pymol-users Mailing List for PyMOL Molecular Graphics System

> There is also something like
> Batch: prepare_receptor4.py -r /cwd/receptor_1.pdb -o
> /cwd/receptor..pdbqt -A checkhydrogens
> sh: prepare_receptor4.py: not found


Dear Lina,

I also encountered this error when using the Autodock 4 plugin. I believe that there is a bug in the script for adding hydrogens; my solution for some structures was to use a different program to add hydrogens (I did this using TRITON http://ncbr.chemi.muni.cz/triton/). Also, if I remember correctly, it is best to ensure there are no underscores in your PDB filenames or selections.

I hope that is of some help,

Best,

Harry

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

Harry Jubb
Part II Biochemistry
Homerton College

Hi Marilyn,

Your choices for hardware depends on how much you want to spend and
what your main application is.  Here are the basics for a low-cost 3D
setup:
 * 120 Hz monitor
 * NVidia Quadro 570+ Card
 * NVidia NVision 3D Kit (emitter+glasses)

If you will have multiple systems in the same room, and have multiple
users using it at once, I suggest the 3D Vision Pro.  Otherwise, the
standard NVision system is fine.

I recently demoed PyMOL off the following hardware and was pleasantly
surprised by the quality and performance:
 * Planar SA2311W (http://www.planar3d.com/3d-products/sa2311w/)
 * NVidia 3D Vision Pro
(http://www.nvidia.com/object/3d-vision-professional-users.html)
 * NVidia Quadro 3000 video card

Planar does sell the 23" monitor and standard 3D Vision kit for about
$650, I think.  After that you just need the Quadro card.

Let me be clear: GeForce cards are not supported for 3D stereo--even
the high-end cards.  You need a Quadro card.

You can find more here:
http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options (although
the page needs to be cleaned up).

Cheers,

-- Jason

On Fri, Apr 29, 2011 at 12:25 PM, Jorns, Marilyn S
<Mar...@dr...> wrote:
> Hi,
>
>
>
> We plan to build a Windows7 64 bit PC and would like to use it in
> conjunction with a flat screen monitor for 3D viewing.
>
>
>
> Advice on appropriate hardware components (video card, monitor etc) would be
> most appreciated.
>
>
>
>
>
> Thanks,
>
> Marilyn
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



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

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

Hi,

 

We plan to build a Windows7 64 bit PC and would like to use it in
conjunction with a flat screen monitor for 3D viewing.  

 

Advice on appropriate hardware components (video card, monitor etc)
would be most appreciated.

 

 

Thanks,

Marilyn

Hi Nicolas,

Use map_halve or map_double depending on what you want, less or more
wire density, respectively:

# get a map

fetch 1ejg, type=2fofc, async=0

# make an isomesh

isomesh ejgMesh, 1ejg, 1.8


Once the mesh is shown, type the following command to halve the wire density:

map_halve ejgMesh

Cheers,

-- Jason

On Thu, Apr 28, 2011 at 7:32 AM, Harmer, Nicholas
<N.J...@ex...> wrote:
> Dear Pymol users,
>
>
>
> I am trying to edit an electron density map, so that the “chickenwire” is
> less dense (i.e. a greater spacing between each line on the contour
> surface). I looked through all of the settings for mesh, and coul not find a
> suitable parameter to change. Is it possible to alter this feature of the
> map using PyMOL?
>
> I would appreciate any help that anyone can give.
>
>
>
> Best regards,
>
>
>
> Nic Harmer
>
>
>
> =====================
> Dr. Nic Harmer
> Lecturer in Structural Biochemistry
>
> School of Biosciences
> University of Exeter
>
> United Kingdom
> tel: +44 1392 725179
>
>
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



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

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

Hi,

I met such issue

Error: 1
<type 'exceptions.IndexError'> Exception in Tk callback
  Function: <bound method Autodock.generate_receptor of
<pmg_tk.startup.autodock.Autodock instance at 0x2c31758>> (type: <type
'instancemethod'>)
  Args: ()
Traceback (innermost last):
  File "/usr/lib/python2.6/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
    return apply(self.func, args)
  File "/usr/local/lib/python2.6/dist-packages/pmg_tk/startup/autodock.py",
line 1898, in generate_receptor
    tmp_rec_pdb = os.path.join(self.work_dir(),"receptor.%s.pdb" % sel[0])
<type 'exceptions.IndexError'>: tuple index out of range

There is also something like
Batch: prepare_receptor4.py -r /cwd/receptor_1.pdb -o
/cwd/receptor..pdbqt -A checkhydrogens
sh: prepare_receptor4.py: not found

can anyone provide me suggestions?

-- 
Best Regards,

lina

Dear Pymol users,

I am trying to edit an electron density map, so that the "chickenwire" is less dense (i.e. a greater spacing between each line on the contour surface). I looked through all of the settings for mesh, and coul not find a suitable parameter to change. Is it possible to alter this feature of the map using PyMOL?
I would appreciate any help that anyone can give.

Best regards,

Nic Harmer

=====================
Dr. Nic Harmer
Lecturer in Structural Biochemistry
School of Biosciences
University of Exeter
United Kingdom
tel: +44 1392 725179

Hi lina:

      After you reached the mutagenisis wizzard, click on the amino acid you
wish to mutate. To subsitute another amino acid, click on "no mutation" icon
in the wizzard. then you can see all the other aminoacid appearing. From the
list click the one you wish to include and say ok. Jobs done!!!

-mohan

On Wed, Apr 27, 2011 at 1:33 PM, lina <lin...@gm...> wrote:

> How can I mutate one residue into another in pymol?
>
> I tried the wizard--> mutagenesis-->
> but nothing coming out after done.
>
> I might understand wrong.
>
> Please let me know.
>
> --
> Thanks and best regards,
>
> lina
>
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

can i get to know whether my proteins are in same plane or different plane
in pymol..?

How can I mutate one residue into another in pymol?

I tried the wizard--> mutagenesis-->
but nothing coming out after done.

I might understand wrong.

Please let me know.

-- 
Thanks and best regards,

lina

Kasper, not sure if this will help you, but I think the GLEW stuff was
added recently in V1.4.x and it seems to be still somewhat experimental.
May be to get you started you could switch to v1.3r1 from the repository
and try to embedd that version. V1.3.x should not contain the new GL
stuff.

 

Good luck

 

                Carsten

 

 

 

From: Kasper Thofte [mailto:kas...@gm...] 
Sent: Tuesday, April 26, 2011 10:34 AM
To: pym...@li...
Subject: [PyMOL] openGL/GLEW problems when embedding a PyMOL instance in
aPyQt4 widget

 

Dear pymol user and developer community

I am trying to embed a pymol2.PyMOL instance in a PyQt4 widget.

I am using the latest beta v1.4.1 (although it still says v1.4.0 in
layer0/Version.h, I assume you just forgot to update?). I use ubuntu on
a macbook.

I got it to display a black window inside a PyQt4 app, and I was even
able to produce som ugly little white square H atoms one time, plus som
menus only half visible. Yes, kind of strange.

The problem is openGL related. When typing pymol -v at the command line,
it tells me that my openGL version is pre 2.0, which is not true. 

(Well, actually I wasn't entirely sure what precisely to look for in the
synaptic package manager, but libqt4-opengl is v4:4.7.0, python-opengl
is v3.0.1, python-qt4-gl is v4.7.4, freeglut3-dev is v2.6.0,
libglew1.5-dev is, well v1.5.2 glutg3-dev is 3.7-25)

Anyway, when I runt the following code (which may also contain the
source of the problem, I don't know):

class PymolQWidget(QGLWidget):

        def __init__(self, parent=None):
                QGLWidget.__init__(self, parent=parent)

                self.pymolInstance = pymol2.PyMOL()
                self.pymolInstance.start()
 
self.pymolInstance.cmd.load('<home-directory>/GUI/H2.pdb')'

                self.pymolInstance.cmd.draw()
                self.pymolInstance.cmd.show_as("sticks")

app = QtGui.QApplication(sys.argv)
pymolWidget = PymolQWidget()
pymolWidget.show()
sys.exit(app.exec_())

I get the following error message:

ShaderMgrInit-Error: Could not initialize GLEW:Missing GL version

which means that GLEW_OK!=err at line 145 in layer0/ShaderMgr.c, which
means the glew hasn't been initialized, which is as far as I was able to
get.

Needless to say, help would be greatly appreaciated.

Best,
Kasper Thofte
University of Copenhagent

Hi Jason,

Thanks for your response. The colouring is all correct as there is an object for each interaction type, the problem now is splitting the measures back into single objects, which Dr Lerner has mentioned is not currently possible. If this is the case I will try to refine my figures another way, the main objective was to selectively hide all the dashes except for those connected to a residue of interest purely for clarity of presentation.

Thanks once more,

Harry

On 26 Apr 2011, at 15:50, Jason Vertrees wrote:

> Hi Harry,
> 
> For "measures" (distances, angles, dihedrals), PyMOL can color down to
> the level of an object (eg. color blue, measure01).  So, once you add
> another measure into an extant object, PyMOL cannot separate those two
> colors.  My suggestion is that you measure into new objects if you
> need new coloring.  If you have lots of measurements as a result, then
> you can group them and color by wildcard.
> 
> Cheers,
> 
> -- Jason
> 
> On Tue, Apr 26, 2011 at 5:47 AM, Harry Jubb <hj...@ca...> wrote:
>> Hi Everyone,
>> 
>> I'd like to ask for some help with dash/distance objects. I have PyMOL session files  which show inter-molecular interactions using PyMOL distance objects. These were created using a script which colours each distance object and merges them according to type of interaction. The problem I'm having is that I would prefer to visualise the interactions on a per-residue basis, i.e. showing all the interactions for one or more residues but not the others, but as the dashes are merged by interaction type I can only hide by that category. Extensive Googling has not led me to a solution to select and hide individual dashes that are merged into one UI object, so I'd like to ask if it is possible to do this? I'm unfortunately no longer able to run the script again (I am at the end of a time limited project and am preparing figures) and I would prefer not to replace each dash manually.
>> 
>> I hope this is clear, the crux of what I am asking is if it is possible to select and/or hide individual distance objects in a pymol session after they have been merged into one object. Un-merging them would also be an attractive solution.
>> 
>> Thanks,
>> 
>> Harry
>> ------------------------------------------------------------------------------
>> WhatsUp Gold - Download Free Network Management Software
>> The most intuitive, comprehensive, and cost-effective network
>> management toolset available today.  Delivers lowest initial
>> acquisition cost and overall TCO of any competing solution.
>> http://p.sf.net/sfu/whatsupgold-sd
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>> 
> 
> 
> 
> -- 
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
> 
> (e) Jas...@sc...
> (o) +1 (603) 374-7120

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

Harry Jubb
Part II Biochemistry
Homerton College

UTN: 131 2726
M: 0790 813 4735

Thanks for the feedback. Yes, the idea was to expose the PyMOL function 
to Python. I'll check out the relevant pages mentioned.


On 26.04.11 14:52, Hongbo Zhu wrote:
> you can write your own loop in python to implement the function.
>
> fh = open(pdbfilename)
> coords =
> numpy.array([[float(line[30:38]),float(line[38:46]),float(line[46:54])]
> for line in fh.readlines() if line.startswith('ATOM  ') or
> line.startswith('HETATM')])
> fh.close()
> extent = (numpy.min(coords,axis=0), numpy.max(coords,axis=0))
>
> or course the code needs to be tuned if you need only the first MODEL or
> only the first alternate position etc.
>
> cheers,hongbo
>
> On 04/26/2011 01:40 PM, Martin Hediger wrote:
>> Dear all
>>
>> I found that PyMOL offer the cmd.get_extent('protein') function, which
>> returns the dimensions of the selection.
>> Is it complicated to make this function available from within an
>> ordinary Pythonscript?
>>
>> Thanks for hints.
>> Martin
>>
>>
>> ------------------------------------------------------------------------------
>> WhatsUp Gold - Download Free Network Management Software
>> The most intuitive, comprehensive, and cost-effective network
>> management toolset available today.  Delivers lowest initial
>> acquisition cost and overall TCO of any competing solution.
>> http://p.sf.net/sfu/whatsupgold-sd
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> 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 pymol user and developer community

I am trying to embed a pymol2.PyMOL instance in a PyQt4 widget.

I am using the latest beta v1.4.1 (although it still says v1.4.0 in
layer0/Version.h, I assume you just forgot to update?). I use ubuntu on a
macbook.

I got it to display a black window inside a PyQt4 app, and I was even able
to produce som ugly little white square H atoms one time, plus som menus
only half visible. Yes, kind of strange.

The problem is openGL related. When typing pymol -v at the command line, it
tells me that my openGL version is pre 2.0, which is not true.

(Well, actually I wasn't entirely sure what precisely to look for in the
synaptic package manager, but libqt4-opengl is v4:4.7.0, python-opengl is
v3.0.1, python-qt4-gl is v4.7.4, freeglut3-dev is v2.6.0, libglew1.5-dev is,
well v1.5.2 glutg3-dev is 3.7-25)

Anyway, when I runt the following code (which may also contain the source of
the problem, I don't know):

class PymolQWidget(QGLWidget):

        def __init__(self, parent=None):
                QGLWidget.__init__(self, parent=parent)

                self.pymolInstance = pymol2.PyMOL()
                self.pymolInstance.start()
                self.pymolInstance.cmd.load('<home-directory>/GUI/H2.pdb')'

                self.pymolInstance.cmd.draw()
                self.pymolInstance.cmd.show_as("sticks")

app = QtGui.QApplication(sys.argv)
pymolWidget = PymolQWidget()
pymolWidget.show()
sys.exit(app.exec_())

I get the following error message:

ShaderMgrInit-Error: Could not initialize GLEW:Missing GL version

which means that GLEW_OK!=err at line 145 in layer0/ShaderMgr.c, which means
the glew hasn't been initialized, which is as far as I was able to get.

Needless to say, help would be greatly appreaciated.

Best,
Kasper Thofte
University of Copenhagent

Hi Harry,

For "measures" (distances, angles, dihedrals), PyMOL can color down to
the level of an object (eg. color blue, measure01).  So, once you add
another measure into an extant object, PyMOL cannot separate those two
colors.  My suggestion is that you measure into new objects if you
need new coloring.  If you have lots of measurements as a result, then
you can group them and color by wildcard.

Cheers,

-- Jason

On Tue, Apr 26, 2011 at 5:47 AM, Harry Jubb <hj...@ca...> wrote:
> Hi Everyone,
>
> I'd like to ask for some help with dash/distance objects. I have PyMOL session files  which show inter-molecular interactions using PyMOL distance objects. These were created using a script which colours each distance object and merges them according to type of interaction. The problem I'm having is that I would prefer to visualise the interactions on a per-residue basis, i.e. showing all the interactions for one or more residues but not the others, but as the dashes are merged by interaction type I can only hide by that category. Extensive Googling has not led me to a solution to select and hide individual dashes that are merged into one UI object, so I'd like to ask if it is possible to do this? I'm unfortunately no longer able to run the script again (I am at the end of a time limited project and am preparing figures) and I would prefer not to replace each dash manually.
>
> I hope this is clear, the crux of what I am asking is if it is possible to select and/or hide individual distance objects in a pymol session after they have been merged into one object. Un-merging them would also be an attractive solution.
>
> Thanks,
>
> Harry
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



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

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

Dear pymol user and developer community

I am trying to embed a pymol2.PyMOL instance in a PyQt4 widget.

I am using the latest beta v1.4.1 (although it still says v1.4.0 in
layer0/Version.h, I assume you just forgot to update?). I use ubuntu on a
macbook.

I got it to display a black window inside a PyQt4 app, and I was even able
to produce som ugly little white square H atoms one time, plus som menus
only half visible. Yes, kind of strange.

The problem is openGL related. When typing pymol -v at the command line, it
tells me that my openGL version is pre 2.0, which is not true.

(Well, actually I wasn't entirely sure what precisely to look for in the
synaptic package manager, but libqt4-opengl is v4:4.7.0, python-opengl is
v3.0.1, python-qt4-gl is v4.7.4, freeglut3-dev is v2.6.0, libglew1.5-dev is,
well v1.5.2 glutg3-dev is 3.7-25)

Anyway, when I runt the following code (which may also contain the source of
the problem, I don't know):

class PymolQWidget(QGLWidget):

        def __init__(self, parent=None):
                QGLWidget.__init__(self, parent=parent)

                self.pymolInstance = pymol2.PyMOL()
                self.pymolInstance.start()
                self.pymolInstance.cmd.load('<home-directory>/GUI/H2.pdb')'

                self.pymolInstance.cmd.draw()
                self.pymolInstance.cmd.show_as("sticks")

app = QtGui.QApplication(sys.argv)
pymolWidget = PymolQWidget()
pymolWidget.show()
sys.exit(app.exec_())

I get the following error message:

ShaderMgrInit-Error: Could not initialize GLEW:Missing GL version

which means that GLEW_OK!=err at line 145 in layer0/ShaderMgr.c, which means
the glew hasn't been initialized, which is as far as I was able to get.

Needless to say, help would be greatly appreaciated.

Best,
Kasper Thofte
University of Copenhagent

Hi Harry,

As far as I know, this is not currently possible in PyMOL, but perhaps
someone will correct me on this.

-Michael

On Tue, Apr 26, 2011 at 9:27 AM, Harry Jubb <hj...@ca...> wrote:

> Hi Michael,
>
> Thank you for your response. The problem is that for types of
> inter-molecular interaction all of the visual distances are merged into one
> object in the sidebar (as if created using the measurement wizard with the
> "merge with previous" option on), for which unfortunately the ungroup
> command doesn't seem to work for. Left-clicking on the interaction type in
> the GUI sidebar toggles show/hide for every distance of that interaction
> type, and there are no further disclosure squares which indicates that the
> distances are grouped rather than merged. Ideally I'd like to be able to
> un-merge these objects to make each dash an object that I can hide or show
> individually so I can switch off the ones not connected to a residue of
> interest. Even better (if possible) would be to only show dashes connected
> to a residue of choice.
>
> I hope that makes sense. Thank you for your help,
>
> Harry
>
>
> On 26 Apr 2011, at 13:59, Michael Lerner wrote:
>
> Hi Harry,
>
> If they've been combined using the group command, you can ungroup them:
>
> fetch 1rx1
> # make some distance objects
> dist measure01, 19/C, 20/C
> dist measure02, 20/C, 21/C
> dist measure03, 158/C, 159/C
> dist measure04, 157/C, 159/C
> # group them
> group g1, measure01 or measure02
> group g2, measure03 or measure04
> #ungroup all of them (this leaves empty groups, which you can delete if
> you'd like)
> ungroup measure*
>
> Hope that helps,
>
> -Michael
>
> On Tue, Apr 26, 2011 at 5:47 AM, Harry Jubb <hj...@ca...> wrote:
>
>> Hi Everyone,
>>
>> I'd like to ask for some help with dash/distance objects. I have PyMOL
>> session files  which show inter-molecular interactions using PyMOL distance
>> objects. These were created using a script which colours each distance
>> object and merges them according to type of interaction. The problem I'm
>> having is that I would prefer to visualise the interactions on a per-residue
>> basis, i.e. showing all the interactions for one or more residues but not
>> the others, but as the dashes are merged by interaction type I can only hide
>> by that category. Extensive Googling has not led me to a solution to select
>> and hide individual dashes that are merged into one UI object, so I'd like
>> to ask if it is possible to do this? I'm unfortunately no longer able to run
>> the script again (I am at the end of a time limited project and am preparing
>> figures) and I would prefer not to replace each dash manually.
>>
>> I hope this is clear, the crux of what I am asking is if it is possible to
>> select and/or hide individual distance objects in a pymol session after they
>> have been merged into one object. Un-merging them would also be an
>> attractive solution.
>>
>> Thanks,
>>
>> Harry
>>
>> ------------------------------------------------------------------------------
>> WhatsUp Gold - Download Free Network Management Software
>> The most intuitive, comprehensive, and cost-effective network
>> management toolset available today.  Delivers lowest initial
>> acquisition cost and overall TCO of any competing solution.
>> http://p.sf.net/sfu/whatsupgold-sd
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
>
>
>   -----------------------------------
>
> Harry Jubb
> Part II Biochemistry
> Homerton College
>
> UTN: 131 2726
> M: 0790 813 4735
>
>


-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)

Hi Michael,

Thank you for your response. The problem is that for types of inter-molecular interaction all of the visual distances are merged into one object in the sidebar (as if created using the measurement wizard with the "merge with previous" option on), for which unfortunately the ungroup command doesn't seem to work for. Left-clicking on the interaction type in the GUI sidebar toggles show/hide for every distance of that interaction type, and there are no further disclosure squares which indicates that the distances are grouped rather than merged. Ideally I'd like to be able to un-merge these objects to make each dash an object that I can hide or show individually so I can switch off the ones not connected to a residue of interest. Even better (if possible) would be to only show dashes connected to a residue of choice.

I hope that makes sense. Thank you for your help,

Harry


On 26 Apr 2011, at 13:59, Michael Lerner wrote:

> Hi Harry,
> 
> If they've been combined using the group command, you can ungroup them:
> 
> fetch 1rx1
> # make some distance objects
> dist measure01, 19/C, 20/C
> dist measure02, 20/C, 21/C
> dist measure03, 158/C, 159/C
> dist measure04, 157/C, 159/C
> # group them
> group g1, measure01 or measure02
> group g2, measure03 or measure04
> #ungroup all of them (this leaves empty groups, which you can delete if you'd like)
> ungroup measure*
> 
> Hope that helps,
> 
> -Michael
> 
> On Tue, Apr 26, 2011 at 5:47 AM, Harry Jubb <hj...@ca...> wrote:
> Hi Everyone,
> 
> I'd like to ask for some help with dash/distance objects. I have PyMOL session files  which show inter-molecular interactions using PyMOL distance objects. These were created using a script which colours each distance object and merges them according to type of interaction. The problem I'm having is that I would prefer to visualise the interactions on a per-residue basis, i.e. showing all the interactions for one or more residues but not the others, but as the dashes are merged by interaction type I can only hide by that category. Extensive Googling has not led me to a solution to select and hide individual dashes that are merged into one UI object, so I'd like to ask if it is possible to do this? I'm unfortunately no longer able to run the script again (I am at the end of a time limited project and am preparing figures) and I would prefer not to replace each dash manually.
> 
> I hope this is clear, the crux of what I am asking is if it is possible to select and/or hide individual distance objects in a pymol session after they have been merged into one object. Un-merging them would also be an attractive solution.
> 
> Thanks,
> 
> Harry
> ------------------------------------------------------------------------------
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> 
> -- 
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)

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

Harry Jubb
Part II Biochemistry
Homerton College

UTN: 131 2726
M: 0790 813 4735

Hi, Harry,

I am curious. How do you merge objects resulting from >>distance<< ? Do 
you mean to "group" them? If so, you can use ungroup command to, well, 
ungroup them. But if the merged object is generated using a CGO, I doubt 
you can unmerge the CGO object. But I don't know dash CGOs, either. 
(Unless you make dashes using small line fragments :)

So do you have dashes or solid lines? Do you see a plus sign before the 
object in PyMOL?

hongbo

On 04/26/2011 11:47 AM, Harry Jubb wrote:
> Hi Everyone,
>
> I'd like to ask for some help with dash/distance objects. I have PyMOL session files  which show inter-molecular interactions using PyMOL distance objects. These were created using a script which colours each distance object and merges them according to type of interaction. The problem I'm having is that I would prefer to visualise the interactions on a per-residue basis, i.e. showing all the interactions for one or more residues but not the others, but as the dashes are merged by interaction type I can only hide by that category. Extensive Googling has not led me to a solution to select and hide individual dashes that are merged into one UI object, so I'd like to ask if it is possible to do this? I'm unfortunately no longer able to run the script again (I am at the end of a time limited project and am preparing figures) and I would prefer not to replace each dash manually.
>
> I hope this is clear, the crux of what I am asking is if it is possible to select and/or hide individual distance objects in a pymol session after they have been merged into one object. Un-merging them would also be an attractive solution.
>
> Thanks,
>
> Harry
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
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Hi Harry,

If they've been combined using the group command, you can ungroup them:

fetch 1rx1
# make some distance objects
dist measure01, 19/C, 20/C
dist measure02, 20/C, 21/C
dist measure03, 158/C, 159/C
dist measure04, 157/C, 159/C
# group them
group g1, measure01 or measure02
group g2, measure03 or measure04
#ungroup all of them (this leaves empty groups, which you can delete if
you'd like)
ungroup measure*

Hope that helps,

-Michael

On Tue, Apr 26, 2011 at 5:47 AM, Harry Jubb <hj...@ca...> wrote:

> Hi Everyone,
>
> I'd like to ask for some help with dash/distance objects. I have PyMOL
> session files  which show inter-molecular interactions using PyMOL distance
> objects. These were created using a script which colours each distance
> object and merges them according to type of interaction. The problem I'm
> having is that I would prefer to visualise the interactions on a per-residue
> basis, i.e. showing all the interactions for one or more residues but not
> the others, but as the dashes are merged by interaction type I can only hide
> by that category. Extensive Googling has not led me to a solution to select
> and hide individual dashes that are merged into one UI object, so I'd like
> to ask if it is possible to do this? I'm unfortunately no longer able to run
> the script again (I am at the end of a time limited project and am preparing
> figures) and I would prefer not to replace each dash manually.
>
> I hope this is clear, the crux of what I am asking is if it is possible to
> select and/or hide individual distance objects in a pymol session after they
> have been merged into one object. Un-merging them would also be an
> attractive solution.
>
> Thanks,
>
> Harry
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)

you can write your own loop in python to implement the function.

fh = open(pdbfilename)
coords = 
numpy.array([[float(line[30:38]),float(line[38:46]),float(line[46:54])] 
for line in fh.readlines() if line.startswith('ATOM  ') or 
line.startswith('HETATM')])
fh.close()
extent = (numpy.min(coords,axis=0), numpy.max(coords,axis=0))

or course the code needs to be tuned if you need only the first MODEL or 
only the first alternate position etc.

cheers,hongbo

On 04/26/2011 01:40 PM, Martin Hediger wrote:
> Dear all
>
> I found that PyMOL offer the cmd.get_extent('protein') function, which
> returns the dimensions of the selection.
> Is it complicated to make this function available from within an
> ordinary Pythonscript?
>
> Thanks for hints.
> Martin
>
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> 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 Martin,

The following works for me, although I needed to change 'protein' to
'polymer'. Is 'protein' normally supported as a selection? It doesn't seem
to be in 1.4.1.

from pymol import cmd
cmd.fetch('1rx1')
a = cmd.get_extent('polymer')
print "a is",a

Hope that helps,

-Michael

On Tue, Apr 26, 2011 at 7:40 AM, Martin Hediger <ma...@bl...> wrote:

> Dear all
>
> I found that PyMOL offer the cmd.get_extent('protein') function, which
> returns the dimensions of the selection.
> Is it complicated to make this function available from within an
> ordinary Pythonscript?
>
> Thanks for hints.
> Martin
>
>
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)

On 04/26/2011 01:40 PM, Martin Hediger wrote:
> Dear all
>
> I found that PyMOL offer the cmd.get_extent('protein') function, which
> returns the dimensions of the selection.
> Is it complicated to make this function available from within an
> ordinary Pythonscript?

what do you mean with "ordinary Pythonscript"? Either your script is 
called by PyMOL directly (with "pymol -cqr yourscript.py"), or you have 
set up PYTHONPATH, PYMOL_PATH and PYMOL_DATA, run python and launch the 
PyMOL process within the script.

Maybe these pages will help:
http://pymolwiki.org/index.php/Launching_From_a_Script
http://pymolwiki.org/index.php/Python_Integration

Cheers,
   Thomas

--
Thomas Holder
MPI for Developmental Biology

Dear all

I found that PyMOL offer the cmd.get_extent('protein') function, which 
returns the dimensions of the selection.
Is it complicated to make this function available from within an 
ordinary Pythonscript?

Thanks for hints.
Martin

Hi Everyone,

I'd like to ask for some help with dash/distance objects. I have PyMOL session files  which show inter-molecular interactions using PyMOL distance objects. These were created using a script which colours each distance object and merges them according to type of interaction. The problem I'm having is that I would prefer to visualise the interactions on a per-residue basis, i.e. showing all the interactions for one or more residues but not the others, but as the dashes are merged by interaction type I can only hide by that category. Extensive Googling has not led me to a solution to select and hide individual dashes that are merged into one UI object, so I'd like to ask if it is possible to do this? I'm unfortunately no longer able to run the script again (I am at the end of a time limited project and am preparing figures) and I would prefer not to replace each dash manually.

I hope this is clear, the crux of what I am asking is if it is possible to select and/or hide individual distance objects in a pymol session after they have been merged into one object. Un-merging them would also be an attractive solution.

Thanks,

Harry

As Tsjerk pointed out!!.. it is exactly 8.3

ATOM    604  OG  SER A  77      37.493  60.526-103.507  1.00 26.47
O
                              123456781234567812345678


cheers,
Abhi

On Mon, Apr 25, 2011 at 12:59 PM, kanika sharma <ksh...@gm...>wrote:

> in the y-z coordinate the 8.3% format is not there..
>
>
> On Mon, Apr 25, 2011 at 4:09 PM, Tsjerk Wassenaar <ts...@gm...>wrote:
>
>> Hi Kanika,
>>
>> No, the spacing, or in this case the lack of it, is correct. The
>> coordinate section of the pdb file is %8.3f%8.3f%8.3f, i.e. each
>> coordinate eight characters wide with three decimal precision.
>>
>> Cheers,
>>
>> Tsjerk
>>
>>
>> On Mon, Apr 25, 2011 at 12:28 PM, kanika sharma <ksh...@gm...>
>> wrote:
>> > i have attached a small section of the file after applying the matrix..
>> > the spacing between x,y and z axis is abnormal
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
>>
>
>
>
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