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
B. Ch
On Wed, Feb 15, 2012 at 12:20 PM, Bachar Cheaib <cheaib.bac...@gmail.com>wrote:
> 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-requ...@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 <li...@cowsandmilk.net>
>> Subject: Re: [PyMOL] Open Source PyMOL v1.5.0.1
>> To: Jason Vertrees <jason.vertr...@schrodinger.com>
>> Cc: pymol-users@lists.sourceforge.net
>> Message-ID:
>> <
>> capuwn_9wwuwpcaa6htud3vsmbxmwguynqnj-kzdwowdt7b_...@mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> On Mon, Feb 13, 2012 at 2:27 PM, Jason Vertrees
>> <jason.vertr...@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.vertr...@schrodinger.com>
>> Subject: Re: [PyMOL] solid objects
>> To: Daniel Larsson <lars...@xray.bmc.uu.se>
>> Cc: pymol-users@lists.sourceforge.net
>> Message-ID:
>> <
>> caax+4zfqqdafwyiqmmdm3hkuiyrtvhoin70bc5eof4hbeae...@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 <lars...@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 <
>> lars...@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
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>> 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.vertr...@schrodinger.com
>> >> (o) +1 (603) 374-7120
>> >
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schr?dinger, LLC
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
>>
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Tue, 14 Feb 2012 09:32:54 -0800
>> From: "Thomas Stout" <tst...@exelixis.com>
>> Subject: [PyMOL] compiling Open Source PyMOL v1.5.0.1
>> To: <pymol-users@lists.sourceforge.net>
>> Message-ID:
>> <c5f9061847b41144899dc5637aef2d2201519...@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.vertr...@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.vertr...@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 <stanev...@wisc.edu>
>> Subject: [PyMOL] 1.5 version runs slow with "large" objects
>> To: pymol-users@lists.sourceforge.net
>> Message-ID:
>> <
>> caenulopwx566+1gotkjv1njwoeqnv1fssuwsulhqnm3-o90...@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
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Wed, 15 Feb 2012 13:30:30 +0300
>> From: ?????? ?????? <gontc...@gmail.com>
>> Subject: Re: [PyMOL] Open Source PyMOL v1.5.0.1
>> To: pymol-users@lists.sourceforge.net
>> Message-ID:
>> <
>> cacfscuydp4j7qmdps-bacd3d8vblcrsuhhkxuapf9opngy7...@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
>>
>>
>>
>> ------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>> Virtualization & Cloud Management Using Capacity Planning
>> Cloud computing makes use of virtualization - but cloud computing
>> also focuses on allowing computing to be delivered as a service.
>> http://www.accelacomm.com/jaw/sfnl/114/51521223/
>>
>> ------------------------------
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> PyMOL-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>> End of PyMOL-users Digest, Vol 69, Issue 12
>> *******************************************
>>
>
>
------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
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