Re: [PyMOL] PyMOL-users Digest, Vol 69, Issue 12

[Bachar C. <che...@gm...>]

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, <pym...@li...
> wrote:

> Send PyMOL-users mailing list submissions to
>        pym...@li...
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
>        pym...@li...
>
> You can reach the person managing the list at
>        pym...@li...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
>
>
> 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...@co...>
> Subject: Re: [PyMOL] Open Source PyMOL v1.5.0.1
> To: Jason Vertrees <jas...@sc...>
> Cc: pym...@li...
> Message-ID:
>        <CAP...@ma...
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Mon, Feb 13, 2012 at 2:27 PM, Jason Vertrees
> <jas...@sc...> 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 <jas...@sc...>
> Subject: Re: [PyMOL] solid objects
> To: Daniel Larsson <la...@xr...>
> Cc: pym...@li...
> Message-ID:
>        <CAA...@ma...
> >
> 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 <la...@xr...>
> 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 <
> la...@xr...> 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!
> >>> http://p.sf.net/sfu/learndevnow-d2d
> >>> _______________________________________________
> >>> 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
> >> Schr?dinger, LLC
> >>
> >> (e) Jas...@sc...
> >> (o) +1 (603) 374-7120
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schr?dinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 14 Feb 2012 09:32:54 -0800
> From: "Thomas Stout" <ts...@ex...>
> Subject: [PyMOL] compiling Open Source PyMOL v1.5.0.1
> To: <pym...@li...>
> Message-ID:
>        <C5F...@EX...>
> 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:jas...@sc...]
> Sent: Mon 2/13/2012 11:27 AM
> To: pym...@li...
> 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) Jas...@sc...
> (o) +1 (603) 374-7120
>
>
> ------------------------------------------------------------------------------
> Try before you buy = See our experts in action!
> 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!
> http://p.sf.net/sfu/learndevnow-dev2
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> This email (including any attachments) may contain material
> that is confidential and privileged and is for the sole use of
> the intended recipient. Any review, reliance or distribution by
> others or forwarding without express permission is strictly
> prohibited. If you are not the intended recipient, please
> contact the sender and delete all copies.
> Exelixis, Inc. reserves the right, to the extent and under
> circumstances permitted by applicable law, to retain, monitor
> and intercept e-mail messages to and from its systems.
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 4
> Date: Tue, 14 Feb 2012 16:27:32 -0600
> From: Vitali Stanevich <sta...@wi...>
> Subject: [PyMOL] 1.5 version runs slow with "large" objects
> To: pym...@li...
> Message-ID:
>        <CAE...@ma...
> >
> 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: ?????? ?????? <gon...@gm...>
> Subject: Re: [PyMOL] Open Source PyMOL v1.5.0.1
> To: pym...@li...
> Message-ID:
>        <CAC...@ma...
> >
> 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
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> End of PyMOL-users Digest, Vol 69, Issue 12
> *******************************************
>