Re: [PyMOL] New Feature Ideas
Hi all, Being a user of Adobe products, I am use to having a very customizable working environment so that you could easily improve overall workflow and decrease fumbling time. I find myself wanting my productivity to increase when using PyMOL. While I do input a lot of my commands by hand, I find that a lot of my time is wasted when I use the point-and-click method of doing things (from the object menu). Most of the time it just takes me too long to find the menu item, say, for renaming or deleting an object. I know that it's in the Actions pull-down menu but I often overlook what I need since the position/arrangement of certain available actions can vary depending on the object. What I would like to see is customizable menus for the objects where the user can, ahead of time, specify or arrange their menus they way that they like along with the actions/commands that they use most often (or sometimes, most recent). Perhaps this could be accomplished through the pymolrc file. With a customized action menu, I know for certain that rename object and delete object will always be positioned at the top and the less used zoom and center options will be lower. Sean _ -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
Hi all, Another feature that I find myself always wanting is a kill script button and/or command. This comes in handy when I am testing a new python script and, accidentally, throw in an infinite loop. It would be nice to have some sort of kill switch not only for python scripts but even for something as simple as ray-tracing. There are times when I am ray-tracing a complicated scene and realize that half-way through the ray-tracing process that something was missing. In that case, I normally have to kill PyMOL and start all over again (and hopefully, I'll have the scene/session saved). Having this function would greatly enhance my productivity. Thanks! Sean _ -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
Hi Sean, On Fri, Feb 12, 2010 at 12:39 PM, Sean Law magic...@hotmail.com wrote: Hi all, Another feature that I find myself always wanting is a kill script button and/or command. This comes in handy when I am testing a new python script and, accidentally, throw in an infinite loop. It would be nice to have some sort of kill switch not only for python scripts but even for something as simple as ray-tracing. There are times when I am ray-tracing a complicated scene and realize that half-way through the ray-tracing process that something was missing. In that case, I normally have to kill PyMOL and start all over again (and hopefully, I'll have the scene/session saved). Having this function would greatly enhance my productivity. You should see a button labeled Abort at the bottom right of the external GUI window. You can click it to stop the ray tracer. It used to only work if you started the ray tracer by clicking the Ray button in that same window, but it appears to work no matter how you start the ray tracer now (1.2r2). Cheers, -Michael Thanks! Sean -- Not using Hotmail on your phone? Why not? Get it now.http://go.microsoft.com/?linkid=9708120 -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
Hi Sean e.a., In reply to your messages, first an overview as I picked up from the other mails: 1. eMovie integration (Simon Kolstoe) 2. Powerpoint plugin (Roger Rowlett) 3. Enhanced morphing (ibid) 4. Foolproof download (David Hall) 5. DynoPlot integration (ibid) 6. Improved undo/redo (ibid) 7. Ray/png size/resolution (Georg Steinkeller) 8. Set mirrors for downloading (Adrian Schreyer) 9. WebGL output (ibid) 10. Vector graphics support (Sean Law) 11. PDF support (ibid) 12. Trajectory support (ibid) 13. CG object GUI (ibid) As noted 2 and 3 are available in the incentive version. 4, 7 and 8 seem relatively straightforward to implement. For 5 steps should probably be taken by the DynoPlot crew, or at least it should be done in collaboration. 6 is indeed problematic but highly desirable. Undoing operations on states would require to store the differences between states, which can be huge, e.g. in the case of splitting accidentally. On the other hand, using wild cards makes it trivial to remove the splitted states again, so I don't think that particular point is worth the trouble. On the other hand, a view is not memory demanding, and it would be easy to keep a stack of those to allow undo/redo. 9. Yea :) 10. Yea. Not by any means trivial though. But I'd be happy to brainstorm on that one. 11. Would be cool. 12. Definite yea. I fear that this requires some serious changes inside though to allow efficient viewing of a trajectory, such as VMD and Yasara offer. The lack of trajectory support is a reason for many working on MD to use VMD rather than Pymol. On the other hand, for the open source/freeware version, the gromacs trajectory API could be interesting to aid in realization of it. In relation to this I'd really like to have support added for reading topology information, and to use this to set bonds, atom types, masses and charges, rather than the internal databases. Especially with the momentum of coarse grained simulations these days, it would be required to keep Pymol favoured over VMD. 13. Errm, yea, but... This would almost come down to integration of Pymol with Blender. Oh, please do, yea, yea! :D In relation to the last point, I would (14.) really like to see improved POV-Ray output. The mesh that is output currently is a mess, and highly inefficient. A correct mesh would require for each mesh object (cartoon, surface, ... per object) to be written as a set of nodes, with a set of pigments and a set of triangles, referring to the node list. Now each triangle is its own mesh2 object, which is terrible. In addition, I would also like to write POV-Ray include files on a per object basis, maybe as a setting split_povray_output. That makes it much more easy to modify the scene. The master file would only contain the global settings (camera, light, etc.) and a number of include statements for the other objects. Actually, this is what I'm now usually doing by hand, enabling/writing/disabling each object and each representation... O, it's also almost trivial to include all views in the master file, so that a complete scene can be written out as a set of POV-Ray files. I'd be happy to streamline and contribute my POV-Ray code for that. Another thing on my mind is the desire to (15.) read in images as objects, or, better, as pigment/texture on an object. That will make it easy to overlay a structure on a graph for instance. Finally, unless I think of more later, I would like to be able to (16.) read and change coordinates quicker. Now, iterating over states to fiddle with coordinates is painstakingly slow. I'm afraid though that this is heavily tied in with the internal structure of Pymol, regarding objects and states. But if that were streamlined, probably together with 12, then probably Pymol would be able to become a true platform for analysis of trajectories. Cheers, Tsjerk On Wed, Jan 20, 2010 at 5:26 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: PyMOLers, We need to move forward on PyMOL development, so I'm collecting ideas from all our users on what they most want in future versions of PyMOL. We already have a page on the PyMOL wiki for this (http://pymolwiki.org/index.php/Ideas) from 2008/2009. We can discuss the ideas here and on the wiki; this list is more for two-way communication and the wiki for one-way. If you have a specific request for an enhancement you can also email it directly to h...@schrodinger.com; please put PyMOL in the subject so I can get them easily. Each request submitted will be considered for implementation. Last, you're particularly passionate about your feature request, email me directly and we can chat about it via phone/skype. Thanks, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the
Re: [PyMOL] New Feature Ideas
On Thu, Jan 21, 2010 at 10:47 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Sean e.a., I really meant Jason e.a. :$ T. -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] New Feature Ideas
Jason, here are my feature requests, only slightly biased by the fact that some of them would be useful for my paper now (-: 1) arbitrary clipping planes bound to an object with an intelligent gui to place them. Something akin to be found in Maestro or semi-transparent CGO objects which can be manipulated freely in space and then used to define clipping planes 2) Implementation of bounding planes in raytracing to avoid showing the inside of clipped surfaces, raster3D has this option. I know one can fumble around in Povray to get the same effect, but I'd rather spend my time on something more productive. 3) If 2) is not an easy option, how about raster3D output in addition to povray? Pymol can read raster3d, why not have the output as well. 4) A better density wizard, let's just copy coot and be done with it. Ability to dynamically bind density levels or some other properties to the scroll-wheel for that matter. 5) Updated documentation. One thing that always irritated me as a paying subscriber was the fact that the documentation never kept up with development and the search capabilities were not that great. Don't get me wrong the Wiki and BB are great resources, but I'd expect a bit more of the docs. Also having the internal help functionality for functions and the API up to date would be great. Some functions don't seem to have a doc-string. 6) Integration/bundling of wxPython as an alternative to TCL/Tk?? 7) Internal FFT routines to be able to read map-coefficients 8) A CGO library for commonly used objects like arrows and such Cheers, Carsten -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] New Feature Ideas
I think a page where features ideas can be posted and voted up or down would be very helpful (like Google product ideas) to collect feature requests and see which ones are the most demanded. Adrian -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
- It would be nice if pymol could deal with/generate viral surfaces similar to this one: http://www.pnas.org/content/100/12/6899/F2.medium.gif I make all my images with pymol but have to switch to chimera for the viral surface. - I would also find useful if pymol could easily export a list of residues/atoms/whatever with given properties, e.g. all the surface residues or all the charged residues in an interface. Maybe it's just my ignorance but I don't know how to do this right now. Thanks, Luca attachment: luca_varani.vcf-- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
On Thu, Jan 21, 2010 at 9:19 AM, Adrian Schreyer ams...@cam.ac.uk wrote: I think a page where features ideas can be posted and voted up or down would be very helpful (like Google product ideas) to collect feature requests and see which ones are the most demanded. Adrian Let's do this. Head over to http://pymolwiki.org/index.php/Ideas and find the idea you like. If it's not there, add it in the format on the page. If you want to vote for a feature you like, simply edit the page, find the yea () associated with your feature and inside the parentheses put ~~~. In the wiki if you insert the text ~~~ it expands to your user name. This will make a list of usernames for each feature. I don't want to do vote counting and we'd have to search the history if someone double voted. -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
On Thu, Jan 21, 2010 at 6:10 AM, Schubert, Carsten [PRDUS] cschu...@its.jnj.com wrote: 4) A better density wizard, let's just copy coot and be done with it. Ability to dynamically bind density levels or some other properties to the scroll-wheel for that matter. +1 6) Integration/bundling of wxPython as an alternative to TCL/Tk?? Also +1. Warren mentioned this last year as a possibility for integrating PyMOL with the Phenix GUI, and in theory support for embedding a PyMOL view in wxPython is already present. However, that code appears to be very old and not maintained - I couldn't get it to work even after updating it to use the newer wx modules. I suspect there is not much work to do in order to resurrect it, but I don't know enough about PyMOL internals, or have time to learn. Note that this feature (if it were open-source) would allow anyone to make a native Mac PyMOL GUI and distribute that, so it isn't something I'd ask Schrodinger to subsidize. (If anyone else is interested in helping figure this out, however, let me know.) 7) Internal FFT routines to be able to read map-coefficients +2. I believe the CCP4 libraries for this are open-source, so those are one option. CCTBX is another (I have tried this and it works), but this will be a lot more overhead. -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
Hi Jason, I think the number one feature I would like to see is eMovie incorporated into the standard build of PyMOL. The built in movie making facilities in PyMOL may be powerful but the scripting is a bit beyond those of us biologists who use computers especially if one is trying to make longer and more involved movies. eMovie is a really nice and easy to understand interface that is only spoiled by how buggy it is (especially on a Mac where it seems to disagree violently with the video card/chips). Secondly, more and more academic structural biologists use Macs - at the recent British Crystallographic Association winter meeting ten out of twelve speakers used Macs. If Mac support is decreased it will stop being used by academics. Finally, although I understand the reasons for PyMOL being sold to Schrodinger, I have to admit I was disappointed as in the past I have found Schrodinger singularly unhelpful in making their software available free(ish) to academics. I really really hope that all the great stuff in PyMOL isn't stolen for other applications whilst PyMOL itself is left to wither away. Simon On 20 Jan 2010, at 04:26, Jason Vertrees wrote: PyMOLers, We need to move forward on PyMOL development, so I'm collecting ideas from all our users on what they most want in future versions of PyMOL. We already have a page on the PyMOL wiki for this (http://pymolwiki.org/index.php/Ideas) from 2008/2009. We can discuss the ideas here and on the wiki; this list is more for two-way communication and the wiki for one-way. If you have a specific request for an enhancement you can also email it directly to h...@schrodinger.com; please put PyMOL in the subject so I can get them easily. Each request submitted will be considered for implementation. Last, you're particularly passionate about your feature request, email me directly and we can chat about it via phone/skype. Thanks, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol- us...@lists.sourceforge.net -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] New Feature Ideas
Hi Jason, here are two minor improvements: 1) set pdb_mirror option to be able to use a European (EBI) mirror for example. The RCSB mirror is rather slow from Europe. 2) uppercase support for fetch_path; currently only lowercase file names are loaded. Something more challenging: 3) Export scenes as webGL.This is a bit more ambitious to be honest but the benefits could be huge. A couple of problems could be solved at once, such as integration into web pages or documents, mobile devices, etc. without any plugins or Java stuff. Adrian -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
- Original Message From: Adrian Schreyer ams...@cam.ac.uk To: jason.vertr...@schrodinger.com; PyMOL-users@lists.sourceforge.net Sent: Wed, January 20, 2010 10:00:03 AM Subject: [PyMOL] New Feature Ideas Something more challenging: 3) Export scenes as webGL.This is a bit more ambitious to be honest but the benefits could be huge. A couple of problems could be solved at once, such as integration into web pages or documents, mobile devices, etc. without any plugins or Java stuff. Adrian +1000 People really need to jump on the bandwagon of getting rid of Java plugins. I wish the pdb het atom pages would get rid of JMol for 3D viewing of molecules and hop onto twirlymol. Just as a question, what version of OpenGL does pymol rely on? WebGL is based around OpenGL ES 2.0 which is based around OpenGL 2.0. I assume pymol doesn't use OpenGL 3.0, since its not even in OS X right now. This area is something I'm hugely ignorant of though. -David -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
Two items come to mind: 1. A Powerpoint plugin for live Pymol viewing in presentations. 2. A simpler method of doing structure morphs in Pymol. Intelligent morphing is incredibly powerful for visualizing protein conformational changes based on "endpoint" protein structures, or just evaluating/understanding the differences between point mutations of proteins. I think both of these were on the radar screen for Pymol feature enhancement at some point in the recent past. Cheers. On 1/19/2010 11:26 PM, Jason Vertrees wrote: PyMOLers, We need to move forward on PyMOL development, so I'm collecting ideas from all our users on what they most want in future versions of PyMOL. We already have a page on the PyMOL wiki for this (http://pymolwiki.org/index.php/Ideas) from 2008/2009. We can discuss the ideas here and on the wiki; this list is more for two-way communication and the wiki for one-way. If you have a specific request for an enhancement you can also email it directly to h...@schrodinger.com; please put "PyMOL" in the subject so I can get them easily. Each request submitted will be considered for implementation. Last, you're particularly passionate about your feature request, email me directly and we can chat about it via phone/skype. Thanks, -- Jason -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
Adrian, My comments follow. 1) set pdb_mirror option to be able to use a European (EBI) mirror for example. The RCSB mirror is rather slow from Europe. This is a good idea; allowing people to set their own server. 2) uppercase support for fetch_path; currently only lowercase file names are loaded. Do you mean the PDB ids are all lower case or the fetch_paths themselves? One caveat for paths is the cross-platform inconsistency in path naming: Windows and some Apple systems are case insensitive. Something more challenging: 3) Export scenes as webGL.This is a bit more ambitious to be honest but the benefits could be huge. A couple of problems could be solved at once, such as integration into web pages or documents, mobile devices, etc. without any plugins or Java stuff. Interesting. -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
Roger, Both of these features are available to PyMOL subscribers already. You can get AxPyMOL which has the ActiveX plugin for PowerPoint. There is no need to tab out of your presentation. Also in the incentive version is RigiMOL the molecular morpher. We could probably clean up the interface for this, as currently you have to be able to do simple Python programming. Warren went through alot of work to realize these two features, which is why he charged for them. Once I rebuild the AxPyMOL builds you can test out the demo version. If you have an immediate need for AxPyMOL, please contact me directly and I might be able to push out that Eval build more quickly. Thanks, -- Jason On Wed, Jan 20, 2010 at 11:08 AM, Roger Rowlett rrowl...@colgate.edu wrote: Two items come to mind: 1. A Powerpoint plugin for live Pymol viewing in presentations. 2. A simpler method of doing structure morphs in Pymol. Intelligent morphing is incredibly powerful for visualizing protein conformational changes based on endpoint protein structures, or just evaluating/understanding the differences between point mutations of proteins. I think both of these were on the radar screen for Pymol feature enhancement at some point in the recent past. Cheers. On 1/19/2010 11:26 PM, Jason Vertrees wrote: PyMOLers, We need to move forward on PyMOL development, so I'm collecting ideas from all our users on what they most want in future versions of PyMOL. We already have a page on the PyMOL wiki for this (http://pymolwiki.org/index.php/Ideas) from 2008/2009. We can discuss the ideas here and on the wiki; this list is more for two-way communication and the wiki for one-way. If you have a specific request for an enhancement you can also email it directly to h...@schrodinger.com; please put PyMOL in the subject so I can get them easily. Each request submitted will be considered for implementation. Last, you're particularly passionate about your feature request, email me directly and we can chat about it via phone/skype. Thanks, -- Jason -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
1) I would love it if the PDB Loader Service Plugin would clean up what it left in /tmp on pymol exit. I have a feeling this might be complicated though. I just have a bad memory when I first entered this world and I had pymol open and I was trying to load a pdb and the plugin just would not work. The previous graduate student using the system had previously loaded the same pdb using the plugin and the file had written in /tmp and the PDB Loader would therefore not get me the file. When you're just starting a rotation in a new lab, that type of problem can scar you as you have to explain why it took you half an hour to open a pdb in pymol... An alternative solution is to check for the filename before trying to write there. And be like Firefox and just name them 1ACB-1.pdb when 1ACB.pdb can't be written to. 2) This might be out of your range as it is a plug in written by the community, but DynoPlot could become something really cool with a little love and care. My big problem right now is that you are only able to create a plot with a single selection. I teach a lab once a year where we have the students use dynoplot to make ramachandran plots of the helices, then they have to restart pymol before they can select the beta sheets and make a ramachandran plot of them as well. As we all know, losing a pymol session can be a painful experience. Having to restart is also rough. 3) A more extensive undo/redo system. It would be nice to be able to undo anything. And then redo it. I'm talking fetch 2no8; split_states, realizing there's 60 models and just doing undo and having a single model again. Or I accidentally change my view, I can go back. I don't know what level of granularity it should be, but something would be good. Again, losing that perfect view or such can be painful. -David - Original Message From: Jason Vertrees jason.vertr...@schrodinger.com To: pymol-users@lists.sourceforge.net Sent: Tue, January 19, 2010 11:26:39 PM Subject: [PyMOL] New Feature Ideas PyMOLers, We need to move forward on PyMOL development, so I'm collecting ideas from all our users on what they most want in future versions of PyMOL. We already have a page on the PyMOL wiki for this (http://pymolwiki.org/index.php/Ideas) from 2008/2009. We can discuss the ideas here and on the wiki; this list is more for two-way communication and the wiki for one-way. If you have a specific request for an enhancement you can also email it directly to h...@schrodinger.com; please put PyMOL in the subject so I can get them easily. Each request submitted will be considered for implementation. Last, you're particularly passionate about your feature request, email me directly and we can chat about it via phone/skype. Thanks, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] New Feature Ideas
David, Some good suggestions, but I think too localized to you, specifically. My comments follow. 1) I would love it if the PDB Loader Service Plugin would clean up what it left in /tmp on pymol exit. I have a feeling this might be complicated though. I just have a bad memory when I first entered this world and I had pymol open and I was trying to load a pdb and the plugin just would not work. The previous graduate student using the system had previously loaded the same pdb using the plugin and the file had written in /tmp and the PDB Loader would therefore not get me the file. When you're just starting a rotation in a new lab, that type of problem can scar you as you have to explain why it took you half an hour to open a pdb in pymol... First time I've heard this request. PyMOL attempts to cache the data, so you don't have to keep re-downloading the PDB files. Also, if PyMOL crashes or is suddenly killed, there's no way to clean up the remaining PDBs. Plus, there could be security issues with removing files: fetch '/bin/rm -r *' might allow for some kind of evilness. To be serious about this, many more people need to show interest in it. An alternative solution is to check for the filename before trying to write there. And be like Firefox and just name them 1ACB-1.pdb when 1ACB.pdb can't be written to. Maybe this smacks of a different solution altogether: project-based sessions? 2) This might be out of your range as it is a plug in written by the community, but DynoPlot could become something really cool with a little love and care. My big problem right now is that you are only able to create a plot with a single selection. I teach a lab once a year where we have the students use dynoplot to make ramachandran plots of the helices, then they have to restart pymol before they can select the beta sheets and make a ramachandran plot of them as well. As we all know, losing a pymol session can be a painful experience. Having to restart is also rough. You would have to work with the DynoPlot author to improve this. 3) A more extensive undo/redo system. It would be nice to be able to undo anything. And then redo it. I'm talking fetch 2no8; split_states, realizing there's 60 models and just doing undo and having a single model again. Or I accidentally change my view, I can go back. I don't know what level of granularity it should be, but something would be good. Again, losing that perfect view or such can be painful. This is a definite must, especially for molecular editing. In PyMOL, sadly, this is very hard. Warren fretted about this for months, and even started a basic level of undo. I predict this will be around after we do some major refactoring--possibly in PyMOL 2.0. :-) Thanks for your suggestions. -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] New Feature Ideas
PyMOLers, We need to move forward on PyMOL development, so I'm collecting ideas from all our users on what they most want in future versions of PyMOL. We already have a page on the PyMOL wiki for this (http://pymolwiki.org/index.php/Ideas) from 2008/2009. We can discuss the ideas here and on the wiki; this list is more for two-way communication and the wiki for one-way. If you have a specific request for an enhancement you can also email it directly to h...@schrodinger.com; please put PyMOL in the subject so I can get them easily. Each request submitted will be considered for implementation. Last, you're particularly passionate about your feature request, email me directly and we can chat about it via phone/skype. Thanks, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
