PyMOL Wiki - User contributions [en]

Ideas

2010-01-21T17:21:21Z

Gregori:

=== Ideas for PyMOL Development ===

This page was originally developed for the 2008 Google Summer of Code competition, but seeing as PyMOL wasn't selected, this page can instead serve as a resource for ongoing PyMOL development efforts.

== Where to Start ==

Always start with Python and only delve down into the C code when absolutely necessary. Although PyMOL is mostly a C-based application, much of the that code is opaque, fragile, and unforgiving. Although C code refactoring is an important project goal, such work may not be ideal since once mistake could potentially to destabilize the entire platform.

Fortunately, the Python interpreter and the PyMOL command and selection languages make it possible to extend PyMOL safely and quickly. Even when performance is critical, Python should be the interface between external C, C++, and Java code and PyMOL's internal C data structures.

== Choosing a Topic ==

The best open-source code is usually written by an end-users attempting to meet their own pressing needs. So if you have already have a specific need which relates to PyMOL, then we strongly encourage you to follow up on that first!

If you are looking for ideas, then try to seek out enhancements and/or integrations that will impact the largest potential user base. For example, imagine what new things might be useful to virtually all medicinal chemists, all structural biologists, all movie-makers, all paper-writers, and so forth.

The ideas below are organized by category. Right now, integration with other open-source projects seems like the approach most likely to yield significant benefit, so those ideas are first.

== Integration Ideas (Linking Out to Useful Open-Source Tools) ==

In most cases, depending on the need, integration can be accomplished through standalone Python scripts, through new PyMOL commands, through PyMOL Wizards, or via Tkinter plugins.

* APBS (electrostatics calculations): Improve the existing plugin. Michael Lerner is currently leading this effort. See [[APBS]]
:: yea ([[User:Inchoate|Tree]] [[User:Jedgold|Jedgold]]) / nay (0)
* RDKit (cheminformatics, depiction, UFF cleanup, etc.): Lots of potential here, however C++ coding may be necessary for more advanced integration tasks. [http://www.rdkit.org RDKit home]
:: yea ([[User:Markvanraaij|Markvanraaij]]) / nay (0)
* GIMP (image manipulation): Streamline & document the process of exporting images from PyMOL into GIMP and preparing them for submission to scientific Journals.
:: yea (0) / nay (0)
* Jmol (publishing visualizations inside of web pages): Liason between PyMOL & Jmol projects to develop a shared molecular visualization data model compatible with both applications.
:: yea (0) / nay (0)
* Firefox (plugin): Develop an PyMOL plugin compatible with Firefox.
:: yea ([[User:Vvostri|Vvostri]]) / nay (0)
* MMTK (molecular mechanics -- Python/flexible): Develop the ability to round-trip molecular systems from PyMOL, into MMTK, and back.
:: yea (0) / nay (0)
* GROMACS (molecular mechanics -- C/fast) - Maybe some ideas can be shared with this guy. [http://www.kde-apps.org/content/show.php/Gromacs+GUI+?content=47665 Gromacs GUI]
:: yea ([[User:Jedgold|Jedgold]]) / nay (0)
* OpenOffice (escape Microsoft hegemony): Develop an PyMOL plugin.
:: yea (0) / nay (0)
* IPython integration (interactive shell): a robust alternative to the PyMOL command line?
:: yea (0) / nay (0)
* R (statistics): PyMOL a 3D viewer environment for visualizating & manipulating large statistical data sets?

Are there other key open-source packages we might specifically target for integration with PyMOL, either through GSoC or beyond?

== High-Level Enhancement Ideas (Mostly Python-oriented) ==

* Work on [[#More Ideas (Please add your own!)| MolViz]]
:: yea (0) / nay (0)
* Develop new plugins which automate routine tasks.
:: yea ([[User:Vvostri|Vvostri]]) / nay (0)
* Improve the Python API documentation.
:: yea (0) / nay (0)
* Flesh out the new "from pymol2 import PyMOL" instance-based PyMOL API.
:: yea (0) / nay (0)
* Develop alternate Tkinter "skins" (for custom OEM-like applications).
:: yea (0) / nay (0)
* Develop a Tkinter/TOGL widget which holds a PyMOL viewer instance.
:: yea (0) / nay (0)
* Develop a PyQt widget which holds a PyMOL viewer instance.
:: yea (0) / nay (0)
* Create a plugin-manager GUI in the style of Firefox, Rythmbox, Gedit, Eclipse. A GUI where it is easy to turn off/on plugins, configure them and see help-contents for them. Maybe also some way to paste a url to install a new Plugin.
:: yea ([[User:Vvostri|Vvostri]]) / nay (0)
* Add a plugin for a GUI window with the same functionality as the "Control Panel" window in SwissPDB Viewer.
:: yea ([[User:Vvostri|Vvostri]]) / nay (0)
* Extend and modify the PyMOL command language so as to be compatible with existing RasMol and/or Jmol scripts.
:: yea (0) / nay (0)
* Enhance the Mutagenesis Wizard in order to support Nucleic acids and/or Sugars.
:: yea (0) / nay (0)

== Low-Level Enhancement Ideas (Mostly C-oriented) ==

* Enable editing of displayed sequence alignments.
:: yea ([[User:Jedgold|Jedgold]], [[User:Aschreyer|Aschreyer]]) / nay (0)
::: Would this then feed back to the structural alignment? [[User:Jedgold|Jedgold]]
* Add multi-line textual annotations
:: yea (0) / nay (0)
* Support additional annotation object including: arrow, lines, and blobs.
:: yea ([[User:Aschreyer|Aschreyer]], [[User:Vvostri|Vvostri]]) / nay (0)
* Add display of secondary structure into the sequence viewer.
:: yea (0) / nay (0)
* Enable per-object Z clipping (especially in the ray tracer)
:: yea ([[User:Gregori|Gregori]]) / nay (0)
::: I would go a step further with fully customizable selection-based clipping planes (XYZ, color and transparency) ([[User:Gregori|Gregori]])
* Highlight H-bonds, salt bridges, Pi-stacking, Pi-cations, etc.
:: yea (0) / nay (0)
* Build in a simple forcefield and energy minimizer suitable for use with Mutagenesis.
:: yea (0) / nay (0)
* Incorporate a suite of standard NMR visualizations (restraint violations, per-residue RMS, etc.)
:: yea ([[User:Vvostri|Vvostri]]) / nay (0)
* Enumeration and display of low-energy conformers.
:: yea ([[User:Jedgold|Jedgold]]) / nay (0)
::: This could be done by integrating RDKit, I think. [[User:Aschreyer|Aschreyer]]
* Automated structure grafting (poor-man's homology modeling).
:: yea (0) / nay ([[User:Jedgold|Jedgold]])
::: Perhaps a plugin to Modeller instead? [[User:Jedgold|Jedgold]]
* Import of alignment files.
:: yea ([[User:Jedgold|Jedgold]]) / nay (0)
* Implement IMD (Interactive Molecular Dynamics) Interface, see http://www.ks.uiuc.edu/Research/vmd/imd/

== Difficult C-level Code Refactoring Ideas ==

* Assemble a test suite which thoroughly exercises the existing code (a prerequisite to major refactoring).
:: yea (0) / nay (0)
* Catch & handle memory-allocation failures gracefully (instead of crashing).
:: yea (0) / nay (0)
* Replace PyMOL's memory management & custom containers with a simple runtime object model.
:: yea (0) / nay (0)
* Separate the View and the Controllers from the Model so that they can all run asynchronously (on multiple cores).
:: yea ([[User:Vvostri|Vvostri]]) / nay (0)
* Enable generalized undo of changes made to the Model.
:: yea ([[User:Vvostri|Vvostri]]) / nay (0)
* Clean up the internal matrix handling code.
:: yea (0) / nay (0)

== Ideas Involving Proprietary APIs ==

Since these involve closed-source APIs and infrastructure, they aren't suitable for open-source development efforts. However, such requests are noted here for the sake of complete coverage.

* Create a Windows port with "native" look & feel. <- Could this be done in PyQT or PyGTK?. Then it would look "native", but be cross-platform and not proprietary.
:: yea (0) / nay (0)
* Integrate directly via Mathematica via MathLink.
:: yea (0) / nay ([[User:Aschreyer|Aschreyer]])
* Further enhance JyMOL (Java-JNI/wrapped PyMOL)
:: yea ([[User:Inchoate|Tree]]) / nay (0)
* Integrate with Matlab.
:: yea (0) / nay ([[User:Aschreyer|Aschreyer]])

== More Ideas (Please add your own!) ==
* [http://molviz.cs.toronto.edu/molviz MolViz] is a project to incorporate head tracking input into [http://pymol.sourceforge.net/ PyMol]. This is accomplished through a [[ImmersiveViz]] script written in Python to control the molecule's position using the existing [http://www.pymolwiki.org/index.php/Category:Commands PyMol API]. Related projects would include:
** Improving the existing [[ImmersiveViz]] PyMol plugin for more precise control of the environment.
** Developing new input drivers for the Wiimote form of control. This would require some bluetooth hacking.
** Implementing some other forms of input for head tracking, such as fisheye head tracking, IR webcam tracking, etc (refer to the end of this [[http://www.youtube.com/watch?v=ncShaY4VSac video]] for a better description).
:: yea (0) / nay (0)
* Provide a 2D chemical depiction of the current 3D view.
:: yea ([[User:Aschreyer|Aschreyer]]) / nay (0)
::: RDKit?
* Spreadsheet view with additional information (e.g. IC50's).
:: yea ([[User:Aschreyer|Aschreyer]]) / nay (0)
* Create additional documentation, screen casts, & tutorials.
:: yea ([[User:Markvanraaij|Markvanraaij]]) / nay (0)
* Export 3D PDF images.
:: yea ([[User:Vvostri|Vvostri]]) / nay (0)
* <strike>Add extra "Single Word Selectors" like "nucleic", "protein", "water", "ions", "backbone" (for nucleic acids or proteins), "mainchain", "sidechain"</strike>
:: yea (0) / nay (0)
* Add functionality that allows you to select atoms based on their location (i.e. select (x_coordinate < 10) and (z_coordinate > 0))
:: yea (0) / nay (0)
* set pdb_mirror option to use PDB mirrors other than RCSB for fetching structures (PDBe, PDBj); the EBI mirror is much faster from Europe for example.
:: yea ([[User:Aschreyer|Aschreyer]]) / nay (0)
* have the ability to link the TK console to the viewer so that users don't have to constantly alt+tab between what they want
:: yea (0) / nay (0)
* have the ability to disable typing in the viewer and automatically type in the TK console (I like being able to cut/paste/home/end)
:: yea (0) / nay (0)
* I see a lot of "can pymol do this" threads - any ideas of a good UI for a page of "things PyMOL can do?"
:: yea (0) / nay (0)
* make an option where I can turn on a coordinate grid - perhaps an object that is a cuboid grid around any object in the view so I can still alter how it's rendered?
:: yea (0) / nay (0)
* iPhone / Nexus One app(s)
:: yea (0) / nay (0)
* single-color bonds between nonidentical or any spherical atoms colored specifically
:: yea (0) / nay (0)
* double bonds as two parallel cylinders
:: yea ([[User:Vvostri|Vvostri]]) / nay (0)
* export scenes as [http://www.khronos.org/webgl/ WebGL] / Could make mobile apps, presentation plugins obsolete
:: yea ([[User:Aschreyer|Aschreyer]]) / nay (0)
* export images in vector format
:: yea ([[User:Vvostri|Vvostri]]) / nay (0)

Split states

2010-01-07T08:21:29Z

Gregori: Small typo

'''Split_States''' splits and orients multiple models and multimers from the biological unit file into a set of single-state molecular objects.

== Syntax ==
<source lang="python">
split_states object [, first [, last [, prefix ]]]
</source>

This splits the '''object''' from '''first''' to '''last''' out to the array of objects prefixed by '''prefix'''. The '''prefix''' option is very handy if all your states--or a subset of the states--have the same name.

==Using==
To use '''split_states''' simply
Load your molecule
<source lang="python">
# example usage
load fileName.pdb1, name
split_states name
delete name

# split all the states to objects starting with conf
fetch 1nmr
split_states 1nmr, prefix=conf
</source>

==Example==
'''1VLS''': A dimer.
<source lang="python">
load 1vls.pdb1, 1vls
split_states 1vls
dele 1vls
</source>

<gallery>
Image:1vls1.png|1VLS as a monomer. This is the state of 1VLS when I load the molecule (and select cartoon representation).
Image:1vls1_dimer.png|1VLS as a dimer using the split_states command. Notice PyMOL automatically loads and orients the new molecules.
</gallery>

[[Category:Commands|Split States]]
[[Category:States|Split States]]

Png

2006-01-26T09:35:15Z

Gregori: New comment about transparent png's

===DESCRIPTION===
'''png''' writes a png format image file of the current image to disk.

===USAGE===
png filename

===PYMOL API===
<source lang="python">
cmd.png( string file )
</source>

===COMMENTS===
To obtain transparent png images, use the following command before ray-tracing and exporting your scene:
set ray_opaque_background, 0

[[Category:Commands|png]]

Talk:Main Page

2005-12-21T12:51:01Z

Gregori: /* cmd commands */

== New ==

=== Some Thoughts For Discussion ===
* 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?

* 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.

* 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.

* 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...

* 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?

[[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).
----
=====Begin Inchoate's Comments To Warren=====
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.

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?

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.

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.

I do think organization is good. My way was seemingly obfuscated. Don't you think PyMol commands should somehow be lumped into available categories?
Changes to be made from my POV:
* Much shorter link names
* Kill the hierarchy?
* How to use the Wiki Intro

======Part 2======
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.

======Part 3======
I've made lots of changes:
* 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.
* 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.
* The names of the links should be MUCH easier to handle, and are far less obfuscated.

MediaWiki-style organization is starting to make sense. :-)

[[User:Inchoate|Inchoate]] 00:48, 6 May 2005 (CDT)
----

=====A singular vote from TStout=====

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:
select near , (ll expand 8)
select near , (ll expand 8)
select bb, (name ca,n,c,o )
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

----

=====Where is the anti-spam mechanism/strategy?=====
Manual removing spam contents really sucks.
----

== cmd commands ==

Hi Inchoate

I tried to change the "cmd delete" command into "delete", I moved the page but I couldn't figure out how to change the command name in the command list page...
Any help is welcome! I'm a newbie with Wiki...
Cheers

----
Edit:
Ok now it's gone... Anyway if you want to post the answer I could need it in the future!!

Talk:Main Page

2005-12-21T12:49:19Z

Gregori: cmd commands

Cmd delete

2005-12-20T10:26:32Z

Gregori: Cmd delete moved to Delete

#REDIRECT [[Delete]]

Remove

2005-12-20T10:23:15Z

Gregori: /* SEE ALSO */

===DESCRIPTION===
'''remove''' eleminates a selection of atoms from models.

===USAGE===
remove (selection)

===PYMOL API===
<source lang="python">
cmd.remove( string selection )
</source>

===EXAMPLES===
remove ( resi 124 )

===SEE ALSO===
[[Delete]]

[[Category:Commands|remove]]

Category:FAQ

2005-10-19T08:52:58Z

Gregori: Added a new Q&A (move two object independently)

==FAQ==

===Overview===
Please post your FAQs here. I suggest you write a Q&A style list with a short answer. More involved answers should link to its own page. Just my suggestion. Should we have topics?

----
Q: I've installed PyMol_0_98 correctly but I can't open my files in .mol2 or .pdb format from the menubar. Instead I can open them with the program. I can't even save the images I create in PyMol and obviously the mivie too.

Could you help me to solve these problems.
Thanks
Vittorio

A1: Vittorio, if I understand you correctly, then you need to (a) make sure you have the PDB file on your machine, say Desktop (or home directory, for *nix), then in the GUI click on, "File"->"Open" then use the dialog to find the file you want to load. You can save time if you know where the file is by just using PyMol's "load" command
load fileName, objectName
loads the fileName into a new object called objectName, for example,
load /tmp/1ggz.pdb, 1ggz

See [[Cmd load|load]],

A2: To save images you have a couple options. First, to save a quick raw screen dump type, "png fileName" to save a PNG image (IE and other programs can view these files). Or, secondly, if you prefer a higher quality image with ray-traced shadows and textures you can do, "ray" then, the above "png" command.

See [[Cmd ray|ray]], [[Cmd png|png]], [[:Category:Using_Pymol|Using PyMol]]

Hope this helps. If it didn't please restate your question to make it more clear.
----

Q: I've installed PyMol_0_98, and recently my structures have stopped displaying. I've tried uninstalling PyMol_0_98 and installing PyMol_0_97, and yet i've ran into the same problem...my .pdb files no longer display, although it is evident that they are being loaded and I can edit them.

Does anybody have any clue as to what might be the problem?
Thanks, shebsmehr

----
Q: Hi I have a problem. For some reason PyMOl do not display certain areas (several loops) of my .pdb file (1DAN) when in cartoon. When I display the structure in "lines" or "sticks" everything is ok. Furthermore, other .pdb viewers dont have this problem. I have tried several things:
1. Upgraded to the newest version og PyMol.
2. Redefined secondary structure using the "alter command".
3. Imported the .pdb file into SwissViewer, saved as the imported structure as a .pdb file, and then imported into PyMOl.

None of these things have solved the problem. Help please! (I would hate to have to start using another pdb-viewer!!)
Cheers
Kasper

----
Q: I want to move one object while keeping another fixed. How do I do this?

A: Load the proteins as separate objects, put the mouse into 3-button editing mode, then shift-middle click-and-drag on the molecule to translate and shift-left-click-and-drag to rotate. (Warren DeLano answer)

Color

2005-08-09T13:10:30Z

Gregori: Changed the API definition

===DESCRIPTION===
"color" changes the color of an object or an atom selection.

===USAGE===
color color-name
color color-name, object-name
color color-name, (selection)

===PYMOL API===
<source lang="python">cmd.color( string color, string selection )</source>

===EXAMPLES===
<source lang="python">color yellow, (name C*)</source>

[[Category:Objects_and_Selections]]
[[Category:Commands|color]]

Nuccyl

2005-08-05T07:57:01Z

Gregori: Change of the nuccyl URL

See [http://www.biosci.ki.se/groups/ljo/software/nuccyl.html Nuccyl Home]

==Overview==
'''nuccyl''' is a [http://www.perl.org/ Perl] program that allows [http://www.pymol.org/ PyMOL], a powerful open-source molecular modeling system, to display atomic models of nucleic acids in a highly simplified representation. By depicting the nucleic acid backbone as a cartoon and the bases of nucleotides as cylinders, similarly to the excellent programs [http://sgce.cbse.uab.edu/ribbons/ Ribbons] and [http://www-ibmc.u-strasbg.fr/upr9002/westhof/download.html Drawna], nuccyl and PyMOL allow to quickly grasp the overall folding of an RNA or DNA molecule

[[Image:Phe_trna_small.jpg|thumb|Example Nuccyl Image]]
[[Image:45s_rna_small.jpg|thumb|Example Nuccyl II]]
[[Image:50s_small.jpg|thumb|Example Nuccyl III]]
[[Image:P4p6_small.jpg|thumb|Example Nuccyl IV]]

nuccyl produces base cylinder coordinates and command files to display them with PyMOL. The base pair analysis programs [http://beta-ndb.rutgers.edu/services/download/index.html#rnaview RNAView] and [http://rutchem.rutgers.edu/%7exiangjun/3DNA/ 3DNA] can also be optionally used to obtain starting input files for nuccyl.

[http://beta-ndb.rutgers.edu/services/download/index.html#rnaview RNAView] can be downloaded and installed as [http://ndbserver.rutgers.edu/services/help/rnaview-readme.html described]; a [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12824344&dopt=Abstract publication] describing the program is also available.
Information and download links for [http://rutchem.rutgers.edu/%7exiangjun/3DNA/ 3DNA] may be found at the program's [http://rutchem.rutgers.edu/%7exiangjun/3DNA/ home page]; a [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12930962&dopt=Abstract paper] has also been published.

----
The four example images Copyright © 2000-2005 Luca Jovine. Do '''NOT''' reuse them without contacting him or reading his release license for the images!

[[Category:PyMol_Integration|Nuccyl]]