pymol-users Mailing List for PyMOL Molecular Graphics System

Friends,

I made a cartoon representation of a DNA. now i want to undisplay the base
and sugar of certain residues in the DNA. Could someone please write me how
to do the same. When i select a residue and choose HIDE-> EVERYTHING. It
undisplays the cartoon of the backbone also which i dnt want.

Regards,
Bala

2009/8/29 David Hall <dwa...@ya...>

> pymol.cmd.align("%s" % name_struct1, "%s" % name_struct2)
>
oh, thanks =)

>
> should return a list, the first element of which is the rms, if I remember
> correctly.
> Warren can probably say what the rest of the elements are.
>
> On this note, maybe we could start documenting on the wiki what exactly all
> these commands return.  It would be very useful for scripting.
>
Yeah, it would be great get that information.

>
> -David
>
>


-- 
http://crosvera.blogspot.com

Carlos Ríos V.
Estudiante de Ing. (E) en Computación e Informática.
Universidad del Bío-Bío
VIII Región, Chile

Linux user number 425502

pymol.cmd.align("%s" % name_struct1, "%s" % name_struct2) 


should return a list, the first element of which is the rms, if I remember correctly.

Warren can probably say what the rest of the elements are.


On this note, maybe we could start documenting on the wiki what exactly all these commands return.  It would be very useful for scripting.


-David


Thank you very much Warren,
>
>Now I have a question about PyMOL api,  because when I align two structures, the outpur (rms value) is printed in te screen, but I need to store that value into a variable, is that possible?
>
>I mean, when I do this:
>
>pymol.cmd.do("align %s, %s" %(name_struct1, name_struct2) )
>
>How can I get the rms value into a variable?
>
>
>
>
>
>
>
>


      

2009/8/24 Warren DeLano <wa...@de...>

> Carlos,
>
> The complication is that align outputs RMS values for only those atomic
> pairs remaining following sequence matching following by a refined structure
> alignment (which omits atoms above a cutoff), whereas rms outputs the value
> for all atoms matched by identifier (without any optimization).
>
> To run align without optimization, issue:
>
> align selection1, selection2, cycles=0
>
> where selection1 and selection2 are replaced with your atom selections, but
> remember that unmatched residues will not be included in the output RMS
> value.
>
> Cheers,
> Warren
>
> > -----Original Message-----
> > From: Carlos Ríos Vera [mailto:cro...@gm...]
> > Sent: Monday, August 24, 2009 1:44 PM
> > To: pym...@li...
> > Subject: [PyMOL] RMS
> >
> > Hello people,
> >
> > I'm trying to use pymol from a custom python scrypt. What I have done
> > is to align two structures, but I need get the RMS value from that
> > align but I have no idea how to do it.
> >
> > I tried to use the RMS command but the value differs from the value
> > that I get from the align.
> >
> > Any Idea how to get that value?
> >
> > cheers
> >
> > ps: Sorry if my English is not so good
> >
> > --
> > http://crosvera.blogspot.com
> >
> > Carlos Ríos V.
> > Estudiante de Ing. (E) en Computación e Informática.
> > Universidad del Bío-Bío
> > VIII Región, Chile
> >
> > Linux user number 425502
> >
> >
> --------------------------------------------------------------------------
> > ----
> > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-
> > Day
> > trial. Simplify your report design, integration and deployment - and
> focus
> > on
> > what you do best, core application coding. Discover what's new with
> > Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
> >
> >
> >

Thank you very much Warren,

Now I have a question about PyMOL api,  because when I align two structures,
the outpur (rms value) is printed in te screen, but I need to store that
value into a variable, is that possible?

I mean, when I do this:

pymol.cmd.do("align %s, %s" %(name_struct1, name_struct2) )

How can I get the rms value into a variable?

cheers, and Thanks



-- 
http://crosvera.blogspot.com

Carlos Ríos V.
Estudiante de Ing. (E) en Computación e Informática.
Universidad del Bío-Bío
VIII Región, Chile

Linux user number 425502

Dear all,

in pymol 1.2 I want to run C.Rothers movie.py. But I got errors as:
PyMOL>run /software/pymol/modules/pmg_tk/startup/movie.py
PyMOL>viewport 200,200
PyMOL>mvClear
Traceback (most recent call last):
   File "/software/pymol_beta_64/modules/pymol/parser.py", line 464, in 
parse
   File "<string>", line 1, in <module>
NameError: name 'mvClear' is not defined
PyMOL>select Mooo , ( 1FIQ05000000 and (Resi 603 or Resi 604) and Chain "")

-- 
Joachim

Hugo,

If building PyMOL from source, then please get APBS in source or binary form from the APBS sourceforge project:  http://apbs.sourceforge.net  

Cheers,
Warren

> -----Original Message-----
> From: Hugo G. de Teran [mailto:hug...@us...]
> Sent: Thursday, August 27, 2009 10:06 AM
> Cc: apb...@li...; pym...@li...
> Subject: [PyMOL] APBS in pymol1.2
> 
> Hi,
> 
> I am trying to use APBS in pymol v1.2 (x86_64 linux compilation). I have
> compiled with no problem APBS, but when I try to start a calculation I
> get the following error:
>   File
> "/usr/local/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py",
> line 998, in __init__
>     from freemol import apbs
> ImportError: No module named freemol
> /usr/local/bin/pymol: line 2:   798 Segmentation fault
> /usr/bin/python
> /usr/local/lib64/python2.6/site-packages/pymol/__init__.py "$@"
> 
> I have read previous posts about freemol, but I do not want to mess up
> with
> beta-versions so I only would like to make APBS work with pymol.
> 
> Thanks for help,
> 
> Hugo
> 
> 
> --
> Hugo G. de Teran, PhD.
> "Parga Pondal" Research fellow
> Fundación Pública Galega de Medicina Xenómica - SERGAS
> Santiago de Compostela (SPAIN)
> 
> Phone +34 981563100 ext 13873
> e-mail:hug...@us...       http://web.usc.es/~hugogdt
> 
> 
> 
> --------------------------------------------------------------------------
> ----
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-
> Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
> 
> 
> 

Hi,

I am trying to use APBS in pymol v1.2 (x86_64 linux compilation). I have
compiled with no problem APBS, but when I try to start a calculation I
get the following error:
  File
"/usr/local/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py",
line 998, in __init__
    from freemol import apbs
ImportError: No module named freemol
/usr/local/bin/pymol: line 2:   798 Segmentation fault     
/usr/bin/python
/usr/local/lib64/python2.6/site-packages/pymol/__init__.py "$@"

I have read previous posts about freemol, but I do not want to mess up with
beta-versions so I only would like to make APBS work with pymol.

Thanks for help,

Hugo


-- 
Hugo G. de Teran, PhD.
"Parga Pondal" Research fellow
Fundación Pública Galega de Medicina Xenómica - SERGAS
Santiago de Compostela (SPAIN) 

Phone +34 981563100 ext 13873
e-mail:hug...@us...       http://web.usc.es/~hugogdt       

Hi Andy, hi everyone,

if you only want a few water molecules in a different size you can always 
change the size by altering their van-der-Waals radii. For example, if you 
want to change water number 3:

alter r. hoh & i. 3, vdw=vdw+3

The CA atoms could be changed similarly, but if you want to change of all them 
you might want to change the b value column and adjust the vdWs by the "B" 
column by:

alter n. ca, vdw=b (you might want to adjust the values by e.g. dividing with 
a constant)

I hope this answers your question sufficiently.

Regards,
Mark

Stuart,

Hmm...it appear that QuietException is being thrown when the input pattern fails to match any valid object name (but without an error message being printed).

The easiest immediate workaround is to simply swallow the exception.

for i in range(10):
    try: 
        cmd.color(colors[i], "sym0" + str(i) + "*")
    except cmd.QuietException:
        pass

Cheers,
Warren

________________________________________
From: Stuart Ballard [mailto:srb...@wi...] 
Sent: Wednesday, August 26, 2009 4:35 PM
To: pymol-users
Subject: [PyMOL] Inexplicable exception raised by cmd.color()

Hello Warren, all,


When attempting to execute this block of code:

    colors = ["red","orange","yellow","green","blue","purple","salmon","grey","pink","teal","brown"]
    for i in range(10):
        cmd.color(colors[i], "sym0" + str(i) + "*")

The following error message is displayed:

Traceback (most recent call last):
  File "/Users/delwarl/MacPyMOL090405/build/Deployment-py25/MacPyMOL.app/pymol/modules/pymol/parser.py", line 153, in parse
  File "<string>", line 3, in <module>
  File "/Users/delwarl/MacPyMOL090405/build/Deployment-py25/MacPyMOL.app/pymol/modules/pymol/viewing.py", line 2425, in color
QuietException: <pymol.parsing.QuietException instance at 0x104ea698>

Furthermore, the object corresponding to sym00* is colored red, as expected. I've looked up the code in parser.py and viewing.py which generates the exception itself, and that has shed no light. Function color in viewing.py is as follows:

        # preprocess selection
        selection = selector.process(selection)
        color = _self._interpret_color(_self,str(color))
        #
        r = DEFAULT_ERROR      
        try:
            _self.lock(_self)
            r = _cmd.color(_self._COb,str(color),str(selection),int(flags),int(quiet))
        finally:
            _self.unlock(r,_self)
        if _self._raising(r,_self): raise QuietException
        return r

Any explanation of the bug, or an effective workaround would be greatly appreciated.


Thanks,
Stuart Ballard
Dept. of Biochemistry
UW-Madison

Hello Warren, all,


When attempting to execute this block of code:

    colors =
["red","orange","yellow","green","blue","purple","salmon","grey","pink","teal","brown"]
    for i in range(10):
        cmd.color(colors[i], "sym0" + str(i) + "*")

The following error message is displayed:

Traceback (most recent call last):
  File
"/Users/delwarl/MacPyMOL090405/build/Deployment-py25/MacPyMOL.app/pymol/modules/pymol/parser.py",
line 153, in parse
  File "<string>", line 3, in <module>
  File
"/Users/delwarl/MacPyMOL090405/build/Deployment-py25/MacPyMOL.app/pymol/modules/pymol/viewing.py",
line 2425, in color
QuietException: <pymol.parsing.QuietException instance at 0x104ea698>

Furthermore, the object corresponding to sym00* is colored red, as expected.
I've looked up the code in parser.py and viewing.py which generates the
exception itself, and that has shed no light. Function color in viewing.py
is as follows:

        # preprocess selection
        selection = selector.process(selection)
        color = _self._interpret_color(_self,str(color))
        #
        r = DEFAULT_ERROR
        try:
            _self.lock(_self)
            r =
_cmd.color(_self._COb,str(color),str(selection),int(flags),int(quiet))
        finally:
            _self.unlock(r,_self)
        if _self._raising(r,_self): raise QuietException
        return r

Any explanation of the bug, or an effective workaround would be greatly
appreciated.


Thanks,
Stuart Ballard
Dept. of Biochemistry
UW-Madison

I want to show different water molecules in an image with spheres of different radii. Is there any way to do that in Pymol? Can the same be done with different Ca atoms?

Thank you



      

tested, works, brilliant, thanks.

Stephen

2009/8/25 Warren DeLano <wa...@de...>:
> Stephen,
>
> ramp_new ramp-name, ...
>
> disable ramp-name
>
> Cheers,
> Warren
>
>> -----Original Message-----
>> From: Stephen Graham [mailto:ste...@st...]
>> Sent: Tuesday, August 25, 2009 10:09 AM
>> To: pym...@li...
>> Subject: [PyMOL] invoke ramp_new without drawing 'ramp' CGO
>>
>> Dear all,
>>
>> Is it possible to invoke ramp_new and have it not draw the 'ramp' CGO?
>>  It's easy enough to hide the CGO when working interactively, but I've
>> yet to find a way to zap it from a script (without also getting rid of
>> the colour ramping itself).
>>
>> 'hide everything, my_ramp' doesn't seem to hide the CGO, and issuing
>> 'delete my_ramp' from within a script kills the colour ramp before it
>> gets applied (to a surface, in this case, despite the order of
>> operations in the script).
>>
>> Thanks,
>>
>> Stephen
>>
>> --
>> Dr Stephen Graham
>> Division of Structural Biology
>> Wellcome Trust Centre for Human Genetics
>> Roosevelt Drive
>> Oxford OX3 7BN
>> United Kingdom
>> Phone: +44 1865 287 549
>>
>>
> ------------------------------------------------------------------------
> --
>> ----
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
> 30-
>> Day
>> trial. Simplify your report design, integration and deployment - and
> focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives:
> http://www.mail-archive.com/pym...@li...
>>
>>
>>
>
>
>



-- 
Dr Stephen Graham
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
Phone: +44 1865 287 549

Stephen,

ramp_new ramp-name, ...

disable ramp-name

Cheers,
Warren

> -----Original Message-----
> From: Stephen Graham [mailto:ste...@st...]
> Sent: Tuesday, August 25, 2009 10:09 AM
> To: pym...@li...
> Subject: [PyMOL] invoke ramp_new without drawing 'ramp' CGO
> 
> Dear all,
> 
> Is it possible to invoke ramp_new and have it not draw the 'ramp' CGO?
>  It's easy enough to hide the CGO when working interactively, but I've
> yet to find a way to zap it from a script (without also getting rid of
> the colour ramping itself).
> 
> 'hide everything, my_ramp' doesn't seem to hide the CGO, and issuing
> 'delete my_ramp' from within a script kills the colour ramp before it
> gets applied (to a surface, in this case, despite the order of
> operations in the script).
> 
> Thanks,
> 
> Stephen
> 
> --
> Dr Stephen Graham
> Division of Structural Biology
> Wellcome Trust Centre for Human Genetics
> Roosevelt Drive
> Oxford OX3 7BN
> United Kingdom
> Phone: +44 1865 287 549
> 
>
------------------------------------------------------------------------
--
> ----
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
30-
> Day
> trial. Simplify your report design, integration and deployment - and
focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives:
http://www.mail-archive.com/pym...@li...
> 
> 
> 

Dear all,

Is it possible to invoke ramp_new and have it not draw the 'ramp' CGO?
 It's easy enough to hide the CGO when working interactively, but I've
yet to find a way to zap it from a script (without also getting rid of
the colour ramping itself).

'hide everything, my_ramp' doesn't seem to hide the CGO, and issuing
'delete my_ramp' from within a script kills the colour ramp before it
gets applied (to a surface, in this case, despite the order of
operations in the script).

Thanks,

Stephen

-- 
Dr Stephen Graham
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
Phone: +44 1865 287 549

Carlos,

The complication is that align outputs RMS values for only those atomic pairs remaining following sequence matching following by a refined structure alignment (which omits atoms above a cutoff), whereas rms outputs the value for all atoms matched by identifier (without any optimization).

To run align without optimization, issue:

align selection1, selection2, cycles=0

where selection1 and selection2 are replaced with your atom selections, but remember that unmatched residues will not be included in the output RMS value.

Cheers,
Warren

> -----Original Message-----
> From: Carlos Ríos Vera [mailto:cro...@gm...]
> Sent: Monday, August 24, 2009 1:44 PM
> To: pym...@li...
> Subject: [PyMOL] RMS
> 
> Hello people,
> 
> I'm trying to use pymol from a custom python scrypt. What I have done
> is to align two structures, but I need get the RMS value from that
> align but I have no idea how to do it.
> 
> I tried to use the RMS command but the value differs from the value
> that I get from the align.
> 
> Any Idea how to get that value?
> 
> cheers
> 
> ps: Sorry if my English is not so good
> 
> --
> http://crosvera.blogspot.com
> 
> Carlos Ríos V.
> Estudiante de Ing. (E) en Computación e Informática.
> Universidad del Bío-Bío
> VIII Región, Chile
> 
> Linux user number 425502
> 
> --------------------------------------------------------------------------
> ----
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-
> Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
> 
> 
> 

Joachim,

I think this is more an issue of driver support rather than hardware.
However, the latest drivers do not necessarily support older cards.
Please see nVidia's site for details:

http://www.nvidia.com/Download/index.aspx?lang=en-us

and click on the "supported hardware" tab after searching.

Cheers,
Warren


> -----Original Message-----
> From: Joachim Reichelt [mailto:Joa...@he...] 
> Sent: Monday, August 24, 2009 6:08 AM
> To: pym...@li...
> Subject: [PyMOL] Zalman 3D Monitor
> 
> Hello,
> 
> does anyone know, which Quadro card supports the Zalman mode.
> The readme states:
>   Stereo options 7, 8, and 9 are only supported on G8xGL and 
> higher GPUs.
> Mode 7 is for the Zalman
> --
> Joachim
> 
> --------------------------------------------------------------
> ----------------
> Let Crystal Reports handle the reporting - Free Crystal 
> Reports 2008 30-Day trial. Simplify your report design, 
> integration and deployment - and focus on what you do best, 
> core application coding. Discover what's new with Crystal 
> Reports now.  http://p.sf.net/sfu/bobj-july 
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: 
> http://www.mail-archive.com/pym...@li...
> 
> 
> 
> 
> 

Stuart,
 
Hmm...whoops, my mistake.  Cmd.extend doesn't actually add a function to
the cmd module -- only to the command keyword dictionary.
 
So, instead, set it explicitly in your .py file:
 
from pymol import cmd
 
def my_fn(...):
    ....
 
cmd.my_fn = my_fn
 
# then later on, in the menu, etc.:
 
cmd.alter_state(..., "cmd.my_fn(...)")
 
Cheers,
Warren
 



________________________________

	From: Stuart Ballard [mailto:srb...@wi...] 
	Sent: Monday, August 24, 2009 4:06 PM
	To: Warren DeLano
	Cc: pymol-users
	Subject: Re: [PyMOL] Calling scripted functions within
alter_state
	
	
	Hello Warren,
	
	
	When adding in the "cmd." I get these error messages:
	
	Traceback (most recent call last):
	  File "<string>", line 1, in <module>
	AttributeError: 'module' object has no attribute 'sym_partner'
	Traceback (most recent call last):
	  File "<string>", line 1, in <module>
	AttributeError: 'module' object has no attribute
'cell_shift_helper'
	
	Versus the error I get with the "cmd." not included:
	
	Traceback (most recent call last):
	  File "<string>", line 1, in <module>
	NameError: name 'sym_partner' is not defined
	Traceback (most recent call last):
	  File "<string>", line 1, in <module>
	NameError: name 'cell_shift_helper' is not defined
	
	I'm pretty stumped at this point. Does it seem like the
pymol.cmd namespace isn't acquiring the new functions as it ought to be?
	
	
	Stuart
	
	
	2009/8/24 Warren DeLano <wa...@de...>
	

		Hello Stuart,

		 

		By default, alter_state expressions are evaluated in the
"pymol" namespace of the current PyMOL instance, not the "cmd"
(pymol.cmd) namespace.  The reason why it works with 'run' is that run
also executes in "pymol" by default, and thus, includes any functions
you define.

		 

		Try:

		 

		cmd.alter_state(1, copy, "x,y,z =
cmd.sym_partner([x,y,z], stored.tmpOp)")
		
		

		instead, after using cmd.extend in your startup or GUI
script.

		 

		Cheers,

		Warren

		 

		 

		
________________________________


		From: Stuart Ballard [mailto:srb...@wi...] 
		Sent: Monday, August 24, 2009 3:38 PM
		To: pymol-users
		Subject: [PyMOL] Calling scripted functions within
alter_state

		 

		Hello Warren, all,
		
		
		I've been working on a plugin for PyMOLX11Hybrid, in
which I have a few lines of code such as:
		
		        cmd.alter_state(1, copy, "x,y,z =
sym_partner([x,y,z], stored.tmpOp)")
		
		AND
		
		    cmd.alter_state(1, object, "x,y,z =
cell_shift_helper([x,y,z],stored.shift)")
		
		Both those functions (sym_partner and cell_shift_helper)
are extended through cmd.extend() function, along with several others
which work perfectly well. The issue arises only when I attempt to use
these functions through a menu added to PyMOL GUI, which does not
involve issuing the run /(filepath)/(script).py command in PyMOL, but
rather initializes necessary commands on startup. I've confirmed that
the cmd.extend() calls are made properly, but I can only fix the problem
by issuing the run command independent of my initialization scripts.
		
		Because this script is planned to be incorporated into a
build of PyMOL which will be run from a variety of file paths, I'd like
to know how I can solve this problem without simply jury rigging a run
command. Is there a way to properly make commands available within an
alter_state command without using the run command?
		
		
		Thanks,
		Stuart Ballard
		Dept. of Biochemistry
		UW-Madison

Hello Warren,


When adding in the "cmd." I get these error messages:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
AttributeError: 'module' object has no attribute 'sym_partner'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
AttributeError: 'module' object has no attribute 'cell_shift_helper'

Versus the error I get with the "cmd." not included:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
NameError: name 'sym_partner' is not defined
Traceback (most recent call last):
  File "<string>", line 1, in <module>
NameError: name 'cell_shift_helper' is not defined

I'm pretty stumped at this point. Does it seem like the pymol.cmd namespace
isn't acquiring the new functions as it ought to be?


Stuart

2009/8/24 Warren DeLano <wa...@de...>

>  Hello Stuart,
>
>
>
> By default, alter_state expressions are evaluated in the “pymol” namespace
> of the current PyMOL instance, not the “cmd” (pymol.cmd) namespace.  The
> reason why it works with ‘run’ is that run also executes in “pymol” by
> default, and thus, includes any functions you define.
>
>
>
> Try:
>
>
>
> cmd.alter_state(1, copy, "x,y,z = cmd.sym_partner([x,y,z], stored.tmpOp)")
>
>  instead, after using cmd.extend in your startup or GUI script.
>
>
>
> Cheers,
>
> Warren
>
>
>
>
>   ------------------------------
>
> *From:* Stuart Ballard [mailto:srb...@wi...]
> *Sent:* Monday, August 24, 2009 3:38 PM
> *To:* pymol-users
> *Subject:* [PyMOL] Calling scripted functions within alter_state
>
>
>
> Hello Warren, all,
>
>
> I've been working on a plugin for PyMOLX11Hybrid, in which I have a few
> lines of code such as:
>
>         cmd.alter_state(1, copy, "x,y,z = sym_partner([x,y,z],
> stored.tmpOp)")
>
> AND
>
>     cmd.alter_state(1, object, "x,y,z =
> cell_shift_helper([x,y,z],stored.shift)")
>
> Both those functions (sym_partner and cell_shift_helper) are extended
> through cmd.extend() function, along with several others which work
> perfectly well. The issue arises only when I attempt to use these functions
> through a menu added to PyMOL GUI, which does not involve issuing the run
> /(filepath)/(script).py command in PyMOL, but rather initializes necessary
> commands on startup. I've confirmed that the cmd.extend() calls are made
> properly, but I can only fix the problem by issuing the run command
> independent of my initialization scripts.
>
> Because this script is planned to be incorporated into a build of PyMOL
> which will be run from a variety of file paths, I'd like to know how I can
> solve this problem without simply jury rigging a run command. Is there a way
> to properly make commands available within an alter_state command without
> using the run command?
>
>
> Thanks,
> Stuart Ballard
> Dept. of Biochemistry
> UW-Madison
>

Hello Stuart,

 

By default, alter_state expressions are evaluated in the "pymol"
namespace of the current PyMOL instance, not the "cmd" (pymol.cmd)
namespace.  The reason why it works with 'run' is that run also executes
in "pymol" by default, and thus, includes any functions you define.

 

Try:

 

cmd.alter_state(1, copy, "x,y,z = cmd.sym_partner([x,y,z],
stored.tmpOp)")



instead, after using cmd.extend in your startup or GUI script.

 

Cheers,

Warren

 

 

________________________________

From: Stuart Ballard [mailto:srb...@wi...] 
Sent: Monday, August 24, 2009 3:38 PM
To: pymol-users
Subject: [PyMOL] Calling scripted functions within alter_state

 

Hello Warren, all,


I've been working on a plugin for PyMOLX11Hybrid, in which I have a few
lines of code such as:

        cmd.alter_state(1, copy, "x,y,z = sym_partner([x,y,z],
stored.tmpOp)")

AND

    cmd.alter_state(1, object, "x,y,z =
cell_shift_helper([x,y,z],stored.shift)")

Both those functions (sym_partner and cell_shift_helper) are extended
through cmd.extend() function, along with several others which work
perfectly well. The issue arises only when I attempt to use these
functions through a menu added to PyMOL GUI, which does not involve
issuing the run /(filepath)/(script).py command in PyMOL, but rather
initializes necessary commands on startup. I've confirmed that the
cmd.extend() calls are made properly, but I can only fix the problem by
issuing the run command independent of my initialization scripts.

Because this script is planned to be incorporated into a build of PyMOL
which will be run from a variety of file paths, I'd like to know how I
can solve this problem without simply jury rigging a run command. Is
there a way to properly make commands available within an alter_state
command without using the run command?


Thanks,
Stuart Ballard
Dept. of Biochemistry
UW-Madison

Hello Warren, all,


I've been working on a plugin for PyMOLX11Hybrid, in which I have a few
lines of code such as:

        cmd.alter_state(1, copy, "x,y,z = sym_partner([x,y,z],
stored.tmpOp)")

AND

    cmd.alter_state(1, object, "x,y,z =
cell_shift_helper([x,y,z],stored.shift)")

Both those functions (sym_partner and cell_shift_helper) are extended
through cmd.extend() function, along with several others which work
perfectly well. The issue arises only when I attempt to use these functions
through a menu added to PyMOL GUI, which does not involve issuing the run
/(filepath)/(script).py command in PyMOL, but rather initializes necessary
commands on startup. I've confirmed that the cmd.extend() calls are made
properly, but I can only fix the problem by issuing the run command
independent of my initialization scripts.

Because this script is planned to be incorporated into a build of PyMOL
which will be run from a variety of file paths, I'd like to know how I can
solve this problem without simply jury rigging a run command. Is there a way
to properly make commands available within an alter_state command without
using the run command?


Thanks,
Stuart Ballard
Dept. of Biochemistry
UW-Madison

Hello people,

I'm trying to use pymol from a custom python scrypt. What I have done
is to align two structures, but I need get the RMS value from that
align but I have no idea how to do it.

I tried to use the RMS command but the value differs from the value
that I get from the align.

Any Idea how to get that value?

cheers

ps: Sorry if my English is not so good

-- 
http://crosvera.blogspot.com

Carlos Ríos V.
Estudiante de Ing. (E) en Computación e Informática.
Universidad del Bío-Bío
VIII Región, Chile

Linux user number 425502

Hello,

does anyone know, which Quadro card supports the Zalman mode.
The readme states:
  Stereo options 7, 8, and 9 are only supported on G8xGL and higher GPUs.
Mode 7 is for the Zalman
-- 
Joachim

Hi Sean,

> I could not find a way to search the archived sourceforge messages,

It is indeed easy to miss but at the bottom of every message there is
a link to the searchable archives:
http://www.mail-archive.com/pym...@li...

Henning

On Thu, Aug 20, 2009 at 10:50 PM, Sean Moore<se...@ma...> wrote:
> Hello,
>
> I could not find a way to search the archived sourceforge messages, so
> I apologize if this has been asked and answered.
>
> I am having trouble moving the light source before a ray command (I
> want to shine it into the crevice of a structure from behind and above
> my current view).
>
> I ended up using "light, [1,5,-100].  I know these are X,Y,Z
> coordinates, but relative to what origin and in what units?  After
> wasting way too much time, I concluded that the values might be
> Angstroms relative to the "eyes" of the current view.  In examples I
> found online, the numbers are small, so this doesn't make much sense.
>
> Also, I see there are several light sources available.  As more and
> more lights are turned on, do the XYZ values for each additional get
> taken in order from the top of the list?  Is there a way to change the
> intensity of each light in addition to its position?
>
> Thanks for any help.
>
> -Sean
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

The light and lightN settings are direction vectors, not coordinates.

Intensity (reflect setting) is averaged across all such directional  
sources.

It has recently been suggested that we need better control over  
lighting.

Cheers,
Warren
--
Warren L. DeLano, Ph.D.
wa...@de...

(Sent from a mobile device.  Please forgive brevity and/or typos!)

On Aug 20, 2009, at 4:14 PM, "Sean Moore" <se...@ma...> wrote:

> Hello,
>
> I could not find a way to search the archived sourceforge messages, so
> I apologize if this has been asked and answered.
>
> I am having trouble moving the light source before a ray command (I
> want to shine it into the crevice of a structure from behind and above
> my current view).
>
> I ended up using "light, [1,5,-100].  I know these are X,Y,Z
> coordinates, but relative to what origin and in what units?  After
> wasting way too much time, I concluded that the values might be
> Angstroms relative to the "eyes" of the current view.  In examples I
> found online, the numbers are small, so this doesn't make much sense.
>
> Also, I see there are several light sources available.  As more and
> more lights are turned on, do the XYZ values for each additional get
> taken in order from the top of the list? Is there a way to change the
> intensity of each light in addition to its position?
>
> Thanks for any help.
>
> -Sean
>
>
>
>
>
>
>
> --- 
> --- 
> --- 
> ---------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008  
> 30-Day
> trial. Simplify your report design, integration and deployment - and  
> focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol- 
> us...@li...
>
>

Sean,

Use set_bond instead of set for per-bond properties.

Cheers,
Warren
--
Warren L. DeLano, Ph.D.
wa...@de...

(Sent from a mobile device.  Please forgive brevity and/or typos!)

On Aug 20, 2009, at 4:18 PM, "Sean Moore" <se...@ma...> wrote:

> Hello,
> I am trying to change the stick_radius for a few selected residues so
> they stand out relative to the surrounding mess of sticks.  If I
> command, "set stick_radius, 0.75, <object name>", the report states
> that the stick radius was changes for the correct number of atoms in
> the file, but the displayed residues all show the original value.
>
> Can the stick radius be changed for a sub-set of residues and  
> rendered?
>
> _Sean
>
>
>
> --- 
> --- 
> --- 
> ---------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008  
> 30-Day
> trial. Simplify your report design, integration and deployment - and  
> focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol- 
> us...@li...
>
>