Re: [PyMOL] PyMOL Project Updates & Open Source PyMOL v1.4b1

[Paul Rigor <paul.rigor@uc...>]

Hi David,

I actually ended up using the python distools instead. However, the viewer
flickers =\ Below is the log when starting up PyMol over X-windows from a
Mac OS X 10.6.x client.  Anyone encounter similar issues?

Detected OpenGL version prior to 2.0.  Shaders unavailable.
 OpenGL graphics engine:
  GL_VENDOR: ATI Technologies Inc.
  GL_RENDERER: ATI Radeon HD 2600 OpenGL Engine
  GL_VERSION: 1.4 (2.1 ATI-1.6.26)
 Adjusting settings to improve performance for ATI cards.
 Detected 16 CPU cores.  Enabled multithreaded rendering.
 OpenGL quad-buffer stereo 3D detected and enabled

Thanks,
Paul

--
Paul Rigor
http://www.ics.uci.edu/~prigor



On Wed, Apr 6, 2011 at 3:07 PM, <lists@...> wrote:

> I found the ce_types.h problem happens with autotools, but not with
> setup.py method.
>
> -David
>
> On Apr 6, 2011, at 5:59 PM, Paul Rigor <paul.rigor@...> wrote:
>
> Hi all,
>
> So I tried compiling the 1.4b today and came across a couple of issues.
> 1) The layer3/Executive.c is attempting to include "ce_types.h" locally but
> the header file is actually under 'modules/cealign/src'
>
> 2) With a quick hack, I was able to compile. However, when attempting to
> run the binary, I get the following error:
>     ImportError: /lv_disk00/preserve/tmp/pymol/modules/pymol/_cmd.so:
> undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE
>
> However, it seems that there is no missing library dependency (quick check
> with ldd).
>
> Has anyone run into any of these issues. I'm running python 2.6 on a CentOS
> 5.5 distro on a 64-bit machine.
>
> Thanks,
> paul
>
> --
> Paul Rigor
> <http://www.ics.uci.edu/~prigor>http://www.ics.uci.edu/~prigor
>
>
>
> On Mon, Apr 4, 2011 at 6:07 AM, Tru Huynh < <tru@...>tru@...
> > wrote:
>
>> Hi Jason,
>>
>> On Mon, Apr 04, 2011 at 08:19:17AM -0400, Jason Vertrees wrote:
>> >
>> > As you have discovered, and I forgot to mention, Python 2.5 or later
>> > is now required.  This is due to 64-bit types using Py_ssize_t.
>>
>> If the patch is the only thing needed to support "Py_ssize_t" for python
>> 2.4
>> please consider adding it for "backport".
>>
>> Cheers,
>>
>> Tru
>>
>> --
>> Dr Tru Huynh          | <http://www.pasteur.fr/recherche/unites/Binfs/>;
>> http://www.pasteur.fr/recherche/unites/Binfs/
>> mailto: <tru@...>tru@... | tel/fax +33 1 45 68 87 37/19
>> Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France
>>
>>
>> ------------------------------------------------------------------------------
>> Create and publish websites with WebMatrix
>> Use the most popular FREE web apps or write code yourself;
>> WebMatrix provides all the features you need to develop and
>> publish your website. <http://p.sf.net/sfu/ms-webmatrix-sf>;
>> http://p.sf.net/sfu/ms-webmatrix-sf
>> _______________________________________________
>> PyMOL-users mailing list ( <PyMOL-users@...>
>> PyMOL-users@...)
>> Info Page: <https://lists.sourceforge.net/lists/listinfo/pymol-users>;
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: <http://www.mail-archive.com/pymol-users@...>;
>> http://www.mail-archive.com/pymol-users@...
>>
>
>
> ------------------------------------------------------------------------------
> Xperia(TM) PLAY
> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
> http://p.sf.net/sfu/verizon-sfdev
>
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: <https://lists.sourceforge.net/lists/listinfo/pymol-users>;
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: <http://www.mail-archive.com/pymol-users@...>;
> http://www.mail-archive.com/pymol-users@...
>
>

Re: [PyMOL] PyMOL Project Updates & Open Source PyMOL v1.4b1

[<lists@co...>]

I found the ce_types.h problem happens with autotools, but not with setup.py method.

-David

On Apr 6, 2011, at 5:59 PM, Paul Rigor <paul.rigor@...> wrote:

> Hi all,
> 
> So I tried compiling the 1.4b today and came across a couple of issues.
> 1) The layer3/Executive.c is attempting to include "ce_types.h" locally but the header file is actually under 'modules/cealign/src'
> 
> 2) With a quick hack, I was able to compile. However, when attempting to run the binary, I get the following error:
>     ImportError: /lv_disk00/preserve/tmp/pymol/modules/pymol/_cmd.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE
> 
> However, it seems that there is no missing library dependency (quick check with ldd).
> 
> Has anyone run into any of these issues. I'm running python 2.6 on a CentOS 5.5 distro on a 64-bit machine.
> 
> Thanks,
> paul
> 
> --
> Paul Rigor
> http://www.ics.uci.edu/~prigor
> 
> 
> 
> On Mon, Apr 4, 2011 at 6:07 AM, Tru Huynh <tru@...> wrote:
> Hi Jason,
> 
> On Mon, Apr 04, 2011 at 08:19:17AM -0400, Jason Vertrees wrote:
> >
> > As you have discovered, and I forgot to mention, Python 2.5 or later
> > is now required.  This is due to 64-bit types using Py_ssize_t.
> 
> If the patch is the only thing needed to support "Py_ssize_t" for python 2.4
> please consider adding it for "backport".
> 
> Cheers,
> 
> Tru
> 
> --
> Dr Tru Huynh          | http://www.pasteur.fr/recherche/unites/Binfs/
> mailto:tru@... | tel/fax +33 1 45 68 87 37/19
> Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France
> 
> ------------------------------------------------------------------------------
> Create and publish websites with WebMatrix
> Use the most popular FREE web apps or write code yourself;
> WebMatrix provides all the features you need to develop and
> publish your website. http://p.sf.net/sfu/ms-webmatrix-sf
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...
> 
> ------------------------------------------------------------------------------
> Xperia(TM) PLAY
> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
> http://p.sf.net/sfu/verizon-sfdev
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...

Re: [PyMOL] PyMOL Project Updates & Open Source PyMOL v1.4b1

[Paul Rigor <paul.rigor@uc...>]

Hi all,

So I tried compiling the 1.4b today and came across a couple of issues.
1) The layer3/Executive.c is attempting to include "ce_types.h" locally but
the header file is actually under 'modules/cealign/src'

2) With a quick hack, I was able to compile. However, when attempting to run
the binary, I get the following error:
    ImportError: /lv_disk00/preserve/tmp/pymol/modules/pymol/_cmd.so:
undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE

However, it seems that there is no missing library dependency (quick check
with ldd).

Has anyone run into any of these issues. I'm running python 2.6 on a CentOS
5.5 distro on a 64-bit machine.

Thanks,
paul

--
Paul Rigor
http://www.ics.uci.edu/~prigor



On Mon, Apr 4, 2011 at 6:07 AM, Tru Huynh <tru@...> wrote:

> Hi Jason,
>
> On Mon, Apr 04, 2011 at 08:19:17AM -0400, Jason Vertrees wrote:
> >
> > As you have discovered, and I forgot to mention, Python 2.5 or later
> > is now required.  This is due to 64-bit types using Py_ssize_t.
>
> If the patch is the only thing needed to support "Py_ssize_t" for python
> 2.4
> please consider adding it for "backport".
>
> Cheers,
>
> Tru
>
> --
> Dr Tru Huynh          | http://www.pasteur.fr/recherche/unites/Binfs/
> mailto:tru@... | tel/fax +33 1 45 68 87 37/19
> Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France
>
>
> ------------------------------------------------------------------------------
> Create and publish websites with WebMatrix
> Use the most popular FREE web apps or write code yourself;
> WebMatrix provides all the features you need to develop and
> publish your website. http://p.sf.net/sfu/ms-webmatrix-sf
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...
>

Re: [PyMOL] How to color in a different way different helix types?

[Jason Vertrees <jason.vertrees@sc...>]

Hi Adam,

You could script this using the angle command with specific selections.

Cheers,

-- Jason

On Wed, Apr 6, 2011 at 11:49 AM, H. Adam Steinberg <adam@...> wrote:
> Jason (or someone else),
> Is there way in pymol to look for the following angle in a structure φ=-49o
> and ψ=-26o ? Which is the definition of a 310 helix. And yes we'd have to
> search for a few degrees plus of minus of those angles. They should all
> appear in tight turns and last for about 3 or 4 amino acids (I don't think
> there wouldn't be any cartoon helix shown).
> I don't think there are any pdbs yet that contain pi helices (because of the
> loose packing and steric hindrance of the side chains), does anyone know of
> any?
> Thanks
> Adam
> On Apr 6, 2011, at 8:16 AM, Jason Vertrees wrote:
>
> Hi Ramiro,
>
> PyMOL doesn't differentiate helices, so it cannot color them
> differently.  If you had the residue labels from some other program
> you could read them in and then color by type.
>
> Cheers,
>
> -- Jason
>
> On Wed, Apr 6, 2011 at 5:22 AM, Ramiro Téllez Sanz <urcindalo@...>
> wrote:
>
> Hi and thanks for reading this.
>
> I have googled for a way to achieve what I want and have gone through
>
> the wiki, to no avail.
>
> I would like to color in a different way the different helix types:
>
> alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get
>
> distinct colors for each type by default. But if the same pdb file is
>
> open with PyMOL all helices are treated the same way. Can't PyMOL
>
> distinguish helix types?
>
> Thanks in advance,
>
> Ramiro Téllez Sanz
>
> Dept. Physical Chemistry
>
> University of Almeria
>
> Spain
>
> ------------------------------------------------------------------------------
>
> Xperia(TM) PLAY
>
> It's a major breakthrough. An authentic gaming
>
> smartphone on the nation's most reliable network.
>
> And it wants your games.
>
> http://p.sf.net/sfu/verizon-sfdev
>
> _______________________________________________
>
> PyMOL-users mailing list (PyMOL-users@...)
>
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>
> Archives: http://www.mail-archive.com/pymol-users@...
>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jason.Vertrees@...
> (o) +1 (603) 374-7120
>
> ------------------------------------------------------------------------------
> Xperia(TM) PLAY
> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
> http://p.sf.net/sfu/verizon-sfdev
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...
>
> artforscience
> H. Adam Steinberg
> Artist, Scientist, Developmental Editor
> http://www.artforscience.com
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/729-5944
>



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

(e) Jason.Vertrees@...
(o) +1 (603) 374-7120

Re: [PyMOL] How to color in a different way different helix types?

[H. Adam Steinberg <adam@st...>]

Jason (or someone else),

Is there way in pymol to look for the following angle in a structure φ=-49o and ψ=-26o ? Which is the definition of a 310 helix. And yes we'd have to search for a few degrees plus of minus of those angles. They should all appear in tight turns and last for about 3 or 4 amino acids (I don't think there wouldn't be any cartoon helix shown).

I don't think there are any pdbs yet that contain pi helices (because of the loose packing and steric hindrance of the side chains), does anyone know of any?

Thanks 

Adam

On Apr 6, 2011, at 8:16 AM, Jason Vertrees wrote:

> Hi Ramiro,
> 
> PyMOL doesn't differentiate helices, so it cannot color them
> differently.  If you had the residue labels from some other program
> you could read them in and then color by type.
> 
> Cheers,
> 
> -- Jason
> 
> On Wed, Apr 6, 2011 at 5:22 AM, Ramiro Téllez Sanz <urcindalo@...> wrote:
>> Hi and thanks for reading this.
>> 
>> I have googled for a way to achieve what I want and have gone through
>> the wiki, to no avail.
>> 
>> I would like to color in a different way the different helix types:
>> alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get
>> distinct colors for each type by default. But if the same pdb file is
>> open with PyMOL all helices are treated the same way. Can't PyMOL
>> distinguish helix types?
>> 
>> Thanks in advance,
>> Ramiro Téllez Sanz
>> Dept. Physical Chemistry
>> University of Almeria
>> Spain
>> 
>> ------------------------------------------------------------------------------
>> Xperia(TM) PLAY
>> It's a major breakthrough. An authentic gaming
>> smartphone on the nation's most reliable network.
>> And it wants your games.
>> http://p.sf.net/sfu/verizon-sfdev
>> _______________________________________________
>> PyMOL-users mailing list (PyMOL-users@...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@...
>> 
> 
> 
> 
> -- 
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
> 
> (e) Jason.Vertrees@...
> (o) +1 (603) 374-7120
> 
> ------------------------------------------------------------------------------
> Xperia(TM) PLAY
> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
> http://p.sf.net/sfu/verizon-sfdev
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...

artforscience

H. Adam Steinberg
Artist, Scientist, Developmental Editor

 http://www.artforscience.com
7904 Bowman Rd
Lodi, WI 53555
608/729-5944

Re: [PyMOL] How to color in a different way different helix types?

[H. Adam Steinberg <adam@st...>]

Hi Ramiro,

Like you, I would love to see secondary structure colored by helix type.  Jmol however does not show this as a default. Do you know what steps you took to get Jmol to show secondary structure colored by helix type?

I can't seem to find that setting in any of the menu options.

style/scheme/cartoon
color/structure/cartoon/By Scheme/Secondary Structure

This shows all of the helices in the same color.

Adam


On Apr 6, 2011, at 4:22 AM, Ramiro Téllez Sanz wrote:

> Hi and thanks for reading this.
> 
> I have googled for a way to achieve what I want and have gone through
> the wiki, to no avail.
> 
> I would like to color in a different way the different helix types:
> alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get
> distinct colors for each type by default. But if the same pdb file is
> open with PyMOL all helices are treated the same way. Can't PyMOL
> distinguish helix types?
> 
> Thanks in advance,
> Ramiro Téllez Sanz
> Dept. Physical Chemistry
> University of Almeria
> Spain
> 
> ------------------------------------------------------------------------------
> Xperia(TM) PLAY
> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
> http://p.sf.net/sfu/verizon-sfdev
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...

artforscience

H. Adam Steinberg
Artist, Scientist, Developmental Editor

 http://www.artforscience.com
7904 Bowman Rd
Lodi, WI 53555
608/729-5944

Re: [PyMOL] How to color in a different way different helix types?

[Jason Vertrees <jason.vertrees@sc...>]

Hi Ramiro,

PyMOL doesn't differentiate helices, so it cannot color them
differently.  If you had the residue labels from some other program
you could read them in and then color by type.

Cheers,

-- Jason

On Wed, Apr 6, 2011 at 5:22 AM, Ramiro Téllez Sanz <urcindalo@...> wrote:
> Hi and thanks for reading this.
>
> I have googled for a way to achieve what I want and have gone through
> the wiki, to no avail.
>
> I would like to color in a different way the different helix types:
> alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get
> distinct colors for each type by default. But if the same pdb file is
> open with PyMOL all helices are treated the same way. Can't PyMOL
> distinguish helix types?
>
> Thanks in advance,
> Ramiro Téllez Sanz
> Dept. Physical Chemistry
> University of Almeria
> Spain
>
> ------------------------------------------------------------------------------
> Xperia(TM) PLAY
> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
> http://p.sf.net/sfu/verizon-sfdev
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...
>



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

(e) Jason.Vertrees@...
(o) +1 (603) 374-7120

Re: [PyMOL] Spectrumany bug?

[Anastassis Perrakis <a.perrakis@nk...>]

To wrap up and summarize, a new version of the script is available in  
the wiki that circumvents the minor python trouble,
and this works well with 1.2r2 and I guess later Pymol versions, and  
it works really well!

My favorite 'indian summer' gradients for now:

spectrumany count, paleyellow yelloworange brightorange, chain A
spectrumany count, olive deepolive splitpea, chain B
spectrumany count, orange ruby firebrick , chain C

Thanks -

Tassos


On Apr 6, 2011, at 8:54, Thomas Holder wrote:

> Hi Tassos,
>
> as Folmer already suggested your PyMOL version, or rather your python
> version could be the problem. The line that throws the error uses
> generator syntax, which was introduced in python 2.4. This can easily
> be backported so you don't need another python version. I updated the
> script in the wiki so it should work with older python now. Can you
> download again and try?
>
> Cheers,
>  Thomas
>
> On Tue, Apr 5, 2011 at 8:49 PM, Anastassis Perrakis  
> <a.perrakis@...> wrote:
>> Hi -
>>
>> I am trying to use the script by Thomas Holder, Spectrumany
>>
>> http://www.pymolwiki.org/index.php/Spectrumany
>>
>> When I import the script (run) I get:
>>
>> PyMOL>run sp.pml
>> Traceback (most recent call last):
>>   File "/Applications/MacPyMOL.app/pymol/modules/pymol/parser.py",
>> line 332, in parse
>>
>> parsing
>> .run_file(exp_path(layer.args[0]),self.pymol_names,self.pymol_names)
>>   File "/Applications/MacPyMOL.app/pymol/modules/pymol/parsing.py",
>> line 455, in run_file
>>     execfile(file,global_ns,local_ns)
>>   File "sp.pml", line 81
>>      col_name = '0x%02x%02x%02x' % tuple(i * 255 for i in col_list)
>>                                                    ^
>>  SyntaxError: invalid syntax
>>
>> ==
>>
>> any help?
>>
>> Tassos
>
> -- 
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen

P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

[PyMOL] How to color in a different way different helix types?

[Ramiro Téllez Sanz <urcindalo@gm...>]

Hi and thanks for reading this.

I have googled for a way to achieve what I want and have gone through
the wiki, to no avail.

I would like to color in a different way the different helix types:
alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get
distinct colors for each type by default. But if the same pdb file is
open with PyMOL all helices are treated the same way. Can't PyMOL
distinguish helix types?

Thanks in advance,
Ramiro Téllez Sanz
Dept. Physical Chemistry
University of Almeria
Spain

Re: [PyMOL] Spectrumany bug?

[Thomas Holder <speleo3@us...>]

Hi Tassos,

as Folmer already suggested your PyMOL version, or rather your python
version could be the problem. The line that throws the error uses
generator syntax, which was introduced in python 2.4. This can easily
be backported so you don't need another python version. I updated the
script in the wiki so it should work with older python now. Can you
download again and try?

Cheers,
  Thomas

On Tue, Apr 5, 2011 at 8:49 PM, Anastassis Perrakis <a.perrakis@...> wrote:
> Hi -
>
> I am trying to use the script by Thomas Holder, Spectrumany
>
> http://www.pymolwiki.org/index.php/Spectrumany
>
> When I import the script (run) I get:
>
> PyMOL>run sp.pml
> Traceback (most recent call last):
>   File "/Applications/MacPyMOL.app/pymol/modules/pymol/parser.py",
> line 332, in parse
>
> parsing
> .run_file(exp_path(layer.args[0]),self.pymol_names,self.pymol_names)
>   File "/Applications/MacPyMOL.app/pymol/modules/pymol/parsing.py",
> line 455, in run_file
>     execfile(file,global_ns,local_ns)
>   File "sp.pml", line 81
>      col_name = '0x%02x%02x%02x' % tuple(i * 255 for i in col_list)
>                                                    ^
>  SyntaxError: invalid syntax
>
> ==
>
> any help?
>
> Tassos

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen