[PyMOL] 2nd Call For Papers - 23rd Annual Tcl/Tk Conference (Tcl'2016)

[akupries]

Hello pymol-users, fyi ...

23rd Annual Tcl/Tk Conference (Tcl'2016)
http://www.tcl.tk/community/tcl2016/

November 14 - 18, 2016
Crowne Plaza Houston River Oaks
2712 Southwest Freeway, 77098
Houston, Texas, USA

Important Dates:

[[ Attention!
   Registration is open. Please have a look at
http://www.tcl.tk/community/tcl2016/register.html

   The tutorials are known. See
http://www.tcl.tk/community/tcl2016/tutorials.html
]]

Abstracts and proposals due   September 12, 2016
Notification to authors   September 19, 2016
WIP and BOF reservations open August 22, 2016
Author materials due  October 24, 2016
Tutorials Start   November 14, 2016
Conference starts November 16, 2016

Email Contact:tclconfere...@googlegroups.com

Submission of Summaries

Tcl/Tk 2016 will be held in Houston, Texas, USA from November 14, 2016 to 
November 18, 2016.

The program committee is asking for papers and presentation proposals
from anyone using or developing with Tcl/Tk (and extensions). Past
conferences have seen submissions covering a wide variety of topics
including:

* Scientific and engineering applications
* Industrial controls
* Distributed applications and Network Managment
* Object oriented extensions to Tcl/Tk
* New widgets for Tk
* Simulation and application steering with Tcl/Tk
* Tcl/Tk-centric operating environments
* Tcl/Tk on small and embedded devices
* Medical applications and visualization
* Use of different programming paradigms in Tcl/Tk and proposals for new
  directions.
* New areas of exploration for the Tcl/Tk language

Submissions should consist of an abstract of about 100 words and a
summary of not more than two pages, and should be sent as plain text
to tclconfere...@googlegroups.com no later than September 12, 2016. Authors of 
accepted
abstracts will have until October 24, 2016 to submit their final
paper for the inclusion in the conference proceedings. The proceedings
will be made available on digital media, so extra materials such as
presentation slides, code examples, code for extensions etc. are
encouraged.

Printed proceedings will be produced as an on-demand book at lulu.com

The authors will have 30 minutes to present their paper at
the conference.

The program committee will review and evaluate papers according to the
following criteria:

* Quantity and quality of novel content
* Relevance and interest to the Tcl/Tk community
* Suitability of content for presentation at the conference

Proposals may report on commercial or non-commercial systems, but
those with only blatant marketing content will not be accepted.

Application and experience papers need to strike a balance between
background on the application domain and the relevance of Tcl/Tk to
the application. Application and experience papers should clearly
explain how the application or experience illustrates a novel use of
Tcl/Tk, and what lessons the Tcl/Tk community can derive from the
application or experience to apply to their own development efforts.

Papers accompanied by non-disclosure agreements will be returned to
the author(s) unread. All submissions are held in the highest
confidentiality prior to publication in the Proceedings, both as a
matter of policy and in accord with the U. S. Copyright Act of 1976.

The primary author for each accepted paper will receive registration
to the Technical Sessions portion of the conference at a reduced rate.

Other Forms of Participation

The program committee also welcomes proposals for panel discussions of
up to 90 minutes. Proposals should include a list of confirmed
panelists, a title and format, and a panel description with position
statements from each panelist. Panels should have no more than four
speakers, including the panel moderator, and should allow time for
substantial interaction with attendees. Panels are not presentations
of related research papers.

Slots for Works-in-Progress (WIP) presentations and Birds-of-a-Feather
sessions (BOFs) are available on a first-come, first-served basis
starting in August 22, 2016. Specific instructions for reserving WIP
and BOF time slots will be provided in the registration information
available in August 22, 2016. Some WIP and BOF time slots will be held open
for on-site reservation. All attendees with an interesting work in
progress should consider reserving a WIP slot.

Registration Information

More information on the conference is available the conference Web
site (http://www.tcl.tk/community/tcl2016/) and will be published on
various Tcl/Tk-related information channels.

To keep in touch with news regarding the conference and Tcl events in
general, subscribe to the tcl-announce list. See:
http://code.activestate.com/lists/tcl-announce to subscribe to the
tcl-announce mailing list.


Conference Committee

   * Andreas Kupries Hewlett Packard Enterprise
   * Arjen MarkusDeltares
   * Brian Griffin   Mentor Graphics
   * Clif Flynt  Noumena Corp
   * Gerald 

Re: [PyMOL] Selective valency on bond

[Thomas Holder]

Hi Patrick and Andreas,

"valence" is actually a bond-level setting, so you don't need to create 
individual objects. This should work:

set_bond valence, 1, organic

Cheers,
  Thomas

On 14 Jun 2016, at 10:01, Andreas Warnecke <4ndreas.warne...@gmail.com> wrote:

> The easiest way to deal with this is setting the valence or valence_mode 
> individually for the object.
> 
> set valence, 0, object1
> set valence, 1, object2
> 
> Cheers,
> 
> Andreas
> 
> On Mon, Jun 13, 2016 at 11:56 AM, McIntyre, Patrick  
> wrote:
> Dear PyMol users,
> 
> I have a crystal structure of my protein with an unnatural amino acid 
> present. This amino acid has a double bond within it, which I would like to 
> display as such. However I would like the surrounding protein  side chains to 
> not show double bond character. Is this possible at all?
> 
> So far, I can either keep valence mode set to '0' and see no double bonds 
> across the whole protein, or set to '1' and see all of the double bonds, 
> which I don't want.
> 
> My question is, is it possible to selectively 'set valency' onto a single 
> bond, or is it a global command which is not capable of this fine-tuning? I 
> am using MacPyMol if this makes a difference at all?
> 
> Thanks for your help,
> Patrick

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Selective valency on bond

[Andreas Warnecke]

The easiest way to deal with this is setting the valence or valence_mode
individually for the object.

set valence, 0, object1
set valence, 1, object2

Cheers,

Andreas

On Mon, Jun 13, 2016 at 11:56 AM, McIntyre, Patrick 
wrote:

> Dear PyMol users,
>
> I have a crystal structure of my protein with an unnatural amino acid
> present. This amino acid has a double bond within it, which I would like to
> display as such. However I would like the surrounding protein  side chains
> to not show double bond character. Is this possible at all?
>
> So far, I can either keep valence mode set to '0' and see no double bonds
> across the whole protein, or set to '1' and see all of the double bonds,
> which I don't want.
>
> My question is, is it possible to selectively 'set valency' onto a single
> bond, or is it a global command which is not capable of this fine-tuning? I
> am using MacPyMol if this makes a difference at all?
>
> Thanks for your help,
> Patrick
>
> --
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> patterns at an interface-level. Reveals which users, apps, and protocols
> are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
> ___
> 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
>
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
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[PyMOL] Selective valency on bond

[McIntyre, Patrick]

Dear PyMol users,

I have a crystal structure of my protein with an unnatural amino acid present. 
This amino acid has a double bond within it, which I would like to display as 
such. However I would like the surrounding protein  side chains to not show 
double bond character. Is this possible at all?

So far, I can either keep valence mode set to '0' and see no double bonds 
across the whole protein, or set to '1' and see all of the double bonds, which 
I don't want. 

My question is, is it possible to selectively 'set valency' onto a single bond, 
or is it a global command which is not capable of this fine-tuning? I am using 
MacPyMol if this makes a difference at all?

Thanks for your help,
Patrick 
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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