[PyMOL] 1st 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:

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 Lester   KnG Consulting LLC
   * Joe Mistachkin  Mistachkin Systems
   * Ronald Fox  CAEN Technologies
 NSCL @ Michigan State University

Contact Information tclconfere...@googlegroups.com

[PyMOL] shadows commands

[harold steinberg]

Hi All,

I’m trying to write scripts that include shadow options.

In the menus at the top of the program users can choose: 
Setting/Rendering/Shadows and then they can pick: None, light, medium, heavy, 
black, matte, soft, occlusion 1, and occlusion 2.

How do I put those shadows into a script? (I reached the web and the wiki to no 
avail).

and where are they in the settings? I’d like to modify them.


H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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[PyMOL] Cryo Maps - gaussian isosurface

[harold steinberg]

Hi All,

I’m trying to make an isomesh of EMD-6413 (a cryo map) in Pymol. It’s a large 
map with a lot of extra, not very clean. In Chimera I can just gaussian the map 
with a new map to the level I want with a slider and it looks good, but I’d 
much rather work in PyMOL!

PyMOL can gaussian maps, I do it all the time, but on maps that I create in 
PyMOL. How do I get an isomesh on EMD-6413 that I can gaussian?

Normally I would use:
alter all, q=1
set gaussian_resolution, 5
map_new mapA, gaussian, 1, pdb code, 6
isosurface surfA, mapA

But in in this case I don’t want to use a pdb, just the cryo map.

I can isosurface the cryo map with the following:
isosurface mapname, EMD-6413, 4 (any number between 1-6)

but that doesn’t allow me to apply the gaussian to the map…

How do I create an isosurface with a gaussian?

Thanks for any help,

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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Re: [PyMOL] Problem with ribbon

[Thomas Holder]

Hi Mark,

Thanks for the bug report. Confirming that this is a picking bug with 
ribbon_as_cylinders=1, affecting 1.8.0.0 and later. Picking works correct for 
me with ribbon_as_cylinders=0 (default).

Thomas

On 05 Apr 2016, at 10:47, Mark A Saper  wrote:

> Hi All & Thomas
> 
> There appears to be a problem with ribbon representations.  I am testing 
> MacPyMOL on v 1.8.1.1 but the same behavior is seen with 1.8.0.4.  Create a 
> ribbon of a test protein, for example, 
> 
>   show ribbon, test and (resi 10:20 or resi 25:35)
> 
>   Double click on the endpoints (to see the residue number)
> 
>   The one that should be 25, displays residue 20. 
> 
> Labels do show the correct residue numbers.
> 
> Mark

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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[PyMOL] Problem with ribbon

[Mark A Saper]

Hi All & Thomas

There appears to be a problem with ribbon representations.  I am testing 
MacPyMOL on v 1.8.1.1 but the same behavior is seen with 1.8.0.4.  Create a 
ribbon of a test protein, for example, 

show ribbon, test and (resi 10:20 or resi 25:35)

Double click on the endpoints (to see the residue number)

The one that should be 25, displays residue 20. 

Labels do show the correct residue numbers.

Mark
___
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
Room 3220B, MSRB III   sa...@umich.edu   +1 (734) 764-3353 


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