https://wiki.pymol.org/api.php?action=feedcontributions&user=Mjhsieh&feedformat=atomPyMOL Wiki - User contributions [en]2024-03-29T05:21:53ZUser contributionsMediaWiki 1.35.1https://wiki.pymol.org/index.php?title=Publication_Quality_Images&diff=8481Publication Quality Images2008-02-27T06:17:04Z<p>Mjhsieh: /* typo */</p>
<hr />
<div>==High Resolution (DPI) Images==<br />
<br />
===Creating Resolution Specific Images===<br />
We often get the question:<br />
Q. How do I create a X DPI image using PyMol's 'ray' command?<br />
<br />
The answer is deceivingly simple. There are two steps in the process. First, setup your scene and use [[Cmd ray|ray]] like this<br />
ray 2400, 2400<br />
From this you will get a large square image. You can now resize it to X inches where X=A*B, A and B factors of 2400 (eg: 8 inch photo @ 300DPI, 4 inch photo at 600DPI, 2 inch photo @ 1200DPI). The formula for creating images is:<br />
rayVal = inches * DPI<br />
where rayVal is the value you pass to "ray". Thus, an 8 inch square photo at 72, 100, and 300 DPI would be created by the following commands:<br />
ray 576,576 # 8inch * 72dpi<br />
ray 800,800 # 8inch * 100dpi; or a 4inch * 200 DPI photo; or 1x800.<br />
ray 2400,2400 # 8inch * 300dpi; 6"x400dpi, etc...<br />
<br />
<br />
The '''new and better solution''' is to use the [[Png]] command with the '''dpi''' setting, such as<br />
<source lang="python"><br />
png fileName, dpi=300<br />
</source><br />
If you don't have a new enough version of PyMOL that supports this, then the '''old solution''' is to use [[PhotoShop]] or [[GIMP]] to resize the photo to the appropriate height and width while making sure also to tell the [[PhotoShop]] or [[GIMP]] what resolution the image is.<br />
<br />
<br />
=====GIMP 2.0=====<br />
In Gimp, load your image (it'll most likely be very large) then <br />
*Select:<br />
Image -><br />
Scale Image -><br />
'Print Size & Scale Image Section' change 'New Width' to whatever width you decided on before.<br />
* Save Image (File->Save)<br />
<br />
You should be set.<br />
<br />
=== See Also ===<br />
[[Png]] [[Ray]] [[Draw]] [[CMYK]]<br />
<br />
[[Category:Image_Manipulation|Publication Quality Images]]<br />
[[Category:Publication_Quality|Publication Quality Images]]</div>Mjhsiehhttps://wiki.pymol.org/index.php?title=MAC_Install&diff=6869MAC Install2007-04-07T01:16:11Z<p>Mjhsieh: /* Installing MacPyMOL */</p>
<hr />
<div>[[Category:Installation|Mac]]<br />
http://images.apple.com/powermac/images/solutionsscience20050427.jpg<br />
<br />
__TOC__<br />
<br />
=Installing MacPyMOL=<br />
http://delsci.com/macpymol/macpymol350.jpg<br />
<br />
===Essentials===<br />
<br />
The [http://delsci.com/macpymol/ download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.<br />
<br />
===Warning on Mouse Drivers===<br />
<br />
One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.<br />
<br />
===Invoking pymol from the unix command line===<br />
<br />
The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL<br />
<br />
I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable. I also use [[MacOSX-specific .pymolrc file|this ~/.pymolrc]] file.<br />
<br />
Additional invokation options and further details are discussed under [[Launching_PyMOL#MacOS_X:]]<br />
<br />
===Extras===<br />
<br />
You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.<br />
<br />
====Mighty Mouse====<br />
<br />
http://images.apple.com/mightymouse/images/index360scroll220050802.gif<br />
<br />
A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.<br />
<br />
====PowerMate Dial====<br />
<br />
http://www.griffintechnology.com/assets/images/products/powermate/prod_powermate_sub01b.jpg<br />
<br />
The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].<br />
<br />
====Stereo====<br />
<br />
http://images.apple.com/powermac/images/graphicspymol20051018.jpg<br />
<br />
The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.<br />
<br />
=Installing X-windows based pymol on Mac OS X=<br />
<br />
===Why would you want to do this?===<br />
<br />
#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol<br />
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu<br />
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.<br />
<br />
----<br />
<br />
===Simplest Installation===<br />
<br />
====Install pymol with Fink====<br />
http://pdb.finkproject.org/img/mlogo.png<br />
<br />
By far the simplest way to install the X-windows based version of pymol on OS X is by using the [http://fink.sourceforge.net/ fink package management system]. To compile it, all you need to do is issue the command<br />
<br />
fink install pymol-py24<br />
<br />
(This will install python2.4 in fink, along with an X-windows based tkinter. There are also versions that permit you to install pymol to interact with python2.3 and even python2.2. Fink uses its own unix-type python installation, but you can trick pymol into using the aqua framework to get a prettier GUI after the fact.)<br />
<br />
The [http://pdb.finkproject.org/pdb/package.php/pymol-py24 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:<br />
<br />
sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.<br />
<br />
You might need to create the latter directory if it doesn't already exist, i.e., issue the command<br />
<br />
sudo mkdir -p /sw/fink/dists/local/main/finkinfo<br />
<br />
Be sure to set your display environment in your start up shell script to use pymol. For example in your home directory, the .bashrc (or .bash_profile) file should contain:<br />
<br />
export DISPLAY=":0.0"<br />
<br />
<br />
I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].<br />
<br />
The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.<br />
<br />
====Install APBS and friends with fink====<br />
<br />
[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]<br />
<br />
To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi mpi version of apbs].<br />
<br />
Issuing the command<br />
<br />
fink install apbs<br />
<br />
will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://xanana.ucsc.edu/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].<br />
<br />
'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.<br />
<br />
----<br />
<br />
===Gratuitous Eye-Candy Tweaks===<br />
[[Image:snap_mac.png|thumb|aqua-tkinter]]<br />
<br />
You can get the fink installed X-windows based pymol-py24 to use an aqua-based tkinter menu as follows:<br />
<br />
====Install a Framework build of Python2.4==== <br />
as follows:<br />
<br />
mkdir src<br />
cd src<br />
curl -O http://www.python.org/ftp/python/2.4.2/Python-2.4.2.tgz<br />
tar xvfz Python-2.4.2.tgz<br />
cd Python-2.4.2<br />
export PATH=/usr/bin:$PATH<br />
./configure --enable-framework<br />
make<br />
sudo make frameworkinstall<br />
<br />
====Getting Fink's PyMOL to use a Framework build of Python====<br />
<br />
1. Remove the following empty directory by issuing the command<br />
<br />
sudo rmdir /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages<br />
<br />
2. Make a symbolic link to your fink site-packages directory:<br />
<br />
sudo ln -s /sw/lib/python2.4/site-packages /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages <br />
<br />
This enables your new framework python to use all of the extras, like pmw, that you installed as dependencies for pymol.<br />
<br />
3. Edit the file /sw/bin/python, and change the line<br />
<br />
/sw/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"<br />
<br />
to<br />
<br />
/Library/Frameworks/Python.framework/Versions/Current/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"<br />
<br />
4. Now issue <br />
<br />
/sw/bin/pymol<br />
<br />
and you should see something that looks like this full-size [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png screenshot of pymol with an aqua-tkinter pmw GUI] and X-windows based molecular display window. Also shown in this screenshot is the APBS plugin in action.<br />
<br />
<br />
----<br />
<br />
===PyMOLX11Hybrid=== <br />
<br />
MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.<br />
<br />
Doing this creates the inverse situation of the previous tweak; the molecular viewer window is aqua-based and the tkinter GUI is X11 based. (Naturally, I had to try the trick of making an aqua-tkinter GUI. It sort of works, but the GUI is dead, thanks to a threading bug in the aqua Tcl/Tk framework that comes with Apple. Bummer.)</div>Mjhsiehhttps://wiki.pymol.org/index.php?title=MAC_Install&diff=6868MAC Install2007-04-07T01:15:46Z<p>Mjhsieh: /* Installing MacPyMOL */</p>
<hr />
<div>[[Category:Installation|Mac]]<br />
http://images.apple.com/powermac/images/solutionsscience20050427.jpg<br />
<br />
__TOC__<br />
<br />
=Installing MacPyMOL=<br />
[[Image:http://delsci.com/macpymol/macpymol350.jpg]]<br />
<br />
===Essentials===<br />
<br />
The [http://delsci.com/macpymol/ download] is about as straightforward as it gets, and you can install it wherever it makes you happy. You need a 3 button mouse (clickable scroll wheel = middle button). Apple has finally come to its senses and designed a proper, ergonomically pleasant, [http://www.apple.com/mightymouse/ scrollbutton mouse] that works well with pymol and permits horizontal scrolling. Most other mice will also work well.<br />
<br />
===Warning on Mouse Drivers===<br />
<br />
One word of warning: '''Do not install 3rd party drivers''' for multi-button mice if you can avoid it. These often mess with the mapping of the middle button or have other horrific side effects. Fortunately, with OS X, you should not need to.<br />
<br />
===Invoking pymol from the unix command line===<br />
<br />
The unix executable resides at MacPyMOL.app/Contents/MacOS/MacPyMOL<br />
<br />
I ([[User:Wgscott|Bill Scott]]) wrote a cheezy [http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/pymol pymol] shell script (and zsh function) to invoke this on the command line. It uses mdfind to find the executable. I also use [[MacOSX-specific .pymolrc file|this ~/.pymolrc]] file.<br />
<br />
Additional invokation options and further details are discussed under [[Launching_PyMOL#MacOS_X:]]<br />
<br />
===Extras===<br />
<br />
You don't need any of these to use MacPyMOL. But you didn't really '''need''' a Mac either. Face it: You need these.<br />
<br />
====Mighty Mouse====<br />
<br />
http://images.apple.com/mightymouse/images/index360scroll220050802.gif<br />
<br />
A 3-button mouse is essential. [http://www.apple.com/mightymouse/ Apple's Mighty Mouse] is an extra treat.<br />
<br />
====PowerMate Dial====<br />
<br />
http://www.griffintechnology.com/assets/images/products/powermate/prod_powermate_sub01b.jpg<br />
<br />
The [http://www.chemistry.ucsc.edu/~wgscott/xtal/powermate_pymol_osx.html PowerMate dial works nicely with pymol].<br />
<br />
====Stereo====<br />
<br />
http://images.apple.com/powermac/images/graphicspymol20051018.jpg<br />
<br />
The [http://www.apple.com/powermac/upgrade.html latest Macs] finally support [http://www.apple.com/powermac/graphics.html stereo in a window]. There is more information in the [[Monitors Hardware Options]] section.<br />
<br />
=Installing X-windows based pymol on Mac OS X=<br />
<br />
===Why would you want to do this?===<br />
<br />
#You want to run a [http://www.oreilly.com/openbook/freedom/ free], guilt-free, open-source version of pymol<br />
#You just happen to prefer the [http://wiki.python.org/moin/TkInter tkinter] menu<br />
#You want to use [http://pymol.sourceforge.net/plugins.html plugins], for example, the [http://www-personal.umich.edu/~mlerner/PyMOL/ apbs plugin] for free grasp-like electrostatic calculations.<br />
<br />
----<br />
<br />
===Simplest Installation===<br />
<br />
====Install pymol with Fink====<br />
http://pdb.finkproject.org/img/mlogo.png<br />
<br />
By far the simplest way to install the X-windows based version of pymol on OS X is by using the [http://fink.sourceforge.net/ fink package management system]. To compile it, all you need to do is issue the command<br />
<br />
fink install pymol-py24<br />
<br />
(This will install python2.4 in fink, along with an X-windows based tkinter. There are also versions that permit you to install pymol to interact with python2.3 and even python2.2. Fink uses its own unix-type python installation, but you can trick pymol into using the aqua framework to get a prettier GUI after the fact.)<br />
<br />
The [http://pdb.finkproject.org/pdb/package.php/pymol-py24 fink pymol package] currently exists in the [http://fink.sourceforge.net/faq/usage-fink.php#unstable unstable branch of fink], so you will either have to [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch] or make the following symbolic links:<br />
<br />
sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol-py.* /sw/fink/dists/local/main/finkinfo/.<br />
<br />
You might need to create the latter directory if it doesn't already exist, i.e., issue the command<br />
<br />
sudo mkdir -p /sw/fink/dists/local/main/finkinfo<br />
<br />
Be sure to set your display environment in your start up shell script to use pymol. For example in your home directory, the .bashrc (or .bash_profile) file should contain:<br />
<br />
export DISPLAY=":0.0"<br />
<br />
<br />
I ([[User:wgscott|wgscott]]) have put a whole lot of further information on how to use fink to install crystallographic software on my own [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Main_Page wiki] and [http://chemistry.ucsc.edu/~wgscott/xtal/ website], including instructions on [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Getting_your_fink_installation_to_use_packages_that_I_have_pre-compiled how to install precompiled binary packages using fink].<br />
<br />
The [http://pdb.finkproject.org/pdb/search.php?summary=pymol fink pymol package] is currently maintained by Jack Howarth.<br />
<br />
====Install APBS and friends with fink====<br />
<br />
[[Image:Rna_surface_apbs.png|thumb|APBS calculated electrostatic potential of SARS s2m RNA reveals the colors of a true patriot.]]<br />
<br />
To use the electrostatics plugin, you will need [http://apbs.sourceforge.net/ APBS] and its dependencies. These are also available as fink packages, and include [http://pdb.finkproject.org/pdb/package.php/apbs apbs], [http://pdb.finkproject.org/pdb/package.php/maloc maloc] and [http://pdb.finkproject.org/pdb/package.php/pdb2pqr pdb2pqr]. If you have multiple processors available, you might wish to install the [http://pdb.finkproject.org/pdb/package.php/apbs-mpi mpi version of apbs].<br />
<br />
Issuing the command<br />
<br />
fink install apbs<br />
<br />
will install apbs and its required dependencies for you. The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Here is [http://xanana.ucsc.edu/xtal/pymol_screenshot.png a big screenshot of the fink APBS package being invoked via the pymol plugin].<br />
<br />
'''Nucleic acids''' may prove problematic for the apbs plugin. If so, use the pdb2pqr command-line tool to create a pqr file manually, instead of using the plugin to generate it.<br />
<br />
----<br />
<br />
===Gratuitous Eye-Candy Tweaks===<br />
[[Image:snap_mac.png|thumb|aqua-tkinter]]<br />
<br />
You can get the fink installed X-windows based pymol-py24 to use an aqua-based tkinter menu as follows:<br />
<br />
====Install a Framework build of Python2.4==== <br />
as follows:<br />
<br />
mkdir src<br />
cd src<br />
curl -O http://www.python.org/ftp/python/2.4.2/Python-2.4.2.tgz<br />
tar xvfz Python-2.4.2.tgz<br />
cd Python-2.4.2<br />
export PATH=/usr/bin:$PATH<br />
./configure --enable-framework<br />
make<br />
sudo make frameworkinstall<br />
<br />
====Getting Fink's PyMOL to use a Framework build of Python====<br />
<br />
1. Remove the following empty directory by issuing the command<br />
<br />
sudo rmdir /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages<br />
<br />
2. Make a symbolic link to your fink site-packages directory:<br />
<br />
sudo ln -s /sw/lib/python2.4/site-packages /Library/Frameworks/Python.framework/Versions/Current/lib/python2.4/site-packages <br />
<br />
This enables your new framework python to use all of the extras, like pmw, that you installed as dependencies for pymol.<br />
<br />
3. Edit the file /sw/bin/python, and change the line<br />
<br />
/sw/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"<br />
<br />
to<br />
<br />
/Library/Frameworks/Python.framework/Versions/Current/bin/python2.4 $PYMOL_PATH/modules/pymol/__init__.py "$@"<br />
<br />
4. Now issue <br />
<br />
/sw/bin/pymol<br />
<br />
and you should see something that looks like this full-size [http://www.chemistry.ucsc.edu/%7Ewgscott/xtal/pymol_screenshot.png screenshot of pymol with an aqua-tkinter pmw GUI] and X-windows based molecular display window. Also shown in this screenshot is the APBS plugin in action.<br />
<br />
<br />
----<br />
<br />
===PyMOLX11Hybrid=== <br />
<br />
MacPyMOL for Tiger now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate MacPyMOL.app and rename it "PyMOLX11Hybrid.app" and launch.<br />
<br />
Doing this creates the inverse situation of the previous tweak; the molecular viewer window is aqua-based and the tkinter GUI is X11 based. (Naturally, I had to try the trick of making an aqua-tkinter GUI. It sort of works, but the GUI is dead, thanks to a threading bug in the aqua Tcl/Tk framework that comes with Apple. Bummer.)</div>Mjhsiehhttps://wiki.pymol.org/index.php?title=Talk:Main_Page&diff=395Talk:Main Page2005-12-12T03:53:05Z<p>Mjhsieh: /* New */</p>
<hr />
<div>== New ==<br />
<br />
=== Some Thoughts For Discussion ===<br />
* Would it be helpful to get rid of display of the somewhat awkward "Cmd" prefix for commands, and simply do a better job of separating the sections that cover concepts and ideas from those that discuss specific commands? <br />
<br />
* Empty links discourage. Could we eliminate them sooner rather than later? Yes, they are helpful initially for maintaining some structure, but people do get bummed out when they follow a link for an interesting topic and end up with nothing. If there are too many of these, then they may quit and go home before finding the real content -- and that would be a shame since there is now plenty of real content.<br />
<br />
* For those coming into the Wiki for the first time, we should insure that the most useful content is out front and on top. Right now the TOC has an awful lot of blank links, so having it on top isn't so helpful as a starting point for nagivation. In contrast, the Categories, Script Library, and PyMOL Commands sections all seem like pretty good starting points.<br />
<br />
* For people (like me) who don't know the first thing about Wiki's, more "newbies click here to learn" links would help ease the transition...<br />
<br />
* Categories & subcategories confuse me. The resulting titles baffle. For example, '''Category: Using Pymol Objects and Selections Working with Objects'''. Shouldn't there be another colon in there? '''Category: Using Pymol Objects and Selections: Working with Objects''' Is this just a Wiki thing? <br />
<br />
[[User:Warren|Warren]] (BTW: Please don't weight what I write too heavily here. With respect to PyMolWiki, I am just another user -- and a clueless one at that).<br />
----<br />
=====Begin Inchoate's Comments To Warren=====<br />
First off, thanks for the post. I always welcome better ways to work and organize information. I don't claim to know any more than anyone else, I just took the initiative for PyMolWiki.<br />
<br />
Warren, you're completely right. Something needs to change, to make this more usable for people. I tried to organize the PyMol information via the user manual and user comments. Imposing a hierarchy on a system that doesn't really want one, isn't such a good idea, or my imposition was implemented incorrectly. The link names need to be MUCH shorter: take a look at http://wikipedia.org. They have 500,000+ pages and they have short link names. I tried to make a hierarchy so that if three such people come in and look up "rotate" that they go to the right page. That is, there's "rotate," "cmd.rotate," and camera independent rotations and whatnot. We have name ambiguitities. Do we just make one big page with "rotate" and include all its information there, or do we make "rotate" a category and dole out the pages to the category?<br />
<br />
I'm ambivalent towards empty links. They remind me of what basic concepts that need filling, but are annoying if you're searching for info. and there's nothing there.<br />
<br />
As far as the comments on categories and subcategories, as I understand it, you can't use double ":"s in names. You have categories and then something is made a subcategory by claiming that is'a category of a category. Kinda' strange.<br />
<br />
I do think organization is good. My way was seemingly obfuscated. Don't you think PyMol commands should somehow be lumped into available categories?<br />
Changes to be made from my POV:<br />
* Much shorter link names<br />
* Kill the hierarchy?<br />
* How to use the Wiki Intro<br />
<br />
======Part 2======<br />
I tihnk I found the problem, and I might be able to solve it. I just made things hard by including the hierarchy <u>in</u> the naming scheme, when that's not appropriate. I think the hierarchy's still very important; however, I think the name-ambiguity problem is not solved via this method.<br />
<br />
======Part 3======<br />
I've made lots of changes:<br />
* I actually took Warren's suggestion on epmty links. I sifted through the TOPTOC and made empty links normal text -- but left them there in case anyone wants to make them links by adding content.<br />
* Also, I've gone through all the commands and removed the Cmd prefix. The commands, and all commands buried in modules should be easy to create by simply making a new page as, for example, "Editing.Get_Dihedral" or whatever.<br />
* The names of the links should be MUCH easier to handle, and are far less obfuscated.<br />
<br />
MediaWiki-style organization is starting to make sense. :-)<br />
<br />
[[User:Inchoate|Inchoate]] 00:48, 6 May 2005 (CDT)<br />
----<br />
<br />
=====A singular vote from TStout=====<br />
<br />
One thing that I think has been missing from the manuals and the Wiki (and manuals for many other programs, I might add) are copious EXAMPLES of how to actually use a command. Speaking as an advanced-dummy, I find it terribly imposing to be presented with something like '''"cmd.select(string name, string selection)"''' as an explanation for how a command works. "How does that translate into what I should type?" is the polite version of how I end up reading such things.... :) Recently, I have noticed more "real" examples being entered into the Wiki: THANK YOU! The example given just now also comes complete with an Examples entry with things like: <br />
select near , (ll expand 8)<br />
select near , (ll expand 8)<br />
select bb, (name ca,n,c,o )<br />
For beginning users, such entries are invaluable. In fact, I would extend that to say that an inverted approach to manual/Wiki writing would be even better for the beginning PyMOL user: organize around how to accomplish the usual tasks, not around a glossary of all the possible commands......That said, a HUGE thank you to all who are putting in so much time building, maintaining and getting this to critical mass so that it becomes the invaluable resource it clearly is headed toward! -Tom<br />
<br />
----<br />
<br />
=====Where is the anti-spam mechanism/strategy?=====<br />
Manual removing spam contents really sucks.<br />
----</div>Mjhsiehhttps://wiki.pymol.org/index.php?title=Talk:Main_Page&diff=394Talk:Main Page2005-12-12T03:48:08Z<p>Mjhsieh: </p>
<hr />
<div>== New ==<br />
<br />
=== Some Thoughts For Discussion ===<br />
* Would it be helpful to get rid of display of the somewhat awkward "Cmd" prefix for commands, and simply do a better job of separating the sections that cover concepts and ideas from those that discuss specific commands? <br />
<br />
* Empty links discourage. Could we eliminate them sooner rather than later? Yes, they are helpful initially for maintaining some structure, but people do get bummed out when they follow a link for an interesting topic and end up with nothing. If there are too many of these, then they may quit and go home before finding the real content -- and that would be a shame since there is now plenty of real content.<br />
<br />
* For those coming into the Wiki for the first time, we should insure that the most useful content is out front and on top. Right now the TOC has an awful lot of blank links, so having it on top isn't so helpful as a starting point for nagivation. In contrast, the Categories, Script Library, and PyMOL Commands sections all seem like pretty good starting points.<br />
<br />
* For people (like me) who don't know the first thing about Wiki's, more "newbies click here to learn" links would help ease the transition...<br />
<br />
* Categories & subcategories confuse me. The resulting titles baffle. For example, '''Category: Using Pymol Objects and Selections Working with Objects'''. Shouldn't there be another colon in there? '''Category: Using Pymol Objects and Selections: Working with Objects''' Is this just a Wiki thing? <br />
<br />
[[User:Warren|Warren]] (BTW: Please don't weight what I write too heavily here. With respect to PyMolWiki, I am just another user -- and a clueless one at that).<br />
----<br />
=====Begin Inchoate's Comments To Warren=====<br />
First off, thanks for the post. I always welcome better ways to work and organize information. I don't claim to know any more than anyone else, I just took the initiative for PyMolWiki.<br />
<br />
Warren, you're completely right. Something needs to change, to make this more usable for people. I tried to organize the PyMol information via the user manual and user comments. Imposing a hierarchy on a system that doesn't really want one, isn't such a good idea, or my imposition was implemented incorrectly. The link names need to be MUCH shorter: take a look at http://wikipedia.org. They have 500,000+ pages and they have short link names. I tried to make a hierarchy so that if three such people come in and look up "rotate" that they go to the right page. That is, there's "rotate," "cmd.rotate," and camera independent rotations and whatnot. We have name ambiguitities. Do we just make one big page with "rotate" and include all its information there, or do we make "rotate" a category and dole out the pages to the category?<br />
<br />
I'm ambivalent towards empty links. They remind me of what basic concepts that need filling, but are annoying if you're searching for info. and there's nothing there.<br />
<br />
As far as the comments on categories and subcategories, as I understand it, you can't use double ":"s in names. You have categories and then something is made a subcategory by claiming that is'a category of a category. Kinda' strange.<br />
<br />
I do think organization is good. My way was seemingly obfuscated. Don't you think PyMol commands should somehow be lumped into available categories?<br />
Changes to be made from my POV:<br />
* Much shorter link names<br />
* Kill the hierarchy?<br />
* How to use the Wiki Intro<br />
<br />
======Part 2======<br />
I tihnk I found the problem, and I might be able to solve it. I just made things hard by including the hierarchy <u>in</u> the naming scheme, when that's not appropriate. I think the hierarchy's still very important; however, I think the name-ambiguity problem is not solved via this method.<br />
<br />
======Part 3======<br />
I've made lots of changes:<br />
* I actually took Warren's suggestion on epmty links. I sifted through the TOPTOC and made empty links normal text -- but left them there in case anyone wants to make them links by adding content.<br />
* Also, I've gone through all the commands and removed the Cmd prefix. The commands, and all commands buried in modules should be easy to create by simply making a new page as, for example, "Editing.Get_Dihedral" or whatever.<br />
* The names of the links should be MUCH easier to handle, and are far less obfuscated.<br />
<br />
MediaWiki-style organization is starting to make sense. :-)<br />
<br />
[[User:Inchoate|Inchoate]] 00:48, 6 May 2005 (CDT)<br />
----<br />
<br />
=====A singular vote from TStout=====<br />
<br />
One thing that I think has been missing from the manuals and the Wiki (and manuals for many other programs, I might add) are copious EXAMPLES of how to actually use a command. Speaking as an advanced-dummy, I find it terribly imposing to be presented with something like '''"cmd.select(string name, string selection)"''' as an explanation for how a command works. "How does that translate into what I should type?" is the polite version of how I end up reading such things.... :) Recently, I have noticed more "real" examples being entered into the Wiki: THANK YOU! The example given just now also comes complete with an Examples entry with things like: <br />
select near , (ll expand 8)<br />
select near , (ll expand 8)<br />
select bb, (name ca,n,c,o )<br />
For beginning users, such entries are invaluable. In fact, I would extend that to say that an inverted approach to manual/Wiki writing would be even better for the beginning PyMOL user: organize around how to accomplish the usual tasks, not around a glossary of all the possible commands......That said, a HUGE thank you to all who are putting in so much time building, maintaining and getting this to critical mass so that it becomes the invaluable resource it clearly is headed toward! -Tom<br />
<br />
----</div>Mjhsiehhttps://wiki.pymol.org/index.php?title=Category_talk:FAQ&diff=4087Category talk:FAQ2005-12-12T03:31:27Z<p>Mjhsieh: despam</p>
<hr />
<div></div>Mjhsiehhttps://wiki.pymol.org/index.php?title=Category_talk:Script_Library&diff=4119Category talk:Script Library2005-12-12T03:29:22Z<p>Mjhsieh: despam</p>
<hr />
<div></div>Mjhsiehhttps://wiki.pymol.org/index.php?title=Category:Uncategorized&diff=3960Category:Uncategorized2005-12-12T03:04:47Z<p>Mjhsieh: /* Alter key bindings */</p>
<hr />
<div><br />
==Alter key bindings==<br />
It's not GUI, but you could simply bind a function key such as F1 to a command:<br />
<source lang="python"><br />
cmd.set_key('F1',lambda :cmd.show('sticks'))<br />
</source><br />
<br />
==Coloring Surface with Electrostatic Potential==<br />
You have to load the potential data by Delphi or some other program like AMBER version 9:<br />
<source lang="python"><br />
load sample.pdb, molecule<br />
load sample.delphi, potential<br />
show surface, molecule<br />
ramp_new level, potential, [-7,0,7]<br />
set surface_color, level, molecule<br />
</source></div>Mjhsiehhttps://wiki.pymol.org/index.php?title=User:Mjhsieh&diff=4882User:Mjhsieh2005-12-10T09:34:17Z<p>Mjhsieh: </p>
<hr />
<div>current working on [http://apple.sysbio.info/~mjhsieh/archives/000528.html Displaying Electrostatic Surface with AMBER/PBSA (AMBER 9)]</div>Mjhsiehhttps://wiki.pymol.org/index.php?title=Surface&diff=5630Surface2005-12-10T08:34:47Z<p>Mjhsieh: /* Settings */</p>
<hr />
<div>The surface representation of a protein, in PyMol, shows the "Connolly" surface or the surface that would be traced out by the '''surfaces''' of waters in contact with teh protein at all possible positions. [[Image:Surface_ex.png|thumb|Surface Representation Example|right]]<br />
<br />
<br />
==Enabling==<br />
To enable the surface representation do<br />
show surface, SEL<br />
for any proper selection SEL.<br />
<br />
==Settings==<br />
===Transparency===<br />
To adjust the transparency of surfaces try:<br />
<source lang="python"><br />
set transparency, 0.5<br />
</source><br />
Where 1.0 will be an invisible and 0.0 a completely solid surface.<br />
<br />
===Quality===<br />
To smooth your surface representation try:<br />
<source lang="python"><br />
set surface_quality, 1<br />
</source><br />
or higher if you wish, though it will take longer and might look odd.<br />
<br />
===Probe Radius===<br />
To change the probe radius other than default 1.4 Å, you need to change the solvent radius, say, 1.6 Å:<br />
<source lang="python"><br />
set solvent_radius, 1.6<br />
</source><br />
If the surface does not change correspondingly, use:<br />
<source lang="python"><br />
rebuild<br />
</source><br />
<br />
==Tips==<br />
===Displaying a protein as surface with a ligand as sticks===<br />
The easiest way to do this is to create separate objects for each type of display. <br />
<br />
- Load your protein<br />
- Select the ligand <br />
- Create a separate object for the ligand <br />
- Remove ligand atoms from the protein<br />
- Display both objects separately<br />
<br />
Example:<br />
<source lang="python"><br />
load prot.ent,protein<br />
select ligand,resn FAD<br />
create lig_sticks,ligand<br />
remove ligand<br />
show sticks,lig_sticks<br />
show surface,protein<br />
</source><br />
<br />
<br />
===Calculating a partial surface===<br />
There is, until now, an undocumented way to calculate a surface for only a part of an object without creating a new one:<br />
<source lang="python"><br />
flag ignore, not A/49-63/, set<br />
delete indicate<br />
show surface<br />
</source><br />
If the surface was already computed, then you'll also need to issue the command:<br />
<source lang="python"><br />
rebuild<br />
</source><br />
<br />
<br />
===Displaying surface inside a molecule===<br />
As far as I can tell, setting ambient to zero alone doesn't quite do the job, since some triangles still get lit by the light source. The best combination I can find is:<br />
<source lang="python"><br />
set ambient=0<br />
set direct=0.7<br />
set reflect=0.0<br />
set backface_cull=0<br />
</source><br />
Which gives no shadows and only a few artifacts.<br />
<br />
As an alternative, you might just consider showing the inside of the surface directly...that will create less visual artifacts, and so long as ambient and direct are sufficiently low, it will look reasonable in "ray".<br />
<source lang="python"><br />
util.ray_shadows("heavy")<br />
set two_sided_lighting=1<br />
set backface_cull=0<br />
</source><br />
<br />
===Creating a Closed Surface===<br />
[[Image:Surface_open.png|thumb|Example OPEN Surface|left|200px]]<br />
[[Image:Surface_closed.png|thumb|Example CLOSED Surface|left|200px]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
To create what I'll call a '''closed surface''' (see images), you need to first make your atom selections, then create a new object for that selection then show the surface for that object. Here's an example.<br />
<br />
sel A, id 1-100<br />
create B, A<br />
show surface, B<br />
<br />
[[Category:Representations|Surface]]</div>Mjhsieh