https://wiki.pymol.org/api.php?action=feedcontributions&user=Smg3d&feedformat=atomPyMOL Wiki - User contributions [en]2024-03-29T13:09:30ZUser contributionsMediaWiki 1.35.1https://wiki.pymol.org/index.php?title=Category_talk:Discussion&diff=4109Category talk:Discussion2005-02-17T21:35:55Z<p>Smg3d: FAQ and News</p>
<hr />
<div>This layout seems better to me. Although I am not sure the News and Questions in the Discussion category are necessary, as we have the newsgroup. I would rely more on the newsgroup for news and questions.<br />
--[[User:Smg3d|Smg3d]] 14:53, 17 Feb 2005 (CST)<br />
<br />
== News & Questions ==<br />
<br />
I thought the news section could be just a central place for general news from Warren, plugin developers, or wiki site maintainers to post things concerning everyone. And the Questions area might be more of an ever growing FAQ. I think one of the things we'd like to do is add all the unique questions from the mailing list archives that are still pertinent to modern PyMOL into this wiki somewhere.<br />
<br />
--[[User:Orpheus|Orpheus]] 2004-02-17 3:14pm<br />
<br />
== FAQ and News ==<br />
<br />
I thought you meant "questions from users" in the Question category. Questions as in '''FAQ''' is definitely a '''necessity'''!<br />
<br />
For the News, it may be a good idea to have a compilation of News that are in the Newsgroup, although I guess it would mean for people to put their News to both places. Or would there be an automatic way to have News to be automatically put at both places (wiki and newsgroup)? Personnaly I would rely on the newsgroup for news, but I guess not all PyMOL users are members of the newsgroup... I am assuming that people who are newsgroup members would only come to the wiki when they want want to fix a problem, or to learn PyMOL tricks. In any case, it does not hurt, as long as information does not stop to flow in the newsgroup.<br />
--[[User:Smg3d|Smg3d]] 15:35, 17 Feb 2005 (CST)</div>Smg3dhttps://wiki.pymol.org/index.php?title=Category_talk:Discussion&diff=4104Category talk:Discussion2005-02-17T20:53:00Z<p>Smg3d: I prefer this layout</p>
<hr />
<div>This layout seems better to me. Although I am not sure the News and Questions in the Discussion category are necessary, as we have the newsgroup. I would rely more on the newsgroup for news and questions.<br />
--[[User:Smg3d|Smg3d]] 14:53, 17 Feb 2005 (CST)</div>Smg3dhttps://wiki.pymol.org/index.php?title=User:Smg3d&diff=3074User:Smg3d2005-02-17T18:26:11Z<p>Smg3d: </p>
<hr />
<div>'''Stéphane M. Gagné'''<br />
<br />
I am a structural biologist at [http://www.ulaval.ca Université Laval] (Québec, Canada).<br />
* Mostly NMR.<br />
* Mostly on Gentoo Linux.<br />
* [http://rmn.ulaval.ca/labo/ Lab Web Page]<br />
* [http://rmn.ulaval.ca/labo/software.html Lab Software Page]<br />
<br />
<pre>Stéphane M. Gagné, Ph.D.<br />
Professeur, biochimie et CREFSIP<br />
3255 pavillon Marchand<br />
Université Laval, Québec, Canada G1K 7P4<br />
Téléphone (bureau): (418) 656-7860<br />
Téléphone (labo): (418) 656-2131, poste 4530<br />
Télécopieur (Fax): (418) 656-7176</pre></div>Smg3dhttps://wiki.pymol.org/index.php?title=Main_Page&diff=4433Main Page2005-02-17T15:56:22Z<p>Smg3d: /* Sections */</p>
<hr />
<div>== PyMol Wiki Home ==<br />
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.<br />
<br />
== Moving In ==<br />
Please excuse the mess as we create the PyMolWiki site. The wiki will be a valuable educational & reference tool for PyMol users.<br />
<br />
== Helping ==<br />
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with<br />
<br />
* Wiki schema/design/organization: Below you'll find the current layout design<br />
* Graphic design and CSS layout: We need logos, BG images and CSS layout<br />
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki<br />
* Smoothing out the edges: Editors are needed just to fix our typos!<br />
* Etc...<br />
<br />
=== Editors Needed ===<br />
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].<br />
<br />
We need your help. So join today & happy editing!<br />
<br />
[[User:Tree|Tree]]<br />
<br />
== [[Initial Wiki Layout Suggestion]] == (Warren Delano; [[User:Tree|Tree]]; Doug Kojetin; Michael George Werner; Kristian Rother; Nat Echols; Roger Dodd)<br />
<br />
== Sections ==<br />
# Technical Issues (installation, hardware)<br />
# Basic Usage (controls, rendering, selections)<br />
# Advanced Issues (Ray tracing, settings)<br />
# Scripting<br />
# Plugins<br />
# High-level applications (Crystallography, NMR)<br />
## [[Crystallography Applications]]<br />
### [[Symmetry]]<br />
### [[Electron Density]]<br />
## [[NMR Applications]]<br />
### [[Working with a Family of Structures]]<br />
### [[Superimposition and RMSD]]<br />
### [[NMR Restraints Analysis]]<br />
# 3rd Party Software<br />
# Using PyMol For Unintended Uses (OpenGL Object Renderer)<br />
<br />
=== Subsections ===<br />
We need to put each one of these in a category above, or make a new section above where appropriate.<br />
<br><br />
<br />
* [[Mouse Controls]]<br />
* [[Command Language]]<br />
* [[Atom Selections]]<br />
* [[Ray-tracing]]<br />
* [[Movies and Animations]]<br />
* [[Cartoon Representations]]<br />
* [[Settings Reference (all settings and what they do)]]<br />
* [[Graphics]]<br />
** [[Stereo 3D Display]]<br />
*** [[Hardware Options]]<br />
*** [[Linux XFree86 Configuration]]<br />
* [[Arbitrary Graphics Objects]]<br />
* [[Python Integration]]<br />
* [[Scenes]]<br />
<br />
* [[Installation]]<br />
** [[Hardware Requirements]]<br />
** [[Software Requirements]]<br />
** [[OS Dependent]]<br />
*** [[Linux]]<br />
*** [[MAC]]<br />
*** [[Windows]]<br />
*** [[Script Library]]<br />
<br />
* [[Plugins/Modules]] <br />
** [[APBS Plugin]]<br />
** [[rtools Plugin]]<br />
<br />
* [[Plugins]] <br />
** [[List of Plugins]]<br />
** [[Tutorial on writing plugins]]<br />
** [[Others]]<br />
<br />
* [[Structure Alignment]]<br />
** [[Structure Alignment Editor]]<br />
* [[3rd Party Applications]]<br />
** [[Movies]]<br />
** [[Codecs]]<br />
** [[Image Manipulation]]<br />
*** [[labels]]<br />
*** [[Photoshop/GIMP]]<br />
*** [[Stereo Figures]]<br />
<br />
* [[Rendering molecules]]<br />
** [[Basics of displaying molecules]]<br />
** [[Coloring molecules]]<br />
** [[Displaying biochemical properties]]<br />
<br />
* [[Modeling and editing structures. ]]<br />
** [[Editing atoms]]<br />
** [[Molecular sculpting]]<br />
** [[Homology modeling]]<br />
* [[How to do electrostatics and energy minimization.]]<br />
* [[Launching PyMOL (has been asked often)]]<br />
* [[Some kind of "script collection" would be very useful]]<br />
* [[Creating publication-quality images HOWTO]]<br />
[http://www.example.com link title]<br />
<br />
== [[Proposal for structure]] ==<br />
Most of these points fall into some higher category. Here is a proposal how they could be arranged ([[User:Kristian Rother|krother]]):<br />
* I. Technical issues (installation, hardware)<br />
* II. Basic usage (controls, rendering, selections)<br />
* III. Advanced issues (Ray tracing, settings, movies)<br />
* IV. Scripting <br />
* V. Plugins<br />
* VI. High-level applications (Crystallography, NMR)<br />
<br />
----<br />
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)<br />
----</div>Smg3dhttps://wiki.pymol.org/index.php?title=Main_Page&diff=4432Main Page2005-02-17T15:55:35Z<p>Smg3d: /* Sections */</p>
<hr />
<div>== PyMol Wiki Home ==<br />
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.<br />
<br />
== Moving In ==<br />
Please excuse the mess as we create the PyMolWiki site. The wiki will be a valuable educational & reference tool for PyMol users.<br />
<br />
== Helping ==<br />
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with<br />
<br />
* Wiki schema/design/organization: Below you'll find the current layout design<br />
* Graphic design and CSS layout: We need logos, BG images and CSS layout<br />
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki<br />
* Smoothing out the edges: Editors are needed just to fix our typos!<br />
* Etc...<br />
<br />
=== Editors Needed ===<br />
If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].<br />
<br />
We need your help. So join today & happy editing!<br />
<br />
[[User:Tree|Tree]]<br />
<br />
== [[Initial Wiki Layout Suggestion]] == (Warren Delano; [[User:Tree|Tree]]; Doug Kojetin; Michael George Werner; Kristian Rother; Nat Echols; Roger Dodd)<br />
<br />
== Sections ==<br />
# Technical Issues (installation, hardware)<br />
# Basic Usage (controls, rendering, selections)<br />
# Advanced Issues (Ray tracing, settings)<br />
# Scripting<br />
# Plugins<br />
# High-level applications (Crystallography, NMR)<br />
## Crystallography Applications]]<br />
### [[Symmetry]]<br />
### [[Electron Density]]<br />
## [[NMR Applications]]<br />
### [[Working with a Family of Structures]]<br />
### [[Superimposition and RMSD]]<br />
### [[NMR Restraints Analysis]]<br />
# 3rd Party Software<br />
# Using PyMol For Unintended Uses (OpenGL Object Renderer)<br />
<br />
=== Subsections ===<br />
We need to put each one of these in a category above, or make a new section above where appropriate.<br />
<br><br />
<br />
* [[Mouse Controls]]<br />
* [[Command Language]]<br />
* [[Atom Selections]]<br />
* [[Ray-tracing]]<br />
* [[Movies and Animations]]<br />
* [[Cartoon Representations]]<br />
* [[Settings Reference (all settings and what they do)]]<br />
* [[Graphics]]<br />
** [[Stereo 3D Display]]<br />
*** [[Hardware Options]]<br />
*** [[Linux XFree86 Configuration]]<br />
* [[Arbitrary Graphics Objects]]<br />
* [[Python Integration]]<br />
* [[Scenes]]<br />
<br />
* [[Installation]]<br />
** [[Hardware Requirements]]<br />
** [[Software Requirements]]<br />
** [[OS Dependent]]<br />
*** [[Linux]]<br />
*** [[MAC]]<br />
*** [[Windows]]<br />
*** [[Script Library]]<br />
<br />
* [[Plugins/Modules]] <br />
** [[APBS Plugin]]<br />
** [[rtools Plugin]]<br />
<br />
* [[Plugins]] <br />
** [[List of Plugins]]<br />
** [[Tutorial on writing plugins]]<br />
** [[Others]]<br />
<br />
* [[Structure Alignment]]<br />
** [[Structure Alignment Editor]]<br />
* [[3rd Party Applications]]<br />
** [[Movies]]<br />
** [[Codecs]]<br />
** [[Image Manipulation]]<br />
*** [[labels]]<br />
*** [[Photoshop/GIMP]]<br />
*** [[Stereo Figures]]<br />
<br />
* [[Rendering molecules]]<br />
** [[Basics of displaying molecules]]<br />
** [[Coloring molecules]]<br />
** [[Displaying biochemical properties]]<br />
<br />
* [[Modeling and editing structures. ]]<br />
** [[Editing atoms]]<br />
** [[Molecular sculpting]]<br />
** [[Homology modeling]]<br />
* [[How to do electrostatics and energy minimization.]]<br />
* [[Launching PyMOL (has been asked often)]]<br />
* [[Some kind of "script collection" would be very useful]]<br />
* [[Creating publication-quality images HOWTO]]<br />
[http://www.example.com link title]<br />
<br />
== [[Proposal for structure]] ==<br />
Most of these points fall into some higher category. Here is a proposal how they could be arranged ([[User:Kristian Rother|krother]]):<br />
* I. Technical issues (installation, hardware)<br />
* II. Basic usage (controls, rendering, selections)<br />
* III. Advanced issues (Ray tracing, settings, movies)<br />
* IV. Scripting <br />
* V. Plugins<br />
* VI. High-level applications (Crystallography, NMR)<br />
<br />
----<br />
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)<br />
----</div>Smg3dhttps://wiki.pymol.org/index.php?title=User:Smg3d&diff=3073User:Smg3d2005-02-17T14:05:08Z<p>Smg3d: </p>
<hr />
<div>'''Stéphane M. Gagné'''<br />
<br />
I am a structural biologist at Université Laval (Québec, Canada).<br />
* Mostly NMR.<br />
* Mostly on Gentoo Linux.<br />
* [http://rmn.ulaval.ca/labo/ Lab Web Page]<br />
* [http://rmn.ulaval.ca/labo/software.html Lab Software Page]<br />
<br />
<pre>Stéphane M. Gagné, Ph.D.<br />
Professeur, biochimie et CREFSIP<br />
3255 pavillon Marchand<br />
Université Laval, Québec, Canada G1K 7P4<br />
Téléphone (bureau): (418) 656-7860<br />
Téléphone (labo): (418) 656-2131, poste 4530<br />
Télécopieur (Fax): (418) 656-7176</pre></div>Smg3dhttps://wiki.pymol.org/index.php?title=User:Smg3d&diff=3072User:Smg3d2005-02-17T13:47:26Z<p>Smg3d: </p>
<hr />
<div>'''Stéphane M. Gagné'''<br />
<br />
I am a structural biologist at Université Laval (Québec, Canada).<br />
* Mostly NMR.<br />
* Mostly on Gentoo Linux.<br />
* [http://rmn.ulaval.ca/labo/ Lab Web Page]<br />
* [http://rmn.ulaval.ca/labo/software.html Lab Software Page]<br />
<br />
Stéphane M. Gagné, Ph.D.<br />
Professeur, biochimie et CREFSIP<br />
3255 pavillon Marchand<br />
Université Laval, Québec, Canada G1K 7P4<br />
Téléphone (bureau): (418) 656-7860<br />
Téléphone (labo): (418) 656-2131, poste 4530<br />
Télécopieur (Fax): (418) 656-7176</div>Smg3dhttps://wiki.pymol.org/index.php?title=User:Smg3d&diff=3071User:Smg3d2005-02-17T08:10:57Z<p>Smg3d: </p>
<hr />
<div>'''Stéphane M. Gagné'''<br />
<br />
I am a structural biologist at Université Laval (Québec, Canada).<br />
* Mostly NMR.<br />
* Mostly on Gentoo Linux.<br />
* [http://rmn.ulaval.ca/labo/ Lab Web Page]<br />
* [http://rmn.ulaval.ca/labo/software.html Lab Software Page]</div>Smg3dhttps://wiki.pymol.org/index.php?title=User:Smg3d&diff=3070User:Smg3d2005-02-17T08:01:55Z<p>Smg3d: </p>
<hr />
<div>[[Stéphane M. Gagné]]<br />
<br />
I am a structural biologist at Université Laval (Québec, Canada).<br />
* Mostly NMR.<br />
* Mostly on Gentoo Linux.</div>Smg3dhttps://wiki.pymol.org/index.php?title=User:Smg3d&diff=3069User:Smg3d2005-02-17T07:56:36Z<p>Smg3d: </p>
<hr />
<div>I am a structural biologist at Université Laval (Québec, Canada). Mostly NMR.</div>Smg3dhttps://wiki.pymol.org/index.php?title=Main_Page&diff=4411Main Page2005-02-17T07:37:24Z<p>Smg3d: /* Initial Wiki Layout Suggestion */</p>
<hr />
<div>== PyMol Wiki Home ==<br />
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.<br />
<br />
== Moving In ==<br />
Please excuse the mess as we create the PyMolWiki site. The wiki will be a valuable educational & reference tool for PyMol users.<br />
<br />
== Helping ==<br />
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with<br />
<br />
* Wiki schema/design/organization: Below you'll find the current layout design<br />
* Graphic design and CSS layout: We need logos, BG images and CSS layout<br />
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki<br />
* Smoothing out the edges: Editors are needed just to fix our typos!<br />
* Etc...<br />
<br />
We need your help. So join today & happy editing!<br />
<br />
[[User:Tree|Tree]]<br />
<br />
== [[Initial Wiki Layout Suggestion]] == (Warren Delano; [[User:Tree|Tree]]; Doug Kojetin; Michael George Werner; Kristian Rother; Nat Echols)<br />
* [[Mouse Controls]]<br />
* [[Command Language]]<br />
* [[Atom Selections]]<br />
* [[Ray-tracing]]<br />
* [[Movies and Animations]]<br />
* [[Cartoon Representations]]<br />
* [[Settings Reference (all settings and what they do)]]<br />
* [[Stereo 3D Display]]<br />
** [[Hardware Options]]<br />
** [[Linux XFree86 Configuration]]<br />
* [[Crystallography Applications]]<br />
** [[Symmetry]]<br />
** [[Electron Density]]<br />
* [[NMR Applications]]<br />
** [[Working with a Family of Structures]]<br />
** [[Superimposition and RMSD]]<br />
** [[NMR Restraints Analysis]]<br />
* [[Arbitrary Graphics Objects]]<br />
* [[Python Integration]]<br />
* [[Scenes]]<br />
<br />
* [[Installation]]<br />
** [[Hardware Requirements]]<br />
** [[Software Requirements]]<br />
** [[OS Dependent]]<br />
*** [[Linux]]<br />
*** [[MAC]]<br />
*** [[Windows]]<br />
*** [[Script Library]]<br />
<br />
* [[Plugins/Modules]] <br />
** [[APBS Plugin]]<br />
<br />
* [[Plugins]] <br />
** [[List of Plugins]]<br />
** [[Tutorial on writing plugins]]<br />
** [[Others]]<br />
<br />
* [[Structure Alignment]]<br />
** [[Structure Alignment Editor]]<br />
* [[3rd Party Applications]]<br />
** [[Movies]]<br />
** [[Codecs]]<br />
<br />
* [[Displaying biochemical properties]]<br />
* [[Coloring molecules]]<br />
* [[Rendering molecules]]<br />
** [["basics of displaying molecules".]]<br />
** [["displaying basic chemical properties", like double bonds, h-bonds, bond angles and b-factors.]]<br />
* [[Modeling and editing structures. ]]<br />
* [[How to do electrostatics and energy minimization.]]<br />
* [[Launching PyMOL (has been asked often)]]<br />
* [[Some kind of "script collection" would be very useful.]]<br />
<br />
----<br />
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)<br />
----</div>Smg3dhttps://wiki.pymol.org/index.php?title=Main_Page&diff=4400Main Page2005-02-17T00:21:11Z<p>Smg3d: </p>
<hr />
<div>== PyMol Wiki Home ==<br />
You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.<br />
<br />
== Moving In ==<br />
Please excuse the mess as we create the PyMolWiki site. The wiki will be a valuable educational & reference tool for PyMol users.<br />
<br />
== Helping ==<br />
If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with<br />
<br />
* Wiki schema/design/organization: Below you'll find the current layout design<br />
* Graphic design and CSS layout: We need logos, BG images and CSS layout<br />
* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki<br />
* Smoothing out the edges: Editors are needed just to fix our typos!<br />
* Etc...<br />
<br />
We need your help. So join today & happy editing!<br />
<br />
[[User:Tree|Tree]]<br />
<br />
== [[Initial Wiki Layout Suggestion]] == (Warren Delano)<br />
* [[Mouse Controls]]<br />
* [[Command Language]]<br />
* [[Atom Selections]]<br />
* [[Ray-tracing]]<br />
* [[Movies and Animations]]<br />
* [[Cartoon Representations]]<br />
* [[Settings Reference (all settings and what they do)]]<br />
* [[Stereo 3D Display]]<br />
** [[Hardware Options]]<br />
** [[Linux XFree86 Configuration]]<br />
* [[Crystallography Applications]]<br />
** [[Symmetry]]<br />
** [[Electron Density]]<br />
* [[Arbitrary Graphics Objects]]<br />
* [[Python Integration]]<br />
* [[Scenes]]<br />
<br />
== [[User Additions]] ==<br />
* [[Installation]] ([[User:Tree|Tree]])<br />
** [[Hardware Requirements]]<br />
** [[Software Requirements]]<br />
** [[OS Dependent]]<br />
*** [[Linux]]<br />
*** [[MAC]]<br />
*** [[Windows]]<br />
*** [[Script Library]]<br />
<br />
* [[NMR Applications]] (Doug Kojetin)<br />
* [[Plugins/Modules]] (Doug Kojetin)<br />
** [[APBS Plugin]]<br />
<br />
* [[Plugins]] (Michael George Werner)<br />
** [[List of Plugins]]<br />
** [[Tutorial on writing plugins]]<br />
** [[Others]]<br />
<br />
* [[Structure Alignment]] (Nat Echols)<br />
** [[Structure Alignment Editor]]<br />
* [[3rd Party Applications]]<br />
** [[Movies]]<br />
** [[Codecs]]<br />
<br />
* [[Displaying biochemical properties]] (Kristian Rother)<br />
* [[Coloring molecules]]<br />
* [[Rendering molecules]]<br />
** [["basics of displaying molecules".]]<br />
** [["displaying basic chemical properties", like double bonds, h-bonds, bond angles and b-factors.]]<br />
* [[Modeling and editing structures. ]]<br />
* [[How to do electrostatics and energy minimization.]]<br />
* [[Launching PyMOL (has been asked often)]]<br />
* [[Some kind of "script collection" would be very useful.]]<br />
<br />
----<br />
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)<br />
----</div>Smg3d