pymol-users Mailing List for PyMOL Molecular Graphics System

awesome, thanks
On Tue, Sep 29, 2015 at 7:39 PM, Thomas Holder <
tho...@sc...> wrote:
> Hi Spencer,
>
> This was a threading issue, I have fixed the script.
>
> Passing a wrong name to PutCenterCallback results in the same threading
> issue. Should also be fixed.
>
> Cheers,
> Thomas
>
> On 29 Sep 2015, at 10:47, Spencer Bliven <spe...@gm...> wrote:
>
> > I'm using the callback version of the Axes script (third script at
> http://www.pymolwiki.org/index.php/Axes). In MacPyMol 1.7.6.3 syspython,
> deleting the constructed axes object causes Pymol to crash. It's an old
> script and I'm guessing not well maintained, but the crash is still
> unfortunate.
> >
> > As an aside, you can also crash many versions of pymol by making
> mistakes in the callback, such as passing a different name for the callback
> and the cgo object (yes, this is a silly thing to try, but it shouldn't
> crash).
> >
> > -Spencer
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Hi Carolina,
Can you reproduce the problem with other sdf files? (for example with the
one attached). Could your file be corrupted?
Cheers,
Osvaldo,
On Tue, Sep 29, 2015 at 8:15 PM, Carolina Stephania Castro Segura <
ste...@gm...> wrote:
>
> ---------- Forwarded message ----------
> From: Carolina Stephania Castro Segura <ste...@gm...>
> Date: 2015年09月29日 13:05 GMT-05:00
> Subject: visualization problems with pymol
> To: pym...@li...
>
>
> Hi pymol users!
>
> I installed pymol in a Windows 7 (32 bits). I can load a file without
> problems to pymol, but when i try to change the lines for sticks the
> molecule (a .sdf file) disappear ... so i have been trying to change the
> representations, but pymol online recognize lines.
> Did anyone knows how to fix it ?
>
> Thanks a lot
> Carolina Castro
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

---------- Forwarded message ----------
From: Carolina Stephania Castro Segura <ste...@gm...>
Date: 2015年09月29日 13:05 GMT-05:00
Subject: visualization problems with pymol
To: pym...@li...
Hi pymol users!
I installed pymol in a Windows 7 (32 bits). I can load a file without
problems to pymol, but when i try to change the lines for sticks the
molecule (a .sdf file) disappear ... so i have been trying to change the
representations, but pymol online recognize lines.
Did anyone knows how to fix it ?
Thanks a lot
Carolina Castro

Hi pymol users!
I installed pymol in a Windows 7 (32 bits). I can load a file without
problems to pymol but when i try to change the lines for sticks the
molecule (a .sdf file) disappear ... so i have been trying to change the
representations but pymol online recognize lines.
Did anyone knows how to fix it ?
Thanks a lot
Carolina Castro

Hi Spencer,
This was a threading issue, I have fixed the script.
Passing a wrong name to PutCenterCallback results in the same threading issue. Should also be fixed.
Cheers,
 Thomas
On 29 Sep 2015, at 10:47, Spencer Bliven <spe...@gm...> wrote:
> I'm using the callback version of the Axes script (third script at http://www.pymolwiki.org/index.php/Axes). In MacPyMol 1.7.6.3 syspython, deleting the constructed axes object causes Pymol to crash. It's an old script and I'm guessing not well maintained, but the crash is still unfortunate.
> 
> As an aside, you can also crash many versions of pymol by making mistakes in the callback, such as passing a different name for the callback and the cgo object (yes, this is a silly thing to try, but it shouldn't crash).
> 
> -Spencer
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

I'm using the callback version of the Axes script (third script at
http://www.pymolwiki.org/index.php/Axes). In MacPyMol 1.7.6.3 syspython,
deleting the constructed axes object causes Pymol to crash. It's an old
script and I'm guessing not well maintained, but the crash is still
unfortunate.
As an aside, you can also crash many versions of pymol by making mistakes
in the callback, such as passing a different name for the callback and the
cgo object (yes, this is a silly thing to try, but it shouldn't crash).
-Spencer

Dear pymol user,
I find my pymol installed in win7 system have some problems on the right button of the mouse. It cannot change the size of the the image in the Pymol viewer window; instead, when I click right botton of the mouse and drag, the size of the pymol viewer window changes: dragging the mouse down or up, the pymol viewer window becomes minized or maximaized, while dragging the mouse to the left or the right, the pymol viewer window goes to the left or the right of the computer screen. It is very strange and troubling. Did anyone experience this and how to fix it?  Thank you in advance!
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences

Dear pymol user,
I find my pymol install in win7 system have some problems on the right button of the mouse. It cannot change the size of the the image in the Pymole viewer window; instead, when I click right botton of the mouse and drag, the size of the pymol viewer window changes: dragging the mouse down or up, the 
pymol viewer window becomes minized or maximaized, while dragging the mouse to the left or the right, the 
pymol viewer window goes to the left or the right of the computer screen. It is very strange and troubling. Did anyone experiencing this and how to fix it?  Thank you in advance!
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences

Hi Arthur & Jerome,
I wrote a basic PDBML importer for PyMOL, see attached script which adds a "load_pdbml" command. I meant to assess the complexity of such a project and ended up writing the entire thing. So far, this only reads atoms and symmetry information. If you find this useful we can include that in the next PyMOL release.
Cheers,
 Thomas

Sorry for bumping old thread, but is support for pdbml still 
unimplemented? In such case i think it's a good project for our 
students.
Regards,
Arthur
> From: Thomas Holder <speleo3@us...> - 2013年12月02日 19:23:18
> Hi Jerome,
> 
> I think the simple reason is that nobody ever wrote a PDBML parser for 
> PyMOL. Is that a good reason?
> 
> Cheers,
> Thomas
> 
>> On 28 Nov 2013, at 13:21, Jerome BENOIT <g6299304p@...> wrote:
>> Hello List,
>> 
>> is there any good reason why PyMOL can not read PDBML data files ?
>> 
>> Cheers,
>> Jerome

Thank you so much Tsejrk and Seera for your kind help!!
Thomas replied. He said that I can load the .gro files too by giving a
command on the terminal.
PyMOL> cd your/working/directory
PyMOL> load file.gro
It worked!!
Thank you so much, once again. I'm sharing his reply here so that in case
anybody else faces the same problem, they can view this in the archive.
On Tue, Sep 22, 2015 at 8:24 PM, <pym...@li...>
wrote:
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>
> Today's Topics:
>
> 1. Re: Ploting coordinates (Tsjerk Wassenaar)
> 2. Re: Ploting coordinates (Thomas Holder)
> 3. Re: Ploting coordinates (Suzanne Scott)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: 2015年9月22日 11:34:26 +0200
> From: Tsjerk Wassenaar <ts...@gm...>
> Subject: Re: [PyMOL] Ploting coordinates
> To: Suzanne Scott <suz...@me...>
> Cc: "pym...@li..."
> <pym...@li...>
> Message-ID:
> <
> CAB...@ma...>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Suzanne,
>
> I'll make the guess that it's position and color. Are there any lines to be
> ignored? Probably this will work anyway... Save this in a script called
> holecgo.py:
>
>
> def holecgo(filename,radius=0.1,name="hole"):
> data = [ i.split() for i in open(filename) ]
> data = [ [ float(i) for i in k[:6] ] if len(k) == 7 and
> k[6].startswith("#") ]
> cmd.load_cgo([u for x,y,z,r,g,b in data for u in
> [6.0,r,g,b,7.0,x,y,z,radius]],name)
>
>
> Then in Pymol, do:
>
> run holecgo.py
> holecgo("yourfilename")
>
> You can add radius=0.25 or something else to make the spheres larger.
>
> Hope it helps,
>
> Tsjerk
>
>
>
> On Mon, Sep 21, 2015 at 9:06 PM, Suzanne Scott <
> suz...@me...> wrote:
>
> > Hi everyone,
> >
> > I hope this isn?t a silly question, but I?m not sure how to do it: I want
> > to plot some coordinates in PyMOL. Not atoms, just coordinates - they?re
> > the output of HOLE implemented in Coot, and have the following format:
> >
> > 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000
> > #7278cc
> > 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000
> > #7278cc
> > 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000
> > #7278cc
> > 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000
> > #7278cc
> >
> > Where the first three columns are the x, y and z coordinates, the next
> > three are the size of the object, and the last is the colour (which isn?t
> > so important - neither is the size, really). I can?t work out how to
> > import them into PyMOL. If anybody has any ideas, I?d be really
> grateful!
> >
> > Thanks,
> > Suzanne
> >
> >
> ------------------------------------------------------------------------------
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 2
> Date: 2015年9月22日 10:40:33 -0400
> From: Thomas Holder <tho...@sc...>
> Subject: Re: [PyMOL] Ploting coordinates
> To: Suzanne Scott <suz...@me...>, Tsjerk Wassenaar
> <ts...@gm...>
> Cc: "pym...@li..."
> <pym...@li...>
> Message-ID: <C67...@sc...>
> Content-Type: text/plain; charset=windows-1252
>
> Hi Suzanne & Tsjerk,
>
> To get those points in as pseudoatoms, you could also simply place a CIF
> atom site header above the data and load it as a .cif file.
>
> data_foo
> loop_
> _atom_site.Cartn_x
> _atom_site.Cartn_y
> _atom_site.Cartn_z
> _atom_site.ignore_size_a
> _atom_site.ignore_size_b
> _atom_site.ignore_size_c
> 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000
> #7278cc
>
> The color will be ignored because # is the comment delimiter.
>
> The only issue is that all atoms will have the same (empty) identifiers,
> so in order to select individual atoms, run something like this:
>
> PyMOL> alter all, resi=index
>
> Cheers,
> Thomas
>
> On 22 Sep 2015, at 05:34, Tsjerk Wassenaar <ts...@gm...> wrote:
>
> > Hi Suzanne,
> >
> > I'll make the guess that it's position and color. Are there any lines to
> be ignored? Probably this will work anyway... Save this in a script called
> holecgo.py:
> >
> >
> > def holecgo(filename,radius=0.1,name="hole"):
> > data = [ i.split() for i in open(filename) ]
> > data = [ [ float(i) for i in k[:6] ] if len(k) == 7 and
> k[6].startswith("#") ]
> > cmd.load_cgo([u for x,y,z,r,g,b in data for u in
> [6.0,r,g,b,7.0,x,y,z,radius]],name)
> >
> >
> > Then in Pymol, do:
> >
> > run holecgo.py
> > holecgo("yourfilename")
> >
> > You can add radius=0.25 or something else to make the spheres larger.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> >
> >
> > On Mon, Sep 21, 2015 at 9:06 PM, Suzanne Scott <
> suz...@me...> wrote:
> > Hi everyone,
> >
> > I hope this isn?t a silly question, but I?m not sure how to do it: I
> want to plot some coordinates in PyMOL. Not atoms, just coordinates -
> they?re the output of HOLE implemented in Coot, and have the following
> format:
> >
> > 145.32307 113.91329 116.36907 0.44800 0.47168
> 0.80000 #7278cc
> > 147.35472 113.65778 116.36907 0.44800 0.47168
> 0.80000 #7278cc
> > 149.39126 113.87088 116.36907 0.44800 0.47168
> 0.80000 #7278cc
> > 141.61303 115.28156 115.56962 0.44800 0.47168
> 0.80000 #7278cc
> >
> > Where the first three columns are the x, y and z coordinates, the next
> three are the size of the object, and the last is the colour (which isn?t
> so important - neither is the size, really). I can?t work out how to
> import them into PyMOL. If anybody has any ideas, I?d be really grateful!
> >
> > Thanks,
> > Suzanne
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schr?dinger, Inc.
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: 2015年9月22日 14:54:18 +0000
> From: Suzanne Scott <suz...@me...>
> Subject: Re: [PyMOL] Ploting coordinates
> To: Thomas Holder <tho...@sc...>
> Cc: Tsjerk Wassenaar <ts...@gm...>,
> "pym...@li..."
> <pym...@li...>
> Message-ID: <564...@me...>
> Content-Type: text/plain; charset="windows-1252"
>
> The code threw up a syntax error for me and I don?t know enough python to
> figure out why, but the CIF approach worked well, thanks very much!
>
>
> On 22 Sep 2015, at 15:40, Thomas Holder <tho...@sc...
> <mailto:tho...@sc...>> wrote:
>
> Hi Suzanne & Tsjerk,
>
> To get those points in as pseudoatoms, you could also simply place a CIF
> atom site header above the data and load it as a .cif file.
>
> data_foo
> loop_
> _atom_site.Cartn_x
> _atom_site.Cartn_y
> _atom_site.Cartn_z
> _atom_site.ignore_size_a
> _atom_site.ignore_size_b
> _atom_site.ignore_size_c
> 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000
> #7278cc
>
> The color will be ignored because # is the comment delimiter.
>
> The only issue is that all atoms will have the same (empty) identifiers,
> so in order to select individual atoms, run something like this:
>
> PyMOL> alter all, resi=index
>
> Cheers,
> Thomas
>
> On 22 Sep 2015, at 05:34, Tsjerk Wassenaar <ts...@gm...<mailto:
> ts...@gm...>> wrote:
>
> Hi Suzanne,
>
> I'll make the guess that it's position and color. Are there any lines to
> be ignored? Probably this will work anyway... Save this in a script called
> holecgo.py:
>
>
> def holecgo(filename,radius=0.1,name="hole"):
> data = [ i.split() for i in open(filename) ]
> data = [ [ float(i) for i in k[:6] ] if len(k) == 7 and
> k[6].startswith("#") ]
> cmd.load_cgo([u for x,y,z,r,g,b in data for u in
> [6.0,r,g,b,7.0,x,y,z,radius]],name)
>
>
> Then in Pymol, do:
>
> run holecgo.py
> holecgo("yourfilename")
>
> You can add radius=0.25 or something else to make the spheres larger.
>
> Hope it helps,
>
> Tsjerk
>
>
>
> On Mon, Sep 21, 2015 at 9:06 PM, Suzanne Scott <
> suz...@me...<mailto:suz...@me...>>
> wrote:
> Hi everyone,
>
> I hope this isn?t a silly question, but I?m not sure how to do it: I want
> to plot some coordinates in PyMOL. Not atoms, just coordinates - they?re
> the output of HOLE implemented in Coot, and have the following format:
>
> 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000
> #7278cc
>
> Where the first three columns are the x, y and z coordinates, the next
> three are the size of the object, and the last is the colour (which isn?t
> so important - neither is the size, really). I can?t work out how to
> import them into PyMOL. If anybody has any ideas, I?d be really grateful!
>
> Thanks,
> Suzanne
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schr?dinger, Inc.
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
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> ------------------------------
>
>
> ------------------------------------------------------------------------------
>
>
> ------------------------------
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> End of PyMOL-users Digest, Vol 112, Issue 8
> *******************************************
>
-- 
Regards,
Raag

The code threw up a syntax error for me and I don’t know enough python to figure out why, but the CIF approach worked well, thanks very much!
On 22 Sep 2015, at 15:40, Thomas Holder <tho...@sc...<mailto:tho...@sc...>> wrote:
Hi Suzanne & Tsjerk,
To get those points in as pseudoatoms, you could also simply place a CIF atom site header above the data and load it as a .cif file.
data_foo
loop_
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.ignore_size_a
_atom_site.ignore_size_b
_atom_site.ignore_size_c
 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000 #7278cc
 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000 #7278cc
 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000 #7278cc
 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000 #7278cc
The color will be ignored because # is the comment delimiter.
The only issue is that all atoms will have the same (empty) identifiers, so in order to select individual atoms, run something like this:
PyMOL> alter all, resi=index
Cheers,
 Thomas
On 22 Sep 2015, at 05:34, Tsjerk Wassenaar <ts...@gm...<mailto:ts...@gm...>> wrote:
Hi Suzanne,
I'll make the guess that it's position and color. Are there any lines to be ignored? Probably this will work anyway... Save this in a script called holecgo.py:
def holecgo(filename,radius=0.1,name="hole"):
 data = [ i.split() for i in open(filename) ]
 data = [ [ float(i) for i in k[:6] ] if len(k) == 7 and k[6].startswith("#") ]
 cmd.load_cgo([u for x,y,z,r,g,b in data for u in [6.0,r,g,b,7.0,x,y,z,radius]],name)
Then in Pymol, do:
run holecgo.py
holecgo("yourfilename")
You can add radius=0.25 or something else to make the spheres larger.
Hope it helps,
Tsjerk
On Mon, Sep 21, 2015 at 9:06 PM, Suzanne Scott <suz...@me...<mailto:suz...@me...>> wrote:
Hi everyone,
I hope this isn’t a silly question, but I’m not sure how to do it: I want to plot some coordinates in PyMOL. Not atoms, just coordinates - they’re the output of HOLE implemented in Coot, and have the following format:
 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000 #7278cc
 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000 #7278cc
 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000 #7278cc
 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000 #7278cc
Where the first three columns are the x, y and z coordinates, the next three are the size of the object, and the last is the colour (which isn’t so important - neither is the size, really). I can’t work out how to import them into PyMOL. If anybody has any ideas, I’d be really grateful!
Thanks,
Suzanne
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Suzanne & Tsjerk,
To get those points in as pseudoatoms, you could also simply place a CIF atom site header above the data and load it as a .cif file.
data_foo
loop_
_atom_site.Cartn_x 
_atom_site.Cartn_y 
_atom_site.Cartn_z 
_atom_site.ignore_size_a
_atom_site.ignore_size_b
_atom_site.ignore_size_c
 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000 #7278cc
 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000 #7278cc
 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000 #7278cc
 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000 #7278cc
The color will be ignored because # is the comment delimiter.
The only issue is that all atoms will have the same (empty) identifiers, so in order to select individual atoms, run something like this:
PyMOL> alter all, resi=index
Cheers,
 Thomas
On 22 Sep 2015, at 05:34, Tsjerk Wassenaar <ts...@gm...> wrote:
> Hi Suzanne,
> 
> I'll make the guess that it's position and color. Are there any lines to be ignored? Probably this will work anyway... Save this in a script called holecgo.py:
> 
> 
> def holecgo(filename,radius=0.1,name="hole"):
> data = [ i.split() for i in open(filename) ]
> data = [ [ float(i) for i in k[:6] ] if len(k) == 7 and k[6].startswith("#") ]
> cmd.load_cgo([u for x,y,z,r,g,b in data for u in [6.0,r,g,b,7.0,x,y,z,radius]],name)
> 
> 
> Then in Pymol, do:
> 
> run holecgo.py
> holecgo("yourfilename")
> 
> You can add radius=0.25 or something else to make the spheres larger.
> 
> Hope it helps,
> 
> Tsjerk
> 
> 
> 
> On Mon, Sep 21, 2015 at 9:06 PM, Suzanne Scott <suz...@me...> wrote:
> Hi everyone,
> 
> I hope this isn’t a silly question, but I’m not sure how to do it: I want to plot some coordinates in PyMOL. Not atoms, just coordinates - they’re the output of HOLE implemented in Coot, and have the following format:
> 
> 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000 #7278cc
> 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000 #7278cc
> 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000 #7278cc
> 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000 #7278cc
> 
> Where the first three columns are the x, y and z coordinates, the next three are the size of the object, and the last is the colour (which isn’t so important - neither is the size, really). I can’t work out how to import them into PyMOL. If anybody has any ideas, I’d be really grateful!
> 
> Thanks,
> Suzanne
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Suzanne,
I'll make the guess that it's position and color. Are there any lines to be
ignored? Probably this will work anyway... Save this in a script called
holecgo.py:
def holecgo(filename,radius=0.1,name="hole"):
 data = [ i.split() for i in open(filename) ]
 data = [ [ float(i) for i in k[:6] ] if len(k) == 7 and
k[6].startswith("#") ]
 cmd.load_cgo([u for x,y,z,r,g,b in data for u in
[6.0,r,g,b,7.0,x,y,z,radius]],name)
Then in Pymol, do:
run holecgo.py
holecgo("yourfilename")
You can add radius=0.25 or something else to make the spheres larger.
Hope it helps,
Tsjerk
On Mon, Sep 21, 2015 at 9:06 PM, Suzanne Scott <
suz...@me...> wrote:
> Hi everyone,
>
> I hope this isn’t a silly question, but I’m not sure how to do it: I want
> to plot some coordinates in PyMOL. Not atoms, just coordinates - they’re
> the output of HOLE implemented in Coot, and have the following format:
>
> 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000
> #7278cc
>
> Where the first three columns are the x, y and z coordinates, the next
> three are the size of the object, and the last is the colour (which isn’t
> so important - neither is the size, really). I can’t work out how to
> import them into PyMOL. If anybody has any ideas, I’d be really grateful!
>
> Thanks,
> Suzanne
>
> ------------------------------------------------------------------------------
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
-- 
Tsjerk A. Wassenaar, Ph.D.

Hi Joel,
Were does the shortcut point to (Right-click on the icon > Properties > Target) and does it have any additional flags like forcing stereo? The default shortcut points to "PymolWin.exe -J", which will start PyMOL with "My Documents" as the working directory.
Cheers,
 Thomas
On 10 Sep 2015, at 01:13, Joel Tyndall <joe...@ot...> wrote:
> Hilist,
> 
> Got an annoying issue on my windows 7 and (8 machines). When I open pymol from the icon shortcut it crashes with the error "pymol.exe has stopped working... close program". Same issue from the start menu. I can open the program by double clicking on a pdb file and there are no issues.
> 
> Current version is 1.7.6.2
> 
> Any idea how to fix this? Might be my hardware but just wondering if others see this or there is a fix?
> J
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Albert,
Yes, Incentive PyMOL since version 1.6 can read properties from SD files. Example:
# load a file with all properties
set load_object_props_default, *
load example.sdf
# query loaded properties
get_property_list example
# query the MOLID property
get_property MOLID, example
# version 1.7 also provides a wizard to browse properties:
wizard properties
Hope that helps.
Cheers,
 Thomas 
On 15 Sep 2015, at 03:47, Albert <mai...@gm...> wrote:
> Hello:
> 
> I've got a ligand .sdf file which contains many informations such as: 
> molecule weight, logP, surface area and so on. I am just wondering is it 
> possible to display those properties in Pymol?
> 
> Thank you very much
> 
> Albert
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Albert,
Incentive PyMOL can do that, simply type:
label all, stereo
This feature is provided by a proprietary library and thus not available in Open-Source PyMOL.
Cheers,
 Thomas
On 16 Sep 2015, at 03:15, Albert <mai...@gm...> wrote:
> Hello:
> 
> Does anybody have any idea whether pymol could label the absolute 
> configuration (R/S) for a chiarity atom?
> 
> Thank you very much.
> 
> Albert
-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi everyone,
I hope this isn’t a silly question, but I’m not sure how to do it: I want to plot some coordinates in PyMOL. Not atoms, just coordinates - they’re the output of HOLE implemented in Coot, and have the following format:
 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000 #7278cc
 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000 #7278cc
 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000 #7278cc
 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000 #7278cc
Where the first three columns are the x, y and z coordinates, the next three are the size of the object, and the last is the colour (which isn’t so important - neither is the size, really). I can’t work out how to import them into PyMOL. If anybody has any ideas, I’d be really grateful!
Thanks,
Suzanne

Cmd.get_view gives you a matrix where the 9th, 10th and 11th numbers give
you the origin of rotation relative to the camera, and 15th and 16th gives
you the front and rear plane distance from the camera, respectively. That
plus some math, and I think you are done. Maybe there is an easier way
though.
Cheers,
João
On Sep 17, 2015 4:50 PM, "wtempel" <wt...@gm...> wrote:
> Hello,
> how can I "get" the the current slab settings, that is settings that are
> adjusted with the clip command: current center of slab (relative to
> center of rotation?), depth of slab?
> Thank you,
> Wolfram Tempel
> ​
>
>
> ------------------------------------------------------------------------------
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> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hello,
how can I "get" the the current slab settings, that is settings that are
adjusted with the clip command: current center of slab (relative to center
of rotation?), depth of slab?
Thank you,
Wolfram Tempel
​

Hello:
Does anybody have any idea whether pymol could label the absolute 
configuration (R/S) for a chiarity atom?
Thank you very much.
Albert

Hey Osvaldo,
I wasn't sure whether it was COG or COM. For a ligand it may matter. For a
macromolecule it won't. That's easy to see by considering the COM as the
weighted average of the COGs per atom type. Because the distributions will
be pretty much the same in all directions, the COGs will be approximately
the same and hence the COM will be equal to the COG.
:)
Tsjerk
On Tue, Sep 15, 2015 at 10:09 PM, Osvaldo Martin <alo...@gm...>
wrote:
> Hi,
>
> Tsjerk you are right pseudoatom puts a new atom on the geometric center of
> a selection.
> Just a clarification, the center of mass and the geometric center (AKA
> centroid) are not exactly the same thing. The geometric center is the
> average of the coordinates and the center of mass is the mass-weighted
> average of the coordinates. I understand that for many practical purposes
> both can be used interchangeably since they could be numerically similar.
>
> Cheers,
> Osvaldo.
>
>
>
>
> On Tue, Sep 15, 2015 at 3:36 PM, Tsjerk Wassenaar <ts...@gm...>
> wrote:
>
>> Hi,
>>
>> AFAIK, pseudoatom puts a new atom on the center of mass (or geometry) of
>> the selection. So,
>>
>> import glob
>> from pymol import cmd
>>
>> for pdb in glob.glob("*.pdb"): cmd.pseudoatom(pdb[-3:],"{} and resn
>> LIGANDNAME".format(pdb))
>>
>> Or along those lines. Be creative :)
>>
>> Cheers,
>>
>> Tsjerk
>>
>>
>> On Tue, Sep 15, 2015 at 12:25 AM, Osvaldo Martin <alo...@gm...>
>> wrote:
>>
>>> Hi Zakir,
>>>
>>> The following script computes the Center Of Mass (or alternative the
>>> geometric center) and then draws a pseudoatom
>>> <http://www.pymolwiki.org/index.php/Pseudoatom>. I think you could
>>> adapt the script to your needs if you find difficulties, don’t hesitate to
>>> contact the list again (your question is not silly).
>>>
>>>
>>> import pymol
>>> from pymol import cmd
>>> pymol.finish_launching()
>>> import numpy as np
>>>
>>> def center(selection, com=True):
>>> model = cmd.get_model(selection)
>>> xyz = np.array(model.get_coord_list())
>>> mass = [i.get_mass() for i in model.atom]
>>> xyz_m = xyz * np.array([mass]).T
>>> if com:
>>> return tuple(np.sum(xyz_m, 0)/model.get_mass())
>>> else:
>>> return tuple(np.average(xyz, 0))
>>>
>>>
>>> cmd.load('some_file.pdb')
>>> COM = center('all')
>>> cmd.pseudoatom('center', pos=COM)
>>>
>>> Alternatively, you can use this script
>>> <http://www.pymolwiki.org/index.php/Center_of_mass> to compute the
>>> center of mass.
>>>
>>> Cheers,
>>> Osvaldo
>>>
>>>
>>> On Mon, Sep 14, 2015 at 4:29 PM, Zakir Tnimov <zak...@gm...>
>>> wrote:
>>>
>>> Hi there,
>>>>
>>>> I have no experience in scripting what so ever thus this simple task
>>>> drives me nuts.
>>>> I was using ZDOCK to dock my protein on the complex. It spits me out
>>>> 2000 pdb files that each contain a ligand and receptor. Receptor position
>>>> is fixed, ligand is not. What I want to show is just centre of mass of the
>>>> ligand and a receptor. I understand that I should be doing something like
>>>> this:
>>>>
>>>> from pymol import cmd
>>>> from glob import glob
>>>>
>>>> for file in glob("*.pdb"):
>>>> print file
>>>> cmd.load(file,'prot')
>>>> for a in cmd.index("CYS/SG"):
>>>> identify COM
>>>> print its location as a dot or sphere
>>>> delete loaded file
>>>> go to another one until list is exhousted
>>>>
>>>> cmd.delete("all")
>>>>
>>>> Thank you a lot and sorry for bothering you with such a silly question!
>>>>
>>>>
>>>> zak...@gm...
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyM...@li...)
>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>> ​
>>>
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>>
>
-- 
Tsjerk A. Wassenaar, Ph.D.

Hi,
Tsjerk you are right pseudoatom puts a new atom on the geometric center of
a selection.
Just a clarification, the center of mass and the geometric center (AKA
centroid) are not exactly the same thing. The geometric center is the
average of the coordinates and the center of mass is the mass-weighted
average of the coordinates. I understand that for many practical purposes
both can be used interchangeably since they could be numerically similar.
Cheers,
Osvaldo.
On Tue, Sep 15, 2015 at 3:36 PM, Tsjerk Wassenaar <ts...@gm...> wrote:
> Hi,
>
> AFAIK, pseudoatom puts a new atom on the center of mass (or geometry) of
> the selection. So,
>
> import glob
> from pymol import cmd
>
> for pdb in glob.glob("*.pdb"): cmd.pseudoatom(pdb[-3:],"{} and resn
> LIGANDNAME".format(pdb))
>
> Or along those lines. Be creative :)
>
> Cheers,
>
> Tsjerk
>
>
> On Tue, Sep 15, 2015 at 12:25 AM, Osvaldo Martin <alo...@gm...>
> wrote:
>
>> Hi Zakir,
>>
>> The following script computes the Center Of Mass (or alternative the
>> geometric center) and then draws a pseudoatom
>> <http://www.pymolwiki.org/index.php/Pseudoatom>. I think you could adapt
>> the script to your needs if you find difficulties, don’t hesitate to
>> contact the list again (your question is not silly).
>>
>>
>> import pymol
>> from pymol import cmd
>> pymol.finish_launching()
>> import numpy as np
>>
>> def center(selection, com=True):
>> model = cmd.get_model(selection)
>> xyz = np.array(model.get_coord_list())
>> mass = [i.get_mass() for i in model.atom]
>> xyz_m = xyz * np.array([mass]).T
>> if com:
>> return tuple(np.sum(xyz_m, 0)/model.get_mass())
>> else:
>> return tuple(np.average(xyz, 0))
>>
>>
>> cmd.load('some_file.pdb')
>> COM = center('all')
>> cmd.pseudoatom('center', pos=COM)
>>
>> Alternatively, you can use this script
>> <http://www.pymolwiki.org/index.php/Center_of_mass> to compute the
>> center of mass.
>>
>> Cheers,
>> Osvaldo
>>
>>
>> On Mon, Sep 14, 2015 at 4:29 PM, Zakir Tnimov <zak...@gm...>
>> wrote:
>>
>> Hi there,
>>>
>>> I have no experience in scripting what so ever thus this simple task
>>> drives me nuts.
>>> I was using ZDOCK to dock my protein on the complex. It spits me out
>>> 2000 pdb files that each contain a ligand and receptor. Receptor position
>>> is fixed, ligand is not. What I want to show is just centre of mass of the
>>> ligand and a receptor. I understand that I should be doing something like
>>> this:
>>>
>>> from pymol import cmd
>>> from glob import glob
>>>
>>> for file in glob("*.pdb"):
>>> print file
>>> cmd.load(file,'prot')
>>> for a in cmd.index("CYS/SG"):
>>> identify COM
>>> print its location as a dot or sphere
>>> delete loaded file
>>> go to another one until list is exhousted
>>>
>>> cmd.delete("all")
>>>
>>> Thank you a lot and sorry for bothering you with such a silly question!
>>>
>>>
>>> zak...@gm...
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>
>> ​
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>

Hi,
AFAIK, pseudoatom puts a new atom on the center of mass (or geometry) of
the selection. So,
import glob
from pymol import cmd
for pdb in glob.glob("*.pdb"): cmd.pseudoatom(pdb[-3:],"{} and resn
LIGANDNAME".format(pdb))
Or along those lines. Be creative :)
Cheers,
Tsjerk
On Tue, Sep 15, 2015 at 12:25 AM, Osvaldo Martin <alo...@gm...>
wrote:
> Hi Zakir,
>
> The following script computes the Center Of Mass (or alternative the
> geometric center) and then draws a pseudoatom
> <http://www.pymolwiki.org/index.php/Pseudoatom>. I think you could adapt
> the script to your needs if you find difficulties, don’t hesitate to
> contact the list again (your question is not silly).
>
>
> import pymol
> from pymol import cmd
> pymol.finish_launching()
> import numpy as np
>
> def center(selection, com=True):
> model = cmd.get_model(selection)
> xyz = np.array(model.get_coord_list())
> mass = [i.get_mass() for i in model.atom]
> xyz_m = xyz * np.array([mass]).T
> if com:
> return tuple(np.sum(xyz_m, 0)/model.get_mass())
> else:
> return tuple(np.average(xyz, 0))
>
>
> cmd.load('some_file.pdb')
> COM = center('all')
> cmd.pseudoatom('center', pos=COM)
>
> Alternatively, you can use this script
> <http://www.pymolwiki.org/index.php/Center_of_mass> to compute the center
> of mass.
>
> Cheers,
> Osvaldo
>
>
> On Mon, Sep 14, 2015 at 4:29 PM, Zakir Tnimov <zak...@gm...>
> wrote:
>
> Hi there,
>>
>> I have no experience in scripting what so ever thus this simple task
>> drives me nuts.
>> I was using ZDOCK to dock my protein on the complex. It spits me out 2000
>> pdb files that each contain a ligand and receptor. Receptor position is
>> fixed, ligand is not. What I want to show is just centre of mass of the
>> ligand and a receptor. I understand that I should be doing something like
>> this:
>>
>> from pymol import cmd
>> from glob import glob
>>
>> for file in glob("*.pdb"):
>> print file
>> cmd.load(file,'prot')
>> for a in cmd.index("CYS/SG"):
>> identify COM
>> print its location as a dot or sphere
>> delete loaded file
>> go to another one until list is exhousted
>>
>> cmd.delete("all")
>>
>> Thank you a lot and sorry for bothering you with such a silly question!
>>
>>
>> zak...@gm...
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
> ​
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
-- 
Tsjerk A. Wassenaar, Ph.D.

Hi Raag,
Did pymol crash (quit) with a PDB file written by Gromacs? That can (I
think) only happen if the PDB file is corrupted, for example by coordinates
going out of bound during a simulation. What did you do to obtain the PDB
file?
Cheers,
Tsjerk
On Tue, Sep 15, 2015 at 7:20 AM, Raag Saluja <sal...@gm...> wrote:
> Hi!
> I am running a simulation using Gromacs. I was able to visualise the .pdb
> file using pymol. But when I tried to visuals the files created by Gromacs,
> pymol crashed. Can you please help? Thank you in advance!
>
> --
> Regards,
> Raag
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
-- 
Tsjerk A. Wassenaar, Ph.D.