, I set it up so that the povray file has a header (cameras,
lights, etc.) separate from the molecular scene description. Then I would
usually edit the header to apply some #default texture or pigment to use th=
e
povray parlance. So the approach I used to use was to strip out all the
pigment {} statements from the molecular scene descriptor povray input with
a perl script, and then use the #default pigment {image_map{ "
mypicturehere.gif" }} syntax in the header to map the image on to the
surface...the practical uses of having a picture of someone, say,
snowboarding down a mountain mapped onto the surface of some kinase are jus=
t
endless. But that aside, the problem now is that these newer texture_list
statements aren't so amenable to this global pigment removal thing, and I
haven't quite figured out how best to get around this. (Couldn't remove the=
m
entirely and putting in the image_map pigment thing didn't seem to work,
although maybe I just didn't get the right combination of open and closed
brackets {?}}})

Anyone have any experiences along these lines? As near as I can tell, there
was some switch in smooth triangle definitions with Povray 3.5 which was
capitalized on by some pymol 0.98 edition. Perhaps I have to go back to an
old archived version of pymol? Or, more sensibly, perhaps I should recogniz=
e
that pictures of easter bunnies or whatever don't belong on some
wood-textured rendition of a half-submerged albumin, glowing softly in the
warm light(s) of a double sunset over an infinite lake lapping at the shore=
s
of a checkered beach. But for some reason journal editors seem to enjoy
this.

Thanks,
 Seth

[PyMOL] povray image mapping and default pigments

[Seth H. <se...@gm...>]

This is for the povray gurus out there...

Occasionally I muck around with the time-consuming practice of trying to ma=
p
pictures onto molecular surfaces with povray.

I had this working to some extent, but something has changed (I think with
the povray file format produced by pymol & make_pov where now there are
fancy texture_list texture and pigment statements, rather than simple
"pigment" ones.)

In the past, I set it up so that the povray file has a header (cameras,
lights, etc.) separate from the molecular scene description. Then I would
usually edit the header to apply some #default texture or pigment to use th=
e
povray parlance. So the approach I used to use was to strip out all the
pigment {} statements from the molecular scene descriptor povray input with
a perl script, and then use the #default pigment {image_map{ "
mypicturehere.gif" }} syntax in the header to map the image on to the
surface...the practical uses of having a picture of someone, say,
snowboarding down a mountain mapped onto the surface of some kinase are jus=
t
endless. But that aside, the problem now is that these newer texture_list
statements aren't so amenable to this global pigment removal thing, and I
haven't quite figured out how best to get around this. (Couldn't remove the=
m
entirely and putting in the image_map pigment thing didn't seem to work,
although maybe I just didn't get the right combination of open and closed
brackets {?}}})

Anyone have any experiences along these lines? As near as I can tell, there
was some switch in smooth triangle definitions with Povray 3.5 which was
capitalized on by some pymol 0.98 edition. Perhaps I have to go back to an
old archived version of pymol? Or, more sensibly, perhaps I should recogniz=
e
that pictures of easter bunnies or whatever don't belong on some
wood-textured rendition of a half-submerged albumin, glowing softly in the
warm light(s) of a double sunset over an infinite lake lapping at the shore=
s
of a checkered beach. But for some reason journal editors seem to enjoy
this.

Thanks,
Seth

[PyMOL] RE: filter for edit settings window

[Seth H. <se...@gm...>]

Hi Michelle,

In case no one's mentioned it yet, Zac Panepucci has contributed a
grepset.py script which, after being run, allows you to type "grepset xxxxx=
"
to see all settings (and their values) associated with whatever xxxxx is.
It's not directly integrated into the pymol distribution but pretty tidily
achieves what you describe. More info and the script itself is on the wiki:

http://www.pymolwiki.org/index.php/Grepset


Cheers,
Seth (on behalf of Zac and his useful scripts)

Re: [PyMOL] another question about ca trace model.

[Geng T. <gen...@ho...>]

Hi, Noinaj:
Thanks for your suggestion. I feel it is not the assignment problem. I tried 
using "cartoon tube" to show the 2nd structure and the strand part can 
showed up. Then I painted the molecule according to the secondary structure 
by using util.cbss("morphy_01","red","yellow","green") and the strand is 
color as "yellow" correctly in the cartoon tube mode. Then I tried another 
thing, I copy-pasted the second structure information from the ca trace pdb 
to my formal all stoms pdb, the strand showed up correctly. This means these 
information are correct. So I guess under the default "cartoon automatic" 
mode, pymol can't draw arrow for the strand residues which do not have the 
coordinates of N, C, O written in the PDB file. This might be a default 
setting of pymol I can't find to turn off or just an internal problem for 
"cartoon automatic" mode.
Thank you again.
Tiger










>From: "Noinaj" <no...@uk...>
>To: "Geng Tian" <gen...@ho...>,<pym...@li...>
>Subject: Re: [PyMOL] another question about ca trace model.
>Date: Tue, 18 Apr 2006 11:06:49 -0400
>
>Tiger,
>
>Unfortunately I don't have much experience with this procedure.  But one 
>thing came to mind, you can manually assign secondary structure within 
>DEEPVIEW/SWISS PDB Viewer [EDIT].  Not sure how many pdb files you have 
>generated for the morph, but if nothing else works, you could try manually 
>assigning secondary structures and see how that works out.  Yep, a huge 
>pain in the buttocks I know, but it should work, in theory.
>
>Best of Luck.
>
>
>Cheers,
>Nick
>
>
>
>----- Original Message ----- From: "Geng Tian" <gen...@ho...>
>To: <pym...@li...>
>Sent: Tuesday, April 18, 2006 6:24 AM
>Subject: [PyMOL] another question about ca trace model.
>
>
>>Hi, there:
>>I am trying to make a movie following the intruction at 
>>http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html
>>From Lsqman, I got a serial of PDB files morphing between two 
>>conformations. These PDB files contain only alpha carbon and non-hydrogen 
>>side-chain atoms. Then I used DSSP to include the secondary structure 
>>information ito the PDB files. In the pymol, after set cartoon_trace, 1 
>>the helix and loop showed up nicely. But all the strands are missing. I 
>>tried several setting about cartoon but just can't get them out. Do you 
>>have any idea how to solve this problem.
>>Thank you.
>>Tiger
>>
>>_________________________________________________________________
>>Express yourself instantly with MSN Messenger! Download today - it's FREE! 
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>>
>>
>>-------------------------------------------------------
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>>that extends applications into web and mobile media. Attend the live 
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>>_______________________________________________
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>>
>
>
>
>-------------------------------------------------------
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Re: [PyMOL] isomesh for electrostatic potential

[Michael G. L. <ml...@um...>]

On Tue, 18 Apr 2006, Chun Tang wrote:

> Dear PyMoler,
>
> In the pymol apbs tool, there is an option to show the
> negative/positive isosurface (not the molecular surface) upon loading
> an electrostatic map. My question is if there is a way to show the
> electrostatic potential surface as mesh instead of solid surface, also
> if it is possible to show the potential as a series of contours. Thank
> you.
>
> Chun

The plugin doesn't allow you to show a mesh, but it would be a good idea 
to build that in.  You can do it from the command line with the isomesh 
command.  If you're using the plugin to do everything, you can do 
something like this:

isomesh iso_pos_mesh, apbs_map, 0.5
color blue, iso_pos_mesh

If you're not using the plugin, change 'apbs_map' to whatever your map is 
called.

the idea of showing a series of contours is probably a good one.  I'm not 
sure how to make a nice GUI interface for it, though.

I recently switched to a Mac.  It was broken for quite a while, but I 
think I finally got things working properly this weekend.  I'll try to put 
out a new version of the plugin soon.  At the moment, here's what I'm 
planning to add:

  - the ability to use pdb2pqr to generate pqr files
  - the ability to display the APBS version
  - the ability to display isomeshes in addition to isosurfaces

any other big suggestions?

-michael

--
www.umich.edu/~mlerner |                        _  |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
-Torrence,  Bring It On|                       / \ | mlerner@umich

>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting language
> that extends applications into web and mobile media. Attend the live webcast
> and join the prime developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>

[PyMOL] isomesh for electrostatic potential

[Chun T. <tcs...@gm...>]

Dear PyMoler,

In the pymol apbs tool, there is an option to show the
negative/positive isosurface (not the molecular surface) upon loading
an electrostatic map. My question is if there is a way to show the
electrostatic potential surface as mesh instead of solid surface, also
if it is possible to show the potential as a series of contours. Thank
you.

Chun

RE: [PyMOL] anybody have experience with the "get_area" command?

[Warren D. <wa...@de...>]

Hi Tom,

There are some pitfalls with get_area that have led me to recommend =
against its use until we can prepare some more comprehensive =
documentation and examples for its use.  If you have other tools for =
measuring areas, then I recommend using them instead.  If not, then here =
is a partial example:

# load components separately

load my_ligand.pdb
load my_target.pdb

# get hydrogens onto everything (NOTE: must have valid valences on the =
ligand...)

h_add

# make sure all atoms within an object occlude one another

flag ignore, none

# use solvent-accessible surface with high sampling density

set dot_solvent, 1
set dot_density, 3

# measure the components individually

ligand_area=3Dcmd.get_area("my_ligand")
target_area=3Dcmd.get_area("my_target")

# create the complex

create my_complex, my_ligand my_target

# measure the complex

complex_area=3Dcmd.get_area("my_complex")

# now print results

print ligand_area
print target_area
print complex_area
print (ligand_area + target_area) - complex_area

Cheers,
Warren

BTW: thanks for your suggestions about quit/close warnings!


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Thomas Stout
> Sent: Tuesday, April 18, 2006 10:36 AM
> To: pym...@li...
> Subject: [PyMOL] anybody have experience with the "get_area" command?
>=20
> =20
> Does it work?
> =20
> We're running version 0.99rc6 on both windoze and linux=20
> (RHEL,WS4) and the "get_area" command returns nothing (no=20
> error, no value).
> =20
> I've tried this with a number of situations, including=20
> loading a single object with a single protein chain and=20
> issuing "get_area all", "get_area n+c", "get_area /obj01" et=20
> cetera following the examples listed in Warren's former=20
> e-mail and subsequently replicated on the Wiki.
> =20
> "get_area ?" lists the syntax as "get_area [ selection [,=20
> state [, load_b [, quiet ]]]]", but "help get_area" does not help....
> =20
> Thanks for any suggestions,
> Tom
>=20
>=20
> This email (including any attachments) may contain material=20
> that is confidential and privileged and is for the sole use=20
> of the intended recipient. Any review, reliance or=20
> distribution by others or forwarding without express=20
> permission is strictly prohibited. If you are not the=20
> intended recipient, please contact the sender and delete all copies.
>=20
>=20
> Exelixis, Inc. reserves the right, to the extent and under=20
> circumstances permitted by applicable law, to retain, monitor=20
> and intercept e-mail messages to and from its systems.
>=20
>=20
>=20

[PyMOL] anybody have experience with the "get_area" command?

[Thomas S. <ts...@ex...>]

=20
Does it work?
=20
We're running version 0.99rc6 on both windoze and linux (RHEL,WS4) and
the "get_area" command returns nothing (no error, no value).
=20
I've tried this with a number of situations, including loading a single
object with a single protein chain and issuing "get_area all", "get_area
n+c", "get_area /obj01" et cetera following the examples listed in
Warren's former e-mail and subsequently replicated on the Wiki.
=20
"get_area ?" lists the syntax as "get_area [ selection [, state [,
load_b [, quiet ]]]]", but "help get_area" does not help....
=20
Thanks for any suggestions,
Tom


This email (including any attachments) may contain material
that is confidential and privileged and is for the sole use of
the intended recipient. Any review, reliance or distribution by
others or forwarding without express permission is strictly
prohibited. If you are not the intended recipient, please
contact the sender and delete all copies.


Exelixis, Inc. reserves the right, to the extent and under
circumstances permitted by applicable law, to retain, monitor
and intercept e-mail messages to and from its systems.