If you need publication citation, I would go for the
Cealign   ww.pymolwiki.org/index.php/Cealign

There is references you can read and understand. :-)

See a list of alignment methods and tools
http://www.pymolwiki.org/index.php/Align#SEE_ALSO


Best
T


Troels Emtekær Linnet
Lyongade 24. 4.mf, 2300 København S
Mobil:
+45 60210234



2012/2/15 Bachar Cheaib <cheaib.bachar@gmail.com>
Dear All,

I am a Pymol's user

I would like to know how could I find the algorithm publication of three functions for superimposition of multi-structures?

1- fit
2- align
3- super

I would thanks in advance for your reply

Sincerely



BaCh

On Wed, Feb 15, 2012 at 11:31 AM, <pymol-users-request@lists.sourceforge.net> wrote:
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Today's Topics:

  1. Re: Open Source PyMOL v1.5.0.1 (David Hall)
  2. Re: solid objects (Jason Vertrees)
  3. compiling Open Source PyMOL v1.5.0.1 (Thomas Stout)
  4. 1.5 version runs slow with "large" objects (Vitali Stanevich)
  5. Re: Open Source PyMOL v1.5.0.1 (?????? ??????)


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

Message: 1
Date: Tue, 14 Feb 2012 12:03:33 -0500
From: David Hall <lists@cowsandmilk.net>
Subject: Re: [PyMOL] Open Source PyMOL v1.5.0.1
To: Jason Vertrees <jason.vertrees@schrodinger.com>
Cc: pymol-users@lists.sourceforge.net
Message-ID:
       <CAPUwN_9WwuwpcAa6hTUd3VsMBxmWgUYnQNj-kZdwoWDT7b_qtA@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

On Mon, Feb 13, 2012 at 2:27 PM, Jason Vertrees
<jason.vertrees@schrodinger.com> wrote:
> Greetings,
>
> It is my pleasure to announce the release of open source PyMOL
> v1.5.0.1. The source code has been committed to the open-source
> repository. It is revision 3976. An svn tag and downloadable bz2
> source file were also created. All of this is accessible form the
> PyMOL project page on SourceForge
> (http://sourceforge.net/projects/pymol/).

For those of you on openSUSE, I've updated the pymol packages in the
openSUSE Build Service to this release. You can test this new version
by visiting http://software.opensuse.org/download.html?project=devel:languages:python&package=pymol
and choosing the appropriate openSUSE release and architecture.

-David



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

Message: 2
Date: Tue, 14 Feb 2012 12:40:02 -0500
From: Jason Vertrees <jason.vertrees@schrodinger.com>
Subject: Re: [PyMOL] solid objects
To: Daniel Larsson <larsson@xray.bmc.uu.se>
Cc: pymol-users@lists.sourceforge.net
Message-ID:
       <CAAx+4zfQqDafwyiQMMDm3hKUiyRtVHoin70BC5eoF4HbEaE9tA@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Daniel,

Filling clipped spheres is not yet available. We'll look at adding it.

Cheers,

-- Jason

On Tue, Feb 14, 2012 at 12:00 PM, Daniel Larsson <larsson@xray.bmc.uu.se> wrote:
> Thanks for the quick reply.
>
> A closely related issue is that clipped spheres are rendered very strangely. It seems they only consists of a half-sphere and if the clipping plane intersects the sphere in the front-most half, then you can see straight through it.
>
> Daniel
>
>
> On Feb 14, 2012, at 17:50 , Jason Vertrees wrote:
>
>> Daniel,
>>
>> # reset the setting
>>
>> set ray_interior_color, default
>>
>> # set the setting for each object
>>
>> set ray_interior_color, marine, protA
>>
>> set ray_interior_color, magenta, protB
>>
>>
>> PyMOL does not support this via the 'draw' command (unless you set
>> draw_mode, 3, but that's just ray tracing). Please file an RFE and
>> we'll look into it.
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Tue, Feb 14, 2012 at 11:17 AM, Daniel Larsson <larsson@xray.bmc.uu.se> wrote:
>>> Hi,
>>>
>>> Is there a way to render truncated/clipped objects as "dense". I.e. a "lid" on clipped objects, such as surfaces or spheres.
>>>
>>> Want I want is something similar to the "A sliced image" example in the wiki gallery (http://www.pymolwiki.org/index.php/Gallery), but with that technique I can only pick one color for all molecules. I would like to set "ray_interior_color" different for different molecules or objects. Basically, I want the color to be the same on the inside as on the outside. It would be great if it would work with the "draw" command as well.
>>>
>>> Is it possible with version 1.5? Or is there a chances of having this implemented anytime soon?
>>>
>>> Daniel
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Keep Your Developer Skills Current with LearnDevNow!
>>> The most comprehensive online learning library for Microsoft developers
>>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>>> Metro Style Apps, more. Free future releases when you subscribe now!
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>>> _______________________________________________
>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schr?dinger, LLC
>>
>> (e) Jason.Vertrees@schrodinger.com
>> (o) +1 (603) 374-7120
>



--
Jason Vertrees, PhD
PyMOL Product Manager
Schr?dinger, LLC

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



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

Message: 3
Date: Tue, 14 Feb 2012 09:32:54 -0800
From: "Thomas Stout" <tstout@exelixis.com>
Subject: [PyMOL] compiling Open Source PyMOL v1.5.0.1
To: <pymol-users@lists.sourceforge.net>
Message-ID:
       <C5F9061847B41144899DC5637AEF2D2201519522@EXCL01.exelixis.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi All -

I am trying to compile the open-source code for PyMOL for the first time (on CentOS) and running into all sorts of issues.  Is there a listing somewhere of all the dependencies (and their versions) that I could use as a guide to get everything I need all at once, rather than continuing to fix compile failures one-at-a-time (which is confusing and frustrating)

Conversely, is there a distro that more-or-less "just works"?  I can create a virtual machine in which I compile, but I'm only allowed to have RHEL or CentOS on my physical machine...

Thanks!
-Tom



________________________________

From: Jason Vertrees [mailto:jason.vertrees@schrodinger.com]
Sent: Mon 2/13/2012 11:27 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Open Source PyMOL v1.5.0.1



Greetings,

It is my pleasure to announce the release of open source PyMOL
v1.5.0.1. The source code has been committed to the open-source
repository. It is revision 3976. An svn tag and downloadable bz2
source file were also created. All of this is accessible form the
PyMOL project page on SourceForge
(http://sourceforge.net/projects/pymol/).

Before upgrading PyMOL -- please -- upgrade your video drivers! NVidia
and AMD/ATI cards are known to work well. But, Intel Mobile and other
low-end cards might have issues with the new rendering. The majority
of rendering anomalies are fixed by simply upgrading your video
drivers.

You should be able to pull and build just like normal. You will need Python 2.7.

Some simple testing on my Linux machine shows the following
improvements in real-time rendering performance for a large protein
(58,000 atom Gro-EL, PDB 1AON) with the new open-source PyMOL code:

Lines:
  240% increase (81 FPS to 270 FPS)
Spheres:
  864% increase (28 FPS to 270 FPS)
Sticks:
  2100% increase (8 FPS to 180 FPS)
Cartoon:
  3757% increase (27 to 270 FPS)
Surface:
  2600% increase (10 to 270 FPS)
Mesh:
  33% (180 FPS to 270 FPS)

Your numbers will be different. This Linux machine has a powerful card
used for development
(http://www.amd.com/us/products/workstation/graphics/ati-firepro-3d/v8800/Pages/v8800.aspx).
It was generously donated by AMD. If you use an AMD/ATI card and PyMOL
works for you it's because AMD/ATI helped out. You may want to thank
them. What I've seen is that the more powerful your card the greater
the _difference_ in speed. That is, low-end cards should see
improvements in the range of tens to hundreds of percent while more
powerful cards should register improvements like mine, in the
thousands of percent for some representations.

To quickly test performance of the new code on your machine just load
a large structure (eg. 1AON; 3R8O and 3R8T) and quickly
rotate/translate it. To see the refresh rate, type "set
show_frame_rate". The refresh rate shows up in the lower right hand
corner. Compare the frame rate, smoothness, and rendering quality when
the setting "use_shaders" is turned off and when it's turned on.
Compare different representations, each time turning on and off the
"use_shaders" setting.

You can quickly update old PyMOL session files to the new rendering by
clicking, Settings > Rendering > Modernize after loading the old
session file. PyMOL will flip all the right settings to update
rendering. If the new code doesn't render properly, you can revert to
the old style rendering by typing:

 set use_shaders, 0

 set sphere_mode, 0


Please let us know how it goes.

Cheers,

-- Jason, Blaine & the PyMOL Team

--
Jason Vertrees, PhD
PyMOL Product Manager
Schr?dinger, LLC

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

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

Message: 4
Date: Tue, 14 Feb 2012 16:27:32 -0600
From: Vitali Stanevich <stanevich@wisc.edu>
Subject: [PyMOL] 1.5 version runs slow with "large" objects
To: pymol-users@lists.sourceforge.net
Message-ID:
       <CAENULoPwx566+1GOTkJV1nJwOEqNV1fsSUwsULHqnm3-o90DWw@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi,

I recently installed a new version of licensed pymol 1.5. It works ok with
small molecules (<25 kDa). But, unfortunately, I found that after I load
relatively large molecules (>60 kDa) everything really slows down,
movements become somewhat abrupt and etc. At the same time, I can open this
molecule with coot, generate bunch of symmetry mates, add maps, but
everything runs really smooth. How can I make pymol run smooth again
(version 1.2 worked well before)?

Pymol: PyMOL-v1.5.0-Linux-x86_32-TclTk8.5 (I tried 64-bit with the same
result)
OS: Ubuntu 10.10
Video card: nVidia GeForce 7150M
CPU: AMD Turion(tm) 64 X2 TL-62 (2100 MHz, 64 bits)

Thanks,
Vitali
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Message: 5
Date: Wed, 15 Feb 2012 13:30:30 +0300
From: ?????? ?????? <gontchar@gmail.com>
Subject: Re: [PyMOL] Open Source PyMOL v1.5.0.1
To: pymol-users@lists.sourceforge.net
Message-ID:
       <CACFSCuYdP4j7QMDPs-bACD3d8vbLcrsuHHKxuApf9opnGy7FhQ@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Hi all!
I've just installed a new version of PyMol, but when I select a
repersentation different to the default, it displays a blank screen
and returns

unsupported IR in fragment shader 13
unsupported IR in fragment shader 13
unsupported IR in fragment shader 13
unsupported IR in fragment shader 13
unsupported IR in fragment shader 13

I run PyMol n Debian Squeeze x64, I have an integrated video

 Detected OpenGL version 2.0 or greater.  Shaders available.
 Detected GLSL version 1.20.
 OpenGL graphics engine:
 GL_VENDOR: Tungsten Graphics, Inc
 GL_RENDERER: Mesa DRI Intel(R) G41 GEM 20091221 2009Q4
 GL_VERSION: 2.1 Mesa 7.7.1

--

Andrew Gonchar



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