PyMOL Wiki - User contributions [en]

MediaWiki:Geshi.css

2015-04-27T19:55:44Z

Jarred:

/* CSS placed here will be applied to GeSHi syntax highlighting */

syntaxhighlight,
pre,
.latex.source-latex .de1, .latex.source-latex .de2,
.winbatch.source-winbatch .de1, .winbatch.source-winbatch .de2,
.bash.source-bash .de1, .bash.source-bash .de2,
.diff.source-diff .de1, .diff.source-diff .de2,
.python.source-python .de1, .python.source-python .de2 {
padding: 10px;
background-color: #000;

border: 0 none;
border-left: 10px solid #ddd;

font-size: 1.1em;
line-height: 1.3em;
}

div.mw-geshi ol li + li {
margin-top:-1.8em;
}

MediaWiki:Common.css

2015-04-27T19:53:33Z

Jarred:

/*--------------------------------------------------|
| dTree 2.05 | www.destroydrop.com/javascript/tree/ |
|---------------------------------------------------|
| Copyright (c) 2002-2003 Geir Landr� |
|--------------------------------------------------*/

@import url("/index.php?title=MediaWiki:Geshi.css");

.dtree {
font-family: Verdana, Geneva, Arial, Helvetica, sans-serif;
font-size: 11px;
color: #666;
white-space: nowrap;
}
.dtree img {
border: 0px;
vertical-align: middle;
}
.dtree a {
color: #333;
text-decoration: none;
}
.dtree a.node, .dtree a.nodeSel {
white-space: nowrap;
padding: 1px 2px 1px 2px;
}
.dtree a.node:hover, .dtree a.nodeSel:hover {
color: #333;
text-decoration: underline;
}
.dtree a.nodeSel {
background-color: #c0d2ec;
}
.dtree .clip {
overflow: hidden;
}
/*
* Dynamic menus
*/
.dmenu { width: 180px }

.dmenu, .dmenu ul { /* all lists */
padding: 0;
margin: 0;
list-style: none;
}
.dmenu .selflink { font-weight: normal; }

.dmenu li { /* all list items */
position: relative;
float: left;
width: 172px;
padding: 4px;
z-index: 100;
}

.dmenu li,
.dmenu li.even a,
.dmenu li.odd a,
.dmenu li li,
.dmenu li li a,
.dmenu li li li,
.dmenu li li li a {
color : black;
}

.dmenu li li { margin: 0; }

.dmenu li ul { /* second-level lists */
position: absolute;
left: -999em;
z-index: 101;
border: 1px solid #ccc;
}

.dmenu li ul ul { /* third-and-above-level lists */
position: absolute;
left: -999em;
margin: 0 0 0 0;
z-index: 102;
}

.dmenu li.odd .submenu {
width: 12px;
height: 15px;
float: right;
background: url(/common/images/rarr-lt.png) 0 3px no-repeat;
}
.dmenu li.even .submenu {
width: 12px;
height: 15px;
float: right;
background: url(/common/images/rarr-dk.png) 0 3px no-repeat;
}
.dmenu li.odd {
background: #E9EDF4;
border: 2px solid #E9EDF4;
}
.dmenu li.even {
background: #D0D8E8;
border: 2px solid #D0D8E8;
}

.dmenu li:hover, .dmenu li.sfhover {
border: 2px solid #385D8A;
}

.dmenu li:hover ul ul,
.dmenu li:hover ul ul ul,
.dmenu li.sfhover ul ul,
.dmenu li.sfhover ul ul ul {
left: -999em;
}

.dmenu li:hover ul,
.dmenu li li:hover ul,
.dmenu li li li:hover ul,
.dmenu li.sfhover ul,
.dmenu li li.sfhover ul,
.dmenu li li li.sfhover ul { /* lists nested under hovered list items */
left: 182px;
top: -3px;
}

/* added by Jason */
table.jtable {
font-family: "Lucida Sans Unicode", "Lucida Grande", Sans-Serif;
font-size: 12px;
background: #fff;
margin: 25px;
border-collapse: collapse;
text-align: left;
}
table.jtable th
{
font-size: 14px;
font-weight: normal;
color: #039;
padding: 10px 8px;
border-bottom: 1px solid #ccc;
text-align: center;
}
table.jtable td
{
border-bottom: 1px solid #ccc;
color: #669;
padding: 6px 8px;
text-align: left;
}
table.jtable tbody tr:hover td
{
color: #009;
}

/* for syntax highlighting, see http://pymolwiki.org/index.php/MediaWiki:Geshi.css */

/* pre tags on pages without GeSHi stylesheet */

pre {
padding: 10px;
background-color: #eee;

border: 0 none;
border-left: 10px solid #ddd;

font-size: 1.1em;
line-height: 1.3em;
}

/* Template:Infobox_script-repo */

table.infobox {
width:300px;
float:right;
border:1px solid black;
background-color: #ffe;
margin: 0 0 10px 10px;
clear: right;
}
table.infobox td,
table.infobox th {
text-align: left;
vertical-align: top;
border-bottom: 1px solid #eee;
}
div.didyouknow table.infobox {
display: none;
}

MediaWiki:Geshi.css

2015-04-23T20:35:03Z

Jarred:

MediaWiki:Geshi.css

2015-04-23T20:34:51Z

Jarred:

Pse export version

2015-04-23T20:28:59Z

Jarred:

The [[pse_export_version]] setting switches to a legacy format when saving PSEs, so far possible. The value is the floating point number representation of the targeted legacy PyMOL version, for example '''1.74''' to save a session for PyMOL 1.7.4.

''New in PyMOL 1.7.6''

Session file loading is always backwards compatible, so any newer version of PyMOL can load old session files.

== Examples ==

<syntaxhighlight lang="python">
# current version (default)
set pse_export_version, 0
save current.pse

# compatible with PyMOL 1.7.4
set pse_export_version, 1.74
save 174compat.pse
</syntaxhighlight>

== Known Limitations ==

The following objects are not or only partly supported:

* scenes before 1.7.6
* volumes before 1.7.2
* ramps
* CGOs

== See Also ==

* [[save]]

[[Category:Settings]]

<source lang="python"></source>

Pse export version

2015-04-23T20:28:15Z

Jarred:

Pse export version

2015-04-23T20:27:41Z

Jarred:

[[Category:Plugins]]
[[Category:Biochemical_Scripts]]

Pse export version

2015-04-23T20:26:59Z

Jarred: Replaced content with "Find polar pairs"

Find polar pairs

Pse export version

2015-04-23T20:26:18Z

Jarred:

Find polar pairs with the [[find_pairs|cmd.find_pairs]] function and return them as a list of atom pairs. It finds (more or less) the same contacts like [[distance|cmd.distance(mode=2)]].

== Example ==

<source lang="python">
pairs = polarpairs('chain A', 'chain B')
for p in pairs:
dist = cmd.get_distance('(%s`%s)' % p[0], '(%s`%s)' % p[1])
print p, 'Distance: %.2f' % (dist)
</source>

== The Script ==

<source lang="python">
'''
(c) 2011 Thomas Holder, MPI for Developmental Biology
'''

from pymol import cmd

def polarpairs(sel1, sel2, cutoff=4.0, angle=63.0, name='', state=1, quiet=1):
'''
ARGUMENTS

sel1, sel2 = string: atom selections

cutoff = float: distance cutoff

angle = float: h-bond angle cutoff in degrees. If angle="default", take
"h_bond_max_angle" setting. If angle=0, do not detect h-bonding.

name = string: If given, also create a distance object for visual representation

SEE ALSO

cmd.find_pairs, cmd.distance
'''
cutoff = float(cutoff)
quiet = int(quiet)
state = int(state)
if angle == 'default':
angle = cmd.get('h_bond_max_angle', cmd.get_object_list(sel1)[0])
angle = float(angle)
mode = 1 if angle > 0 else 0
x = cmd.find_pairs('(%s) and donors' % sel1, '(%s) and acceptors' % sel2,
state, state,
cutoff=cutoff, mode=mode, angle=angle) + \
cmd.find_pairs('(%s) and acceptors' % sel1, '(%s) and donors' % sel2,
state, state,
cutoff=cutoff, mode=mode, angle=angle)
x = sorted(set(x))
if not quiet:
print 'Settings: cutoff=%.1fangstrom angle=%.1fdegree' % (cutoff, angle)
print 'Found %d polar contacts' % (len(x))
if len(name) > 0:
for p in x:
cmd.distance(name, '(%s`%s)' % p[0], '(%s`%s)' % p[1])
return x

cmd.extend('polarpairs', polarpairs)
</source>

[[Category:Plugins]]
[[Category:Biochemical_Scripts]]

MediaWiki:Geshi.css

2015-04-23T20:24:06Z

Jarred:

/* CSS placed here will be applied to GeSHi syntax highlighting */

div.mw-code,
pre,
pre.prettyprint,
pre.lang-latex,
pre.lang-winbatch,
pre.lang-bash,
pre.lang-diff,
pre.lang-python,
lang(python)
{
padding: 10px;
background-color: #000;

border: 0 none;
border-left: 10px solid #ddd;

font-size: 1.1em;
line-height: 1.3em;
}

div.mw-geshi ol li + li {
margin-top:-1.8em;
}

.latex.source-latex .de1, .latex.source-latex .de2,
.winbatch.source-winbatch .de1, .winbatch.source-winbatch .de2,
.bash.source-bash .de1, .bash.source-bash .de2,
.diff.source-diff .de1, .diff.source-diff .de2,
.python.source-python .de1, .python.source-python .de2 {
padding: 0;
border: 0 none;

font-size: 1.1em;
line-height: 1.3em;
}

MediaWiki:Geshi.css

2015-04-23T20:22:51Z

Jarred:

/* CSS placed here will be applied to GeSHi syntax highlighting */

div.mw-code,
pre,
pre.prettyprint,
pre.lang-latex,
pre.lang-winbatch,
pre.lang-bash,
pre.lang-diff,
pre.lang-python,
syntaxhighlight,
.python,

{
padding: 10px;
background-color: #000;

border: 0 none;
border-left: 10px solid #ddd;

font-size: 1.1em;
line-height: 1.3em;
}

div.mw-geshi ol li + li {
margin-top:-1.8em;
}

.latex.source-latex .de1, .latex.source-latex .de2,
.winbatch.source-winbatch .de1, .winbatch.source-winbatch .de2,
.bash.source-bash .de1, .bash.source-bash .de2,
.diff.source-diff .de1, .diff.source-diff .de2,
.python.source-python .de1, .python.source-python .de2 {
padding: 0;
border: 0 none;

font-size: 1.1em;
line-height: 1.3em;
}

MediaWiki:Geshi.css

2015-04-23T20:19:22Z

Jarred:

/* CSS placed here will be applied to GeSHi syntax highlighting */

div.mw-code,
pre,
pre.prettyprint,
pre.lang-latex,
pre.lang-winbatch,
pre.lang-bash,
pre.lang-diff,
pre.lang-python, {
padding: 10px;
background-color: #000;

border: 0 none;
border-left: 10px solid #ddd;

font-size: 1.1em;
line-height: 1.3em;
}

div.mw-geshi ol li + li {
margin-top:-1.8em;
}

.latex.source-latex .de1, .latex.source-latex .de2,
.winbatch.source-winbatch .de1, .winbatch.source-winbatch .de2,
.bash.source-bash .de1, .bash.source-bash .de2,
.diff.source-diff .de1, .diff.source-diff .de2,
.python.source-python .de1, .python.source-python .de2 {
padding: 0;
border: 0 none;

font-size: 1.1em;
line-height: 1.3em;
}

MediaWiki:Geshi.css

2015-04-23T20:18:22Z

Jarred:

/* CSS placed here will be applied to GeSHi syntax highlighting */

div.mw-code,
syntaxhighlight.python,
pre,
pre.prettyprint,
pre.lang-latex,
pre.lang-winbatch,
pre.lang-bash,
pre.lang-diff,
pre.lang-python {
padding: 10px;
background-color: #000;

border: 0 none;
border-left: 10px solid #ddd;

font-size: 1.1em;
line-height: 1.3em;
}

div.mw-geshi ol li + li {
margin-top:-1.8em;
}

.latex.source-latex .de1, .latex.source-latex .de2,
.winbatch.source-winbatch .de1, .winbatch.source-winbatch .de2,
.bash.source-bash .de1, .bash.source-bash .de2,
.diff.source-diff .de1, .diff.source-diff .de2,
.python.source-python .de1, .python.source-python .de2 {
padding: 0;
border: 0 none;

font-size: 1.1em;
line-height: 1.3em;
}

Pse export version

2015-04-23T20:16:51Z

Jarred:

MediaWiki:Geshi.css

2015-04-22T18:33:55Z

Jarred:

/* CSS placed here will be applied to GeSHi syntax highlighting */

div.mw-code,
pre,
pre.prettyprint,
pre.lang-latex,
pre.lang-winbatch,
pre.lang-bash,
pre.lang-diff,
pre.lang-python {
padding: 10px;
background-color: #eee;

border: 0 none;
border-left: 10px solid #ddd;

font-size: 1.1em;
line-height: 1.3em;
}

div.mw-geshi ol li + li {
margin-top:-1.8em;
}

.latex.source-latex .de1, .latex.source-latex .de2,
.winbatch.source-winbatch .de1, .winbatch.source-winbatch .de2,
.bash.source-bash .de1, .bash.source-bash .de2,
.diff.source-diff .de1, .diff.source-diff .de2,
.python.source-python .de1, .python.source-python .de2 {
padding: 0;
border: 0 none;

font-size: 1.1em;
line-height: 1.3em;
}

MediaWiki:Geshi.css

2015-04-22T18:33:44Z

Jarred:

/* CSS placed here will be applied to GeSHi syntax highlighting */

div.mw-code,
pre,
pre.prettyprint,
pre.lang-latex,
pre.lang-winbatch,
pre.lang-bash,
pre.lang-diff,
pre.lang-python {
padding: 10px;
background-color: #ee;

border: 0 none;
border-left: 10px solid #ddd;

font-size: 1.1em;
line-height: 1.3em;
}

div.mw-geshi ol li + li {
margin-top:-1.8em;
}

.latex.source-latex .de1, .latex.source-latex .de2,
.winbatch.source-winbatch .de1, .winbatch.source-winbatch .de2,
.bash.source-bash .de1, .bash.source-bash .de2,
.diff.source-diff .de1, .diff.source-diff .de2,
.python.source-python .de1, .python.source-python .de2 {
padding: 0;
border: 0 none;

font-size: 1.1em;
line-height: 1.3em;
}

Pse export version

2015-04-22T18:33:29Z

Jarred:

The [[pse_export_version]] setting switches to a legacy format when saving PSEs, so far possible. The value is the floating point number representation of the targeted legacy PyMOL version, for example '''1.74''' to save a session for PyMOL 1.7.4.

''New in PyMOL 1.7.6''

Session file loading is always backwards compatible, so any newer version of PyMOL can load old session files.

== Examples ==

<source lang="python">
# current version (default)
set pse_export_version, 0
save current.pse

# compatible with PyMOL 1.7.4
set pse_export_version, 1.74
save 174compat.pse
</source>

== Known Limitations ==

The following objects are not or only partly supported:

* scenes before 1.7.6
* volumes before 1.7.2
* ramps
* CGOs

== See Also ==

* [[save]]

[[Category:Settings]]

MediaWiki:Geshi.css

2015-04-22T18:32:53Z

Jarred: Undo revision 12668 by Jarred (talk)

/* CSS placed here will be applied to GeSHi syntax highlighting */

div.mw-code,
syntaxhighlight,
pre,
pre.prettyprint,
pre.lang-latex,
pre.lang-winbatch,
pre.lang-bash,
pre.lang-diff,
pre.lang-python {
padding: 10px;
background-color: #000;

border: 0 none;
border-left: 10px solid #ddd;

font-size: 1.1em;
line-height: 1.3em;
}

div.mw-geshi ol li + li {
margin-top:-1.8em;
}

.latex.source-latex .de1, .latex.source-latex .de2,
.winbatch.source-winbatch .de1, .winbatch.source-winbatch .de2,
.bash.source-bash .de1, .bash.source-bash .de2,
.diff.source-diff .de1, .diff.source-diff .de2,
.python.source-python .de1, .python.source-python .de2 {
padding: 0;
border: 0 none;

font-size: 1.1em;
line-height: 1.3em;
}

MediaWiki:Geshi.css

2015-04-22T18:19:20Z

Jarred:

/* CSS placed here will be applied to GeSHi syntax highlighting */

pre,
.latex.source-latex .de1, .latex.source-latex .de2,
.winbatch.source-winbatch .de1, .winbatch.source-winbatch .de2,
.bash.source-bash .de1, .bash.source-bash .de2,
.diff.source-diff .de1, .diff.source-diff .de2,
.python.source-python .de1, .python.source-python .de2 {
padding: 10px;
background-color: #000;

border: 0 none;
border-left: 10px solid #ddd;

font-size: 1.1em;
line-height: 1.3em;
}

div.mw-geshi ol li + li {
margin-top:-1.8em;
}

.latex.source-latex .de1, .latex.source-latex .de2,
.winbatch.source-winbatch .de1, .winbatch.source-winbatch .de2,
.bash.source-bash .de1, .bash.source-bash .de2,
.diff.source-diff .de1, .diff.source-diff .de2,
.python.source-python .de1, .python.source-python .de2 {
padding: 0;
border: 0 none;

font-size: 1.1em;
line-height: 1.3em;
}

MediaWiki:Geshi.css

2015-04-22T18:13:05Z

Jarred:

MediaWiki:Geshi.css

2015-04-22T18:11:12Z

Jarred:

/* CSS placed here will be applied to GeSHi syntax highlighting */

div.mw-code,
syntaxhighlight,
pre,
pre.prettyprint,
pre.lang-latex,
pre.lang-winbatch,
pre.lang-bash,
pre.lang-diff,
pre.lang-python {
padding: 10px;
background-color: #eee;

border: 0 none;
border-left: 10px solid #ddd;

font-size: 1.1em;
line-height: 1.3em;
}

div.mw-geshi ol li + li {
margin-top:-1.8em;
}

.latex.source-latex .de1, .latex.source-latex .de2,
.winbatch.source-winbatch .de1, .winbatch.source-winbatch .de2,
.bash.source-bash .de1, .bash.source-bash .de2,
.diff.source-diff .de1, .diff.source-diff .de2,
.python.source-python .de1, .python.source-python .de2 {
padding: 0;
border: 0 none;

font-size: 1.1em;
line-height: 1.3em;
}

MediaWiki:Geshi.css

2015-04-22T18:10:05Z

Jarred:

Pse export version

2015-04-22T18:09:34Z

Jarred: Reverted edits by Jarred (talk) to last revision by Bell

MediaWiki:Geshi.css

2015-04-22T18:08:20Z

Jarred:

/* CSS placed here will be applied to GeSHi syntax highlighting */

div.mw-code,
syntaxhighlighter,
pre,
pre.prettyprint,
pre.lang-latex,
pre.lang-winbatch,
pre.lang-bash,
pre.lang-diff,
pre.lang-python {
padding: 10px;
background-color: #000;

border: 0 none;
border-left: 10px solid #ddd;

font-size: 1.1em;
line-height: 1.3em;
}

div.mw-geshi ol li + li {
margin-top:-1.8em;
}

.latex.source-latex .de1, .latex.source-latex .de2,
.winbatch.source-winbatch .de1, .winbatch.source-winbatch .de2,
.bash.source-bash .de1, .bash.source-bash .de2,
.diff.source-diff .de1, .diff.source-diff .de2,
.python.source-python .de1, .python.source-python .de2 {
padding: 0;
border: 0 none;

font-size: 1.1em;
line-height: 1.3em;
}

Pse export version

2015-04-22T17:15:46Z

Jarred:

The [[pse_export_version]] setting switches to a legacy format when saving PSEs, so far possible. The value is the floating point number representation of the targeted legacy PyMOL version, for example '''1.74''' to save a session for PyMOL 1.7.4.

''New in PyMOL 1.7.6''

Session file loading is always backwards compatible, so any newer version of PyMOL can load old session files.

== Examples ==
<syntaxhighlighter lang="python">
# current version (default)
set pse_export_version, 0
save current.pse

# compatible with PyMOL 1.7.4
set pse_export_version, 1.74
save 174compat.pse
</syntaxhighlighter>

== Known Limitations ==

The following objects are not or only partly supported:

* scenes before 1.7.6
* volumes before 1.7.2
* ramps
* CGOs

== See Also ==

* [[save]]

[[Category:Settings]]

MediaWiki:Geshi.css

2015-04-22T17:14:54Z

Jarred: Undo revision 12658 by Jarred (talk)

/* CSS placed here will be applied to GeSHi syntax highlighting */

div.mw-code,
pre,
pre.prettyprint,
pre.lang-latex,
pre.lang-winbatch,
pre.lang-bash,
pre.lang-diff,
pre.lang-python {
padding: 10px;
background-color: #000;

border: 0 none;
border-left: 10px solid #ddd;

font-size: 1.1em;
line-height: 1.3em;
}

div.mw-geshi ol li + li {
margin-top:-1.8em;
}

.latex.source-latex .de1, .latex.source-latex .de2,
.winbatch.source-winbatch .de1, .winbatch.source-winbatch .de2,
.bash.source-bash .de1, .bash.source-bash .de2,
.diff.source-diff .de1, .diff.source-diff .de2,
.python.source-python .de1, .python.source-python .de2 {
padding: 0;
border: 0 none;

font-size: 1.1em;
line-height: 1.3em;
}

Pse export version

2015-04-22T17:13:52Z

Jarred:

The [[pse_export_version]] setting switches to a legacy format when saving PSEs, so far possible. The value is the floating point number representation of the targeted legacy PyMOL version, for example '''1.74''' to save a session for PyMOL 1.7.4.

''New in PyMOL 1.7.6''

Session file loading is always backwards compatible, so any newer version of PyMOL can load old session files.

== Examples ==
<source lang="python">
# current version (default)
set pse_export_version, 0
save current.pse

# compatible with PyMOL 1.7.4
set pse_export_version, 1.74
save 174compat.pse
</source>

== Known Limitations ==

The following objects are not or only partly supported:

* scenes before 1.7.6
* volumes before 1.7.2
* ramps
* CGOs

== See Also ==

* [[save]]

[[Category:Settings]]

MediaWiki:Geshi.css

2015-04-22T17:13:18Z

Jarred:

MediaWiki:Geshi.css

2015-04-22T17:13:01Z

Jarred:

Pse export version

2015-04-22T00:55:59Z

Jarred:

The [[pse_export_version]] setting switches to a legacy format when saving PSEs, so far possible. The value is the floating point number representation of the targeted legacy PyMOL version, for example '''1.74''' to save a session for PyMOL 1.7.4.

''New in PyMOL 1.7.6''

Session file loading is always backwards compatible, so any newer version of PyMOL can load old session files.

== Examples ==
<syntaxhighlight lang="python">
# current version (default)
set pse_export_version, 0
save current.pse

# compatible with PyMOL 1.7.4
set pse_export_version, 1.74
save 174compat.pse
</syntaxhighlight>

== Known Limitations ==

The following objects are not or only partly supported:

* scenes before 1.7.6
* volumes before 1.7.2
* ramps
* CGOs

== See Also ==

* [[save]]

[[Category:Settings]]

Pse export version

2015-04-22T00:54:59Z

Jarred:

The [[pse_export_version]] setting switches to a legacy format when saving PSEs, so far possible. The value is the floating point number representation of the targeted legacy PyMOL version, for example '''1.74''' to save a session for PyMOL 1.7.4.

''New in PyMOL 1.7.6''

Session file loading is always backwards compatible, so any newer version of PyMOL can load old session files.

== Examples ==
<div dir="ltr" class="mw-geshi" style="text-align: left;">
<syntaxhighlight lang="python">
# current version (default)
set pse_export_version, 0
save current.pse

# compatible with PyMOL 1.7.4
set pse_export_version, 1.74
save 174compat.pse
</syntaxhighlight>
</div>

== Known Limitations ==

The following objects are not or only partly supported:

* scenes before 1.7.6
* volumes before 1.7.2
* ramps
* CGOs

== See Also ==

* [[save]]

[[Category:Settings]]

MediaWiki:Geshi.css

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Jarred:

/* CSS placed here will be applied to GeSHi syntax highlighting */

div.mw-code,
pre,
pre.prettyprint,
pre.lang-latex,
pre.lang-winbatch,
pre.lang-bash,
pre.lang-diff,
pre.lang-python {
padding: 10px;
background-color: #000;

border: 0 none;
border-left: 10px solid #ddd;

font-size: 1.1em;
line-height: 1.3em;
}

div.mw-geshi ol li + li {
margin-top:-1.8em;
}

.latex.source-latex .de1, .latex.source-latex .de2,
.winbatch.source-winbatch .de1, .winbatch.source-winbatch .de2,
.bash.source-bash .de1, .bash.source-bash .de2,
.diff.source-diff .de1, .diff.source-diff .de2,
.python.source-python .de1, .python.source-python .de2 {
padding: 0;
border: 0 none;

font-size: 1.1em;
line-height: 1.3em;
}

Main Page

2014-11-21T22:48:22Z

Jarred:

__NOTOC__
{| align="center" style="padding-bottom: 4em;"
|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
| New accounts: email thomas (dot) holder (@) schrodinger dot com
|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
|}
{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
|-
| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
||'''[[GoogleSearch]]'''
|}

{| width="100%"
| style="vertical-align: top; width: 40%" |
{| class="jtable" style="float: left; width: 90%;"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|-
! Official Release
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7.2 have all been released] on August 4, 2014.
|-
! Official Release
| [http://pymol.org PyMOL, AxPyMOL, and JyMOL v1.7 have all been released] today, January 14, 2014.
|-
! New Plugin
| [[Bondpack]] is a collection of PyMOL plugins for easy visualization of atomic bonds.
|-
! New Plugin
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
|-
! 3D using Geforce
| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
|-
! New Plugin
| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.
|-
! New Software
| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
|-
! New Script
| [[cgo_arrow]] draws an arrow between two picked atoms.
|-
! Tips & Tricks
| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
|-
! Older News
| See [[Older_News|Older News]].
|}
|style="vertical-align: top; width: 40%"|
{| class="jtable" style="float: right; width: 90%"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
|-
|<div class="didyouknow" >
<DPL>
namespace=
category=Commands|Plugins|Script_Library|Settings
includepage=*
includemaxlength=1050
escapelinks=false
resultsheader=__NOTOC__ __NOEDITSECTION__
randomcount=1
mode=userformat
addpagecounter=true
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
</DPL>
</div>
<div style="clear: both;"></div>
|}
|
|style="vertical-align: top; width: 18%"|
<DPL>
imagecontainer=Covers
randomcount=1
escapelinks=false
openreferences=true
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n
ordermethod=none
</DPL>

|}

Ray orthoscopic

2014-04-07T23:12:49Z

Jarred:

== Overview ==
This setting controls whether ray-traced images are rendered with or without perspective. Note that this can be in conflict with the setting "orthoscopic"; by default, images are rendered with the same orthoscopic setting as the viewport, unless "ray_orthoscopic" is deliberately set otherwise.

== Settings ==
<source lang="python">
set ray_orthoscopic, off # render ray-traced images with perspective (2-4x SLOWER)
set ray_orthoscopic, on # render ray-traced images without perspective
</source>

== Examples ==
'''For many images, the difference is hardly visible'''
<gallery>
Image:orthoon2.png|orthoscopic on (perspective off)

Image:orthooff2.png |orthoscopic off (perspective on)
</gallery>

'''Especially when straight features parallel to the z axis are shown, the effect may be large'''
<gallery>
Image:orthoon.png|orthoscopic on (perspective off)

Image:orthooff.png |orthoscopic off (perspective on)
</gallery>

[[Category:Settings|Ray orthoscopic]]
[[Category:Image_Manipulation|Ray orthoscopic]]
[[Category:Publication_Quality|Ray orthoscopic]]

Orthoscopic

2014-04-07T23:11:50Z

Jarred:

== Overview ==
'''orthoscopic''' turns on and off the perspective handling. Turning '''on''' orthoscopic rendering removes the effects of perspective. To adjust perspective rendering see, the [[Field_Of_View|Field of View]] command.

=== [[:Category:Performance|Performance]] Notes ===
Turning '''on''' orthoscopic rendering improves the [[Ray|rendering speed]] by a factor of 2x-4x! So, if you have large images, or are rendering a movie that does not need perspective in the images, try turning off perspective by setting orthoscopic to '''1'''.

== Examples ==

'''For many images, the difference is hardly visible'''
<gallery>
Image:orthoon2.png|orthoscopic on (perspective off)

Image:orthooff2.png |orthoscopic off (perspective on)

</gallery>

'''Especially when straight features parallel to the z axis are shown, the effect may be large'''
<gallery>
Image:orthoon.png|orthoscopic on (perspective off)

Image:orthooff.png |orthoscopic off (perspective on)
</gallery>

== Syntax ==
<source lang="python">
set orthoscopic, on
set orthoscopic, off
</source>

== See Also ==
[[Field_Of_View|Field of View]], [[Ray#Perspective_Example_Images|Perspective Settings]]

[[Category:Performance]]

Orthoscopic

2014-04-07T23:00:47Z

Jarred:

== Overview ==
'''orthoscopic''' turns on and off the perspective handling. Turning '''on''' orthoscopic rendering removes the effects of perspective. To adjust perspective rendering see, the [[Field_Of_View|Field of View]] command.

=== [[:Category:Performance|Performance]] Notes ===
Turning '''on''' orthoscopic rendering improves the [[Ray|rendering speed]] by a factor of 2x-4x! So, if you have large images, or are rendering a movie that does not need perspective in the images, try turning off perspective by setting orthoscopic to '''1'''.

== Examples ==
<gallery>
Image:orthoon2.png|orthoscopic on (perspective off)

Image:orthooff2.png |orthoscopic off (perspective on)

For many images, the difference is hardly visible
</gallery>

<gallery>
Image:orthoon.png|orthoscopic on (perspective off)

Image:orthooff.png |orthoscopic off (perspective on)
Especially when straight features parallel to the z axis are shown, the effect may be large
</gallery>

== Syntax ==
<source lang="python">
set orthoscopic, on
set orthoscopic, off
</source>

== See Also ==
[[Field_Of_View|Field of View]], [[Ray#Perspective_Example_Images|Perspective Settings]]

[[Category:Performance]]

Orthoscopic

2014-04-07T22:57:45Z

Jarred:

== Overview ==
'''orthoscopic''' turns on and off the perspective handling. Turning '''on''' orthoscopic rendering removes the effects of perspective. To adjust perspective rendering see, the [[Field_Of_View|Field of View]] command.

=== [[:Category:Performance|Performance]] Notes ===
Turning '''on''' orthoscopic rendering improves the [[Ray|rendering speed]] by a factor of 2x-4x! So, if you have large images, or are rendering a movie that does not need perspective in the images, try turning off perspective by setting orthoscopic to '''1'''.

== Examples ==
<gallery>
Image:orthoon2.png|orthoscopic on (perspective off)

Image:orthooff2.png |orthoscopic off (perspective on)

For many images, the difference is hardly visible.
</gallery>

<gallery>
Image:orthoon.png|orthoscopic on (perspective off)

Image:orthooff.png |orthoscopic off (perspective on)
Especially when straight features parallel to the z axis are shown, the effect may be large.
</gallery>

== Syntax ==
<source lang="python">
set orthoscopic, on
set orthoscopic, off
</source>

== See Also ==
[[Field_Of_View|Field of View]], [[Ray#Perspective_Example_Images|Perspective Settings]]

[[Category:Performance]]

Orthoscopic

2014-04-07T22:53:15Z

Jarred:

== Overview ==
'''orthoscopic''' turns on and off the perspective handling. Turning '''on''' orthoscopic rendering removes the effects of perspective. To adjust perspective rendering see, the [[Field_Of_View|Field of View]] command.

=== [[:Category:Performance|Performance]] Notes ===
Turning '''on''' orthoscopic rendering improves the [[Ray|rendering speed]] by a factor of 2x-4x! So, if you have large images, or are rendering a movie that does not need perspective in the images, try turning off perspective by setting orthoscopic to '''1'''.

== Examples ==
<gallery>
Image:orthoon2.png|orthoscopic on (perspective off)

Image:orthooff2.png |orthoscopic off (perspective on)
For many images, the difference is hardly visible.
</gallery>

<gallery>
Image:orthoon.png|orthoscopic on (perspective off)

Image:orthooff.png |orthoscopic off (perspective on)
Especially when straight features parallel to the z axis are shown, the effect may be large.
</gallery>

== Syntax ==
<source lang="python">
set orthoscopic, on
set orthoscopic, off
</source>

== See Also ==
[[Field_Of_View|Field of View]], [[Ray#Perspective_Example_Images|Perspective Settings]]

[[Category:Performance]]

File:For many images, the difference is hardly visible.

2014-04-07T22:50:14Z

Jarred: Created page with "For many images, the difference is hardly visible."

For many images, the difference is hardly visible.

Orthoscopic

2014-04-07T22:49:51Z

Jarred:

== Overview ==
'''orthoscopic''' turns on and off the perspective handling. Turning '''on''' orthoscopic rendering removes the effects of perspective. To adjust perspective rendering see, the [[Field_Of_View|Field of View]] command.

=== [[:Category:Performance|Performance]] Notes ===
Turning '''on''' orthoscopic rendering improves the [[Ray|rendering speed]] by a factor of 2x-4x! So, if you have large images, or are rendering a movie that does not need perspective in the images, try turning off perspective by setting orthoscopic to '''1'''.

== Examples ==
<gallery>
Image:orthoon2.png|orthoscopic on (perspective off)

Image:orthooff2.png |orthoscopic off (perspective on)
Image: For many images, the difference is hardly visible.
</gallery>

<gallery>
Image:orthoon.png|orthoscopic on (perspective off)

Image:orthooff.png |orthoscopic off (perspective on)
Especially when straight features parallel to the z axis are shown, the effect may be large.
</gallery>

== Syntax ==
<source lang="python">
set orthoscopic, on
set orthoscopic, off
</source>

== See Also ==
[[Field_Of_View|Field of View]], [[Ray#Perspective_Example_Images|Perspective Settings]]

[[Category:Performance]]

File:Especially when straight features parallel to the z axis are shown, the effect may be large.

2014-04-04T18:23:26Z

Jarred: Created page with "For many images, the difference is hardly visible."

For many images, the difference is hardly visible.

File:WarrenDeLanoMosaicized 1536x1152.png

2014-04-04T18:02:22Z

Jarred: Jarred uploaded "File:WarrenDeLanoMosaicized 1536x1152.png"

File:Surface ramp above mode.jpg

2014-04-04T18:00:24Z

Jarred: Jarred uploaded "File:Surface ramp above mode.jpg"

illustration of the surface_ramp_above_mode/surface_solvent setting combinations

File:Surface ramp above mode.jpg.png

2014-04-04T17:57:41Z

Jarred:

File:Sqd.png

2014-04-04T17:56:16Z

Jarred: Jarred uploaded "File:Sqd.png"

surface_quality to default

File:Kchannel-rainbow.png

2014-04-04T17:55:08Z

Jarred: Jarred uploaded "File:Kchannel-rainbow.png"

An example rendering of the K+ Channel from PDB 1BL8

File:It.png

2014-04-04T17:51:44Z

Jarred: Jarred uploaded "File:It.png"

inertia tensor

File:Spec direct.gif

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increasing spec_direct

File:Sticknub default.png

2014-04-04T17:47:58Z

Jarred: Jarred uploaded "File:Sticknub default.png"

File:DNA-ring3-ladder1-na3-finder1.png

2014-04-04T17:45:05Z

Jarred: Jarred uploaded "File:DNA-ring3-ladder1-na3-finder1.png"