pymol-users Mailing List for PyMOL Molecular Graphics System

[i'm sending again; it seems the pymol sourceforge list was down when i 
tried to send this]

Hi All-

In reference to this post:
http://sourceforge.net/mailarchive/message.php?msg_id=6977122

When I gave PyMOL this command, I got the following error:
Error: unknown setting 'cartoon_transparency'.

Is this setting only available on newer versions of PyMOL?  If so, 
anyone working on a *new* Fink version?!?

[ edit: just found out this is only available on 0.91 & greater on the 
changes page -- feel free to reply about the Fink version; I believe 
many are waiting for this to be released! ]

I would simply use the native Apple PyMOL released, but a) I prefer the 
interface of the 'Fink' version, unless there's a way to customize the 
menu interface and b) often, when I minimize/maximize the PyMOL 
interface to the Dock a few times, the native PyMOL crashes -- has 
anyone else experienced this?  I have plenty of free and total memory 
(1.5GB total), so I don't think it's a memory issue.

Also, I could not find any reference to 'cartoon_transparency' on the 
online man pages -- presently, are there updated man pages available 
(to subscribers only?) that include the new settings/etc.?

Many thanks for the help,
Doug

Hi Yunfeng Hu,

You can try the following (which has surely been on the list before :) ):

show sticks, (byres ((protA within 3.5 of protB) or (protB within 3.5 of 
protA)))

You might want to make sure that you only have hydrogen bonds by adding 
additional terms.

Hope it helps. Cheers,

Tsjerk

Yunfeng Hu wrote:

>Hi, I have the following task to do and wonder if anyone can show a simple 
>way to do it. I want to show the residues forming intermolecular hydrogen 
>bonds between two proteins. 
>
>dist protein A, protein B, 3.5
>
>Then I want to show those residues that form hydrogen bonds with each 
>other. How do I chose those residues? Sorry if this question was already 
>anwsered. Thanks. By the way I am using the latest version for OS X.3
>
>Yunfeng
>
>
>
>
>-------------------------------------------------------
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-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Tsjerk A. Wassenaar, M.Sc.
-- :) 	Molecular Dynamics Group
-- :) 	Dept. of Biophysical Chemistry
-- :) 	University of Groningen
-- :) 	Nijenborgh 4
-- :) 	9747 AG Groningen
-- :) 	The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-- :) 	Copy me into your ~/.signature to help me spread!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Hi All-

In reference to this post:
http://sourceforge.net/mailarchive/message.php?msg_id=6977122

When I gave PyMOL this command, I got the following error:
Error: unknown setting 'cartoon_transparency'.

Is this setting only available on newer versions of PyMOL?  If so, 
anyone working on a *new* Fink version?!?

[ edit: just found out this is only available on 0.91 & greater on the 
changes page -- feel free to reply about the Fink version; I believe 
many are waiting for this to be released! ]

I would simply use the native Apple PyMOL released, but a) I prefer the 
interface of the 'Fink' version, unless there's a way to customize the 
menu interface and b) often, when I minimize/maximize the PyMOL 
interface to the Dock a few times, the native PyMOL crashes -- has 
anyone else experienced this?  I have plenty of free and total memory 
(1.5GB total), so I don't think it's a memory issue.

Also, I could not find any reference to 'cartoon_transparency' on the 
online man pages -- presently, are there updated man pages available 
(to subscribers only?) that include the new settings/etc.?

Many thanks for the help,
Doug

[trying a third time]

Hi All-

In reference to this post:
http://sourceforge.net/mailarchive/message.php?msg_id=6977122

When I gave PyMOL this command, I got the following error:
Error: unknown setting 'cartoon_transparency'.

Is this setting only available on newer versions of PyMOL?  If so, 
anyone working on a *new* Fink version?!?

[ edit: just found out this is only available on 0.91 & greater on the 
changes page -- feel free to reply about the Fink version; I believe 
many are waiting for this to be released! ]

I would simply use the native Apple PyMOL released, but a) I prefer the 
interface of the 'Fink' version, unless there's a way to customize the 
menu interface and b) often, when I minimize/maximize the PyMOL 
interface to the Dock a few times, the native PyMOL crashes -- has 
anyone else experienced this?  I have plenty of free and total memory 
(1.5GB total), so I don't think it's a memory issue.

Also, I could not find any reference to 'cartoon_transparency' on the 
online man pages -- presently, are there updated man pages available 
(to subscribers only?) that include the new settings/etc.?

Many thanks for the help,
Doug

Hi Yunfeng,

I ran across the following link in the archives that might get you started.

http://sourceforge.net/mailarchive/message.php?msg_id=6905613

Best,
Morri

On Wed, 28 Jan 2004, Yunfeng Hu wrote:

> Hi, I have the following task to do and wonder if anyone can show a simple
> way to do it. I want to show the residues forming intermolecular hydrogen
> bonds between two proteins.
>
> dist protein A, protein B, 3.5
>
> Then I want to show those residues that form hydrogen bonds with each
> other. How do I chose those residues? Sorry if this question was already
> anwsered. Thanks. By the way I am using the latest version for OS X.3
>
> Yunfeng
>
>
>
>
> -------------------------------------------------------
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

I am new to python and trying to write a small GUI which is called
from within pymol.  I am trying an example script out of my book,
which uses a Tkinter Variable within a Label & and Entry object.
The script works perfectly on its own, but when I try to run
the script within pymol, the variable does not get set.  This has
me baffled (and frustrated), and clearly there is some
relationship which I don't understand.   Please could some
experienced pymol programmer offer me some help.

To run this script on its own I type:
python leigh.py  (and I uncomment the "mainloop" line)
From within python I run this script by typing:
run leigh.py

In the first instance (without pymol), the label & entry get set on
initialisation to "hello". From within pymol, they are blank,
and typing in the entry field does set the label, but the values are not
passed on to the Tkinter variable.  It is as though I have
created 2 separate variables, one which is used by the Label & Entry,
and one which I have initialized to "hello".

Here is my small script, thanks in advance for any help.  Leigh Willard.

from Tkinter import *

class leigh:
    def __init__(self):
        root = Tk()
        frame = Frame(root)
        frame.pack()
        self.tv = StringVar()
        self.tv.set('hello')
        Label(frame, textvariable=self.tv).pack()
        self.entry = Entry(frame, textvariable=self.tv)
        self.entry.pack()

        print "variable name = ", self.entry.cget('textvariable')
        print self.tv.get()

me = leigh()
# uncomment the next line if running without pymol.  ie. python script.py
# mainloop()

Hi, I have the following task to do and wonder if anyone can show a simple 
way to do it. I want to show the residues forming intermolecular hydrogen 
bonds between two proteins. 

dist protein A, protein B, 3.5

Then I want to show those residues that form hydrogen bonds with each 
other. How do I chose those residues? Sorry if this question was already 
anwsered. Thanks. By the way I am using the latest version for OS X.3

Yunfeng

Chris,

	PyMOL only support one kind stereo of stereo: OpenGL
quad-buffered-stereo.  It's unclear to me from your message that your
Octane can support QBS.  Sybyl, I believe, can run using top/bottom
stereo, so I am not sure that is a reliable indicator...

PyMOL usually autodetects QBS on X11-based hardware, if it is available.
If "stereo quadbuffer" doesn't work then you may be out of luck on that
system.

(FYI: On the Indigo2's, if you had a lower-end graphics option, it was
necessary to change the video mode to a lower resolution in order to get
QBS...perhaps the same is true of your system?)

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154=20
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Christian Rummey
> Sent: Wednesday, January 28, 2004 4:42 AM
> To: pym...@li...
> Subject: [PyMOL] SGI Crystal Eyes Problem
>=20
>=20
> Dear all,
>=20
> I'd like to use pymol with our sgi shutter glasses, which are standard
> ones
> on an sgi octane R12000, working fine e.g. with Tripos SYBYL.
>=20
> when I try to use them with pymol, the default stereo setting isn't
> quad-buffer (which means it is not available?), and if I manually set
the
> stereo mode
> to 1 (=3D quad buffer) I can see the correct picture (objects are =
drawn
> 'twice'), but the display doesn't enter stereo mode and the
transmitter
> accordingly
> do not work.
>=20
> Is there something I miss? - that needs to be configured before quad
> buffer
> works on an sgi?
>=20
> any hints ary highly appreciated!
>=20
> thanks,
> christian
>=20
> --
> Christian Rummey
>=20
> --
> +++ GMX - die erste Adresse f=FCr Mail, Message, More +++
> Bis 31.1.: TopMail + Digicam f=FCr nur 29 EUR =
http://www.gmx.net/topmail
>=20
>=20
>=20
> -------------------------------------------------------
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Dear all,

I'd like to use pymol with our sgi shutter glasses, which are standard ones
on an sgi octane R12000, working fine e.g. with Tripos SYBYL.

when I try to use them with pymol, the default stereo setting isn't
quad-buffer (which means it is not available?), and if I manually set the stereo mode
to 1 (= quad buffer) I can see the correct picture (objects are drawn
'twice'), but the display doesn't enter stereo mode and the transmitter accordingly
do not work.

Is there something I miss? - that needs to be configured before quad buffer
works on an sgi?

any hints ary highly appreciated!

thanks,
christian

--
Christian Rummey

-- 
+++ GMX - die erste Adresse für Mail, Message, More +++
Bis 31.1.: TopMail + Digicam für nur 29 EUR http://www.gmx.net/topmail

Doug,

	As far as I know there isn't any resource online, so I'll try to
answer your questions here:

PyMOL does not automatically align structures.

intra_fit is presumably the command you're looking for to do this, since
you're placing models are in one object.

intra_fit name ca, 1

would for example align all of the models to the first model using
alpha-carbon coordinates.

intra_fit resi 10-15, 1

would align all models to the coordinates of atoms in residues 10-15.

As far as RMS statistics go, PyMOL may be the best tool for this yet,
since it doesn't current have the ability to generate statistics for the
ensemble.

What statistics in particular would you like it to provide?  

Also note that if you have you ensemble in a multiple-model pdb file
(with MODEL and ENDMDL records), you can just load it in one command

load ens.pdb

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Douglas Kojetin
> Sent: Monday, January 26, 2004 11:22 AM
> To: pymol
> Subject: [PyMOL] nmr ensemble alignment
> 
> Hi All-
> 
> Will reading in a structural ensemble ....
> 
> load pdb01.pdb, ens
> load pdb02.pdb, ens
> ...
> 
> ... automagically align the structures?  If not, do I need to run
> another command, such as ' intra_fit (name ca) ' ?  Or should I use
> normal 'fit'?
> 
> Also, what is the best method for determining the RMS of the ensemble?
> There are a few commands in the reference manual (rms, rms_cur,
> intra_rms, intra_rms_cur), and I'm confused as to which is best for
> structural ensembles.
> 
> Or, to save typing, is there a current web resource for using PyMOL
> with NMR models (with hints, scripts, etc.)?  One thing I /miss/ from
> MOLMOL is the 'sausage' display -- has anyone implemented this in
PyMOL
> yet?
> 
> Thanks,
> Doug
> 
> 
> 
> -------------------------------------------------------
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi All-

Will reading in a structural ensemble ....

load pdb01.pdb, ens
load pdb02.pdb, ens
...

... automagically align the structures?  If not, do I need to run 
another command, such as ' intra_fit (name ca) ' ?  Or should I use 
normal 'fit'?

Also, what is the best method for determining the RMS of the ensemble?  
There are a few commands in the reference manual (rms, rms_cur, 
intra_rms, intra_rms_cur), and I'm confused as to which is best for 
structural ensembles.

Or, to save typing, is there a current web resource for using PyMOL 
with NMR models (with hints, scripts, etc.)?  One thing I /miss/ from 
MOLMOL is the 'sausage' display -- has anyone implemented this in PyMOL 
yet?

Thanks,
Doug

Hi There,

I've written a little patch to add a filtering capability
on the dialog used to edit the settings.

The patch will add a new menu entry under "Edit all..."
named "Edit All (filter)"

The new dialog has a field where you can type either a word
or a complex regular expression and hit enter and the list 
of settings should narrow down. 

Try for example "sphe|line|surf" (without the quotes)

To go back to the full list, clear the field and hit enter, 
an empty string matches all settings.

Follow the instructions below to patch the file PMGApp.py
and add the attached file to the same directory where PMGApp.py
resides.


Have fun.
  Zac

###
# FILE ./pymol/modules/pmg_tk/PMGapp.py
###

# LINE 20
#
# change it so it reads
from SetEditorFilter import SetEditor, SetEditorFilter



# LINE 1383
#
# add this code (make sure the indentation is correct)

      self.menuBar.addmenuitem('Setting', 'command',
                         'Edit PyMOL Settings',
                         label=self.pad+'Edit All (filter)',
                               command = lambda s=self: SetEditorFilter(s))


###
# FILE ./pymol/modules/pmg_tk/SetEditorFilter.py
###

#add the attached file as SetEditorFilter.py

I have been trying to install Pymol for days but ---.

(On my OSX10.3.2@PowerBookG4; Fink installed)

1. The Diskimage 'pymol-0_93-bin-osx-g4-demos.dmg' and=20
'pymol-0_92-bin-osx-g4-demos.dmg' can not be mounted saying like=20
'mountabe file system missing (In Japanese)'.

2. 'pymol-0_90-bin-osx.dmg' can be mounted and I placed the folder just=20=

downstream of 'Application'. But the message 'cannot continue <<event=20
coreoapp>>' appears saying;
on run
	tell application "Terminal"
		=ABevent coreoapp=BB
		do script with command =
"/Applications/PyMOL/Darwin/pymol.com"
	end tell
end run.

3. (I did this first); Fink installation of '0.86-14' fails as follows;
gcc  -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -I/sw/include/python2.3=20=

-I/sw/include/python2.3 @DEFS@ -I/sw/include  -c ././ExtensionClass.c=20
-o ./ExtensionClass.o
gcc: cannot specify -o with -c or -S and multiple compilations
make[2]: *** [ExtensionClass.o] Error 1
make[1]: *** [make-modules] Error 2
make: *** [.contrib] Error 2
### execution of make failed, exit code 2
Failed: compiling pymol-0.86-14 failed

Any help highly appreciated!

Kazuo

Hi,

I found some strange action when executing pymol command
from external python interpreter.

program1(test1.py) work well.I can see test.pdb with stick.
Buit test2.py does not work well, Pymol launched ,but I can not
see test.pdb.
Additionally when I type program1 in external python interpreter
line by line, Pymol dump.

Why does only program1 work well? Is this a bug?

--- program 1 (test1.py)---
import pymol
pymol.finish_launching()
from pymol import cmd
cmd.load("test.pdb")
cmd.show("stick")

--- program 2 (test2.py)---
def view():
	import pymol
	pymol.finish_launching()
	from pymol import cmd
	cmd.load("test.pdb")
	cmd.show("stick")
view()

Takefumi SORA

Michal,

Unfortunately, beautiful backbones require N and C coordinates as well,
because PYMOL uses AA geometry to determine orientation vectors.  The
best you can do with CA only is a tube.

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: Michal Kurowski [mailto:mi...@ge...]
> Sent: Thursday, January 22, 2004 3:19 PM
> To: Warren L. DeLano
> Cc: pym...@li...
> Subject: Re: c-alpha traces
> 
> Warren L. DeLano [wa...@de...] wrote:
> > Yes,
> >
> > PyMOL can visualize CA-only models, perform CA-based alignments on
CA
> > models, visualize all-atom models, perform CA-based alignments on
all
> > atom models, and perform all-atom alignments on all-atom models.
> 
> Thats great !
> 
> To make sure we both speak of the same thing:
> 
> I specifically meant visualization of pdb files with c-alpha
> - only structure subsets  from rcsb without *any* action on
> already centered molecules. Moreover, showing beautiful
> backbones ;-).
> 
> Is it right ?
> 
> Regards,
> 
> --
> Michal Kurowski
> <mi...@ge...>
> 
> 

Lesley,

	set cartoon_transparency, 0.6

should do the trick.  Note that you may need to ray-trace the image to
avoid transparency artifacts.

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Lesley Debono
> Sent: Wednesday, January 21, 2004 10:56 PM
> To: pym...@li...
> Subject: [PyMOL] translucent proteins
> 
> I would like to be able to make the backbone protein in a structure
> translucent so that the active site is clearly visible through the
> protein. Any ideas on how to do this?
> 
> Lesley
> 
> 
> 
> -------------------------------------------------------
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

On Thu, 22 Jan 2004, Warren L. DeLano wrote:

> Where script.py contains the following sequence:
> 
> import pymol
> pymol.finish_launching()
> 
> [PS If there's anyone out there with a more elegant alternative for
> launching the PyMOL thread from a standalone Python script, I'd sure
> like to hear it : )].

I don't have anything significant to contribute to a revised interface
right now, but I just wanted to say that I think it is strange that an
import statement starts doing things like launching threads. The
import should just make an interface available, and then the script
can use the interface to create a "pymol object" or whatever:

  import pymol

  pymolHandle = pymol.create(options like window size, parent window to create in)
  pymolHandle.cmd.show("sticks", someName)

The pymol.create() blocks until things are ready, so it is sort of the
same as calling pymol.finish_launching(), but it seems more natural to
this programmer. I don't expect import statements to do much. If I
import imaplib it doesn't create an interface to an IMAP server,
right? It just gives me the ability to do so.

It would be up to the application to maintain or pass around
pymolHandle to various modules/objects to get things done.

Perhaps an app could use pymol.create() to create another instance, a
second rendering window? Shared model underneath? Hmmm. . .

When I delete pymolHandle or it goes out of scope, the thread should
shut down and other resources should be released. It should NOT kill
my application as it currently does when I call cmd.quit(). It's just
a thread, it shouldn't be making decisions for my application.

-Bob

> > -----Original Message-----
> > From: pym...@li... [mailto:pymol-users-
> > ad...@li...] On Behalf Of Takefumi Sora
> > Sent: Wednesday, January 21, 2004 10:57 PM
> > To: pym...@li...
> > Subject: RE: [PyMOL] How to send pymol command to pymol by python
> > interpreter
> > 
> > 
> > Hi.
> > 
> > I appreciate your answer, Warren.
> > Thank you.
> > 
> > Please let me ask one more question.
> > 
> > You said I need two lines first:
> > import pymol
> > pymol.finish_launching()
> > 
> > As long as I use,I can't the role of
> > "pymol.finish_launching()"
> > if I don't call this, what troubles will happen ?
> > 
> > Takefumi SORA
> > 
> > 
> > 
> > -------------------------------------------------------
> > The SF.Net email is sponsored by EclipseCon 2004
> > Premiere Conference on Open Tools Development and Integration
> > See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> > http://www.eclipsecon.org/osdn
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> 
> 
> -------------------------------------------------------
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

Thanks for the suggestion, and the solution.  

In Versions >= 0.95, cmd.extend will will adds new commands into the
help dictionary.  

In the meantime

   cmd.help_sc.append('func_name')

will work...

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Michael George Lerner
> Sent: Thursday, January 22, 2004 1:51 PM
> To: Gareth Stockwell
> Cc: pymol-users
> Subject: Re: [PyMOL] Help for user-defined functions
> 
> 
> Hi,
> 
> I haven't seen this documented anywhere, so I have no idea if it's the
> Right Way to do things, but I think all you need to do is add
> 
> cmd.help_sc.append('some_func')
> 
> after the cmd.extend('some_func',some_func) call.  should this be
built in
> to cmd.extend()?
> 
> -michael
> 
> --
> This isn't a democracy;|                        _  |Michael Lerner
>  it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
> -Torrence,  Bring It On|  - against HTML email  X  |  Biophysics
>                        |                       / \ | mlerner@umich
> 
> On Thu, 22 Jan 2004, Gareth Stockwell wrote:
> 
> > Does anyone know if it is possible to add 'help' documentation to my
own
> > user-defined functions?  What I want is to be able to define a new
PyMOL
> > command by executing the following script:
> >
> >
> > #------------------
> >
> > def some_func:
> >
> > 	'''
> > 	Some help docs here...
> >
> > 	'''
> >
> > 	# Python code here...
> >
> > cmd.extend("some_func", some_func)
> >
> > #------------------
> >
> > ... and then type 'help some_func'.
> >
> > Gareth
> >
> > --
> > Gareth Stockwell <ga...@eb...>
> > European Bioinformatics Institute
> >
> >
> >
> > -------------------------------------------------------
> > The SF.Net email is sponsored by EclipseCon 2004
> > Premiere Conference on Open Tools Development and Integration
> > See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> > http://www.eclipsecon.org/osdn
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> 
> 
> -------------------------------------------------------
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
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Takefumi,

You only need to worry about this if you're using an external Python
interpreter with a modular build of PyMOL.  For example, after
installing a late-model linux PyMOL RPM, you run

python script.py

Where script.py contains the following sequence:

import pymol
pymol.finish_launching()

which is needed to insure that PyMOL's API in the parallel thread is
defined ready to receive messages.

The problem is that PyMOL can't launch until "import pymol" completes
and returns and __main__.pymol is defined.  However, that means that the
next command in your script will need to be executed before PYMOL has
had a chance to initialize itself.  So the current approach is to launch
the PyMOL thread, and then call a function which blocks until PyMOL is
all ready to go...

Cheers,
Warren

[PS If there's anyone out there with a more elegant alternative for
launching the PyMOL thread from a standalone Python script, I'd sure
like to hear it : )].

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Takefumi Sora
> Sent: Wednesday, January 21, 2004 10:57 PM
> To: pym...@li...
> Subject: RE: [PyMOL] How to send pymol command to pymol by python
> interpreter
> 
> 
> Hi.
> 
> I appreciate your answer, Warren.
> Thank you.
> 
> Please let me ask one more question.
> 
> You said I need two lines first:
> import pymol
> pymol.finish_launching()
> 
> As long as I use,I can't the role of
> "pymol.finish_launching()"
> if I don't call this, what troubles will happen ?
> 
> Takefumi SORA
> 
> 
> 
> -------------------------------------------------------
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
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> _______________________________________________
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Warren L. DeLano [wa...@de...] wrote:
> Yes, 
> 
> PyMOL can visualize CA-only models, perform CA-based alignments on CA
> models, visualize all-atom models, perform CA-based alignments on all
> atom models, and perform all-atom alignments on all-atom models.

Thats great !

To make sure we both speak of the same thing:

I specifically meant visualization of pdb files with c-alpha 
- only structure subsets  from rcsb without *any* action on 
already centered molecules. Moreover, showing beautiful 
backbones ;-).  

Is it right ?
 
Regards,

-- 
Michal Kurowski
<mi...@ge...>

 

Yes, 

PyMOL can visualize CA-only models, perform CA-based alignments on CA
models, visualize all-atom models, perform CA-based alignments on all
atom models, and perform all-atom alignments on all-atom models.

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Michal Kurowski
> Sent: Wednesday, January 21, 2004 5:37 PM
> To: pym...@li...
> Subject: [PyMOL] c-alpha traces
> 
> Hi,
> 
> Some structure comparison software is only able to generate alignments
> built of c-alpha atoms of both structures compared.
> 
> Is Pymol able to visualize such alignment with (faked) backbone
> shown ?
> 
> If not what could possibly show it ?
> 
> Regards,
> 
> 
> --
> Michal Kurowski
> <mi...@ge...>
> 
> 
> 
> 
> -------------------------------------------------------
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
> http://www.eclipsecon.org/osdn
> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi,

I haven't seen this documented anywhere, so I have no idea if it's the
Right Way to do things, but I think all you need to do is add

cmd.help_sc.append('some_func')

after the cmd.extend('some_func',some_func) call.  should this be built in
to cmd.extend()?

-michael

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

On Thu, 22 Jan 2004, Gareth Stockwell wrote:

> Does anyone know if it is possible to add 'help' documentation to my own
> user-defined functions?  What I want is to be able to define a new PyMOL
> command by executing the following script:
>
>
> #------------------
>
> def some_func:
>
> 	'''
> 	Some help docs here...
>
> 	'''
>
> 	# Python code here...
>
> cmd.extend("some_func", some_func)
>
> #------------------
>
> ... and then type 'help some_func'.
>
> Gareth
>
> --
> Gareth Stockwell <ga...@eb...>
> European Bioinformatics Institute
>
>
>
> -------------------------------------------------------
> The SF.Net email is sponsored by EclipseCon 2004
> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
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>

Package: pymol
Version: 0.93-2

On Thu, Jan 22, 2004 at 08:53:37AM -0800, Morri Feldman wrote:
> On Thu, 22 Jan 2004 11:02:25 +0100 Michael Banck wrote:
> 
> > On Wed, Jan 21, 2004 at 09:11:01PM -0800, Morri Feldman wrote:
> > > Regarding my problems raytracing on my debian/testing machine.
> > 
> > What is the exact version of the pymol .deb you're using? 0.93-2?
> pymol_0.93-2_i386.deb
> 
> > What architecture are you running on? i386 or something else?
> i386, Pentium III
> 
> > Do you use pymol's internal raytracer, or povray? 
> I invoke the raytracer by typing "ray".  I assume this is the internal
> raytracer.
> 
> > Does the raytracing-demo from the demo-menu work?
> The ray tracing demo works.  But after running the raytracing-demo, pymol 
> will crash if I type either:
> hide spheres
> show sticks
> ray
> 
> or:
> hide spheres
> show lines
> ray

Indeed, I can reproduce this here. Thanks for the bug report. I'll try
to debug this during the weekend (won't have time tomorrow I guess),
please nag me if you don't here back next week.


thanks,

Michael

I recently installed a new version of pymol using all-in-one archive 
pymol-0_93-bin-linux-libc6-i386.tgz. When I try to run pymol the program 
crashes and gives this error message:

pymol.com: line 14: 10610 Floating point exception$PYMOL_PATH/pymol.exe $*

I am trying to do this on a PC running SuSe Linux 8.2. Strangely other PCs in 
the lab which use SuSe 8.2 as well do not have this problem. 

Does anyone have an idea where this might come from?

thanks,
mark
-- 
Mark Pfuhl                    fon: 0116 223 1544
Department of Biochemistry    fax: 0116 223 1503
University of Leicester     email: mp...@le...
University Road               www: www.le.ac.uk/biochem/mp84
Leicester LE1 7RH

On Thu, 22 Jan 2004 11:02:25 +0100 Michael Banck wrote:

> On Wed, Jan 21, 2004 at 09:11:01PM -0800, Morri Feldman wrote:
> > Regarding my problems raytracing on my debian/testing machine.
> 
> What is the exact version of the pymol .deb you're using? 0.93-2?
pymol_0.93-2_i386.deb

> What architecture are you running on? i386 or something else?
i386, Pentium III

> Do you use pymol's internal raytracer, or povray? 
I invoke the raytracer by typing "ray".  I assume this is the internal
raytracer.

> Does the raytracing-demo from the demo-menu work?
The ray tracing demo works.  But after running the raytracing-demo, pymol 
will crash if I type either:
hide spheres
show sticks
ray

or:
hide spheres
show lines
ray

Thanks,
Morri

>  
> 
> thanks,
> 
> Michael
> 
> 
> -------------------------------------------------------
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> Premiere Conference on Open Tools Development and Integration
> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA.
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 



Morri Feldman