[PyMOL] Interface for native OS X version.
On 3 nov. 03, at 22:29, pymol-users-requ...@lists.sourceforge.net wrote: 2)The interface for mac is .. well.. very uncomfortable. Is there a chance of improvement soon? What exactly do you mean? I guess Einat talks about the tk interface that is missing in the native OS X version of PyMol. One can use the fink version to get the tk menu. But this version is rarely up-to-date. The menus have to be built using cocoa or tcl/tk aqua could be include in the native release.
RE: [PyMOL] DSSP
Ben, Great response! Indeed, the PDB's limited capacity for secondary structure does indeed represent this as one single helix, not two. > +/- 15 degrees is pretty difficult to see - so I think that DSSPs > +assignment > in this case, while liberal, is certainly acceptable. I hardly think it acceptable that one residue with 3-10 PHI/PSI constitutes a helix when you have so many other telltale characteristics of a Type II' beta turn, including a Glycine in position i+1 and all deviations within 22 deg. of ideal turn, as well as four planer CA atoms (actually five, C-alphas 98-102 are all nearly planer). Some turns do look like helices, but not this one -- not even close. > Great example of where DSSP fails, but perhaps a bit contrived. I don't think this example is contrived. One of the many tests I put PYMOL through regularly is to render the entire PDB over several hours, so I literally see thousands of structures on a routine basis. Such "objective but bogus" assignments are far more common than one would like to think. It is a real problem. > The reason that consistency is of paramount importance in assigning secondary structure > is so that different scientists can talk about the same protein in context. > If everyone uses the same definition of secondary structure - "helix 1" is always "helix 1". Good point, but I disagree. In acknowledging the subjective and relative nature of assignments, I think it is more reasonable to ask scientists to define their terms rather than to perpetuate broken conventions. Given how evolution, crystallization, and protein processing work, even with DSSP, Helix 3 can easily be Helix 2 or 4 in another structure of the identical or a related protein, so the savings in confusion is slight. Also, keep in mind that all numbering is relative and increasingly problematic as more and more homologous structures are solved, and explicit conceptual labels are far more general than numeric ones. But finally, do understand that I would provide DSSP as an option if it were possible to do so, but frankly, it's not. The paper does not enable an exact reimplementation, and the owners of DSSP, instead of making DSSP source code usable and redistributable as an open standard, have decided to use the software for revenue generation (presumed modest at best). It is exatly this kind of short-sighted restrictiveness that PyMOL was created to combat. We must end this dismal pattern of scientists developing research software that is so drastically and artificially limited by licensing terms that it has little or no ability to enable future scientific advances. Computer-dependent scientific fields like structural biology and computational chemistry will be handicapped until we can all effectively access and improve upon existing software systems. That will not happen until research scientists and academic institutions stop viewing such software programs as potentially lucrative intellectual properties and start viewing them as the critical building blocks that will enable future breakthroughs if and when they become widely shared. Imagine... What would happen if all scientists stopped publishing their discoveries and kept all information within one lab or institution? Scientific progress would come to a halt. That's basically what has occurred with so much scientific software over the last 20 years. Don't get me wrong -- some great code has been written -- and some of that code has been shared without cost to some or for a low fee to others. However, most of that code has almost never been shared in such a way as to enable extension, modification, and redistribution. As a result, we are not making much cumulative progress. Software programs resemble ideas: they must be shared, questioned, altered, and refined in order for lasting progress to occur. Otherwise they stagnate just like old ways of thinking. DSSP (circa 1983) is a great example of how many computer-dependent sciences remain trapped in the 1980s. Whether it works better than PyMOL or not is almost beside the point. It is simply not an appropriate standard for us to be using today in this age of open standards, open source, and composite systems. We can and should do better than this. My hope is that if PyMOL and enough similar projects are successful, that governments, companies, and funding agencies will begin to back these kinds of efforts wholeheartedly with money and policies, and thus drive rapid progress and widespread benefits throughout the sciences. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: Ben Hitz [mailto:bh...@exelixis.com] > Sent: Monday, November 03, 2003 11:01 AM > To: Warren L. DeLano; pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] DSSP
[PyMOL] Mac questions
On Nov 3, 2003, at 1:37 AM, Einat Sitbon wrote: Several questions regarding pymol on macs. 1)I'm using a G3. will version 0.93 work on it as the 0.90 version does? It should. I'm still waiting for 0.93 to be released via fink, because my compiling skills are minimal. 2)The interface for mac is .. well.. very uncomfortable. Is there a chance of improvement soon? What exactly do you mean? 3)In fink there is only version 0.86 of pymol. At least as much as I can see. Is there a more recent version? 0.90 is in the unstable branch. Just copy pymol.info and pymol.patch into the stable tree: sudo cp /sw//fink/10.2/unstable/main/finkinfo/sci/pymol.* /sw/fink/dists/local/main/finkinfo/ then run: fink index fink install pymol There are a couple of other packages in the unstable branch you will have to copy over too, such as numeric-py22 and pmw-py22 and a couple others too I think Good luck Scott
Re: [PyMOL] DSSP
Warren - Just up front I want to state that I don't think DSSP is the best possible way to algorithmically determine secondary structure. My position is that secondary structure is a subjective assignment anyway - so it will always be open to interpretation. In that case, you are better off assigning to the standard this is in most common usage. Great example of where DSSP fails, but perhaps a bit contrived. First of all, DSSP is assigning this as a "H" helix and "G" 3-10 helix - not really a single continuous helix (although one could interpret it this way). Second, you point about it not really being a 3-10 helix is not strong.. 3-10 helix (-49/-26). (ideal) residue 101 (-63/-12) +/- 15 degrees is pretty difficult to see - so I think that DSSPs assignment in this case, while liberal, is certainly acceptable. Finally the difference between a 3 residue "helix" and a reverse turn is not really easy to quantitate. In fact, any single turn of any helix is basically, well, a turn. Any algorithm that "allows" 3-4 residue helices is going to make such assignments, and in fact any realistic (human) interpretation is going to make the equivalence of short "helices" with turns. Your last point in the URL is critical. There will presumably be "errors" in dss, or stride, or any other algorithm, because frankly, the problem is not very well defined. Hence, it's probably best to just implement something, and leave the interpretation to the user. The reason that consistency is of paramount importance in assigning secondary structure is so that different scientists can talk about the same protein in context. If everyone uses the same definition of secondary structure - "helix 1" is always "helix 1". Ben -- Ben HitzExelixis Computational Biology and Informatics bh...@exelixis.com 650-837-8137 - Original Message - From: "Warren L. DeLano" To: "'Ben Hitz'" ; Sent: Monday, November 03, 2003 10:39 AM Subject: RE: [PyMOL] DSSP > Ben, > > Granted -- and there are certain times when it makes sense for everyone > to be "wrong" in order to be consistent. But is this one such case? I > think not. If DSSP "helices" aren't actually helices, then of what use > is the standard? Neither the resulting statistics nor the cartoon > figures will be correct. > > I've put up one particularly egregious DSSP example on the web at > > http://www.pymol.org/not_helix > > for inspection. If you are comfortable with obvious turn regions (such > as this one) being assigned as helix, then by all means, go right ahead > and continue using DSSP via rTools or the PDB. > > But for me, I am not going to lose sleep over deviating from an existing > standard in PyMOL. As I said before, the DSSP paper wasn't even written > in such a way as to enable exact reproduction of their research other > than by running their proprietary (1000 EURO) software program or by > analyzing their source code. > > PyMOL's new "dss" algorithm is nowhere near validated enough to become a > standard, but I do think that if we are going to agree upon a standard > for secondary structure assignment, that the standard should reflect > common notions of secondary structure, be exactly described, be > reproducible, and be available in an open-source reference > implementation. Does DSSP meet these criteria? No, but STRIDE might > (if one could find it), and "dss" probably could in time. > > Cheers, > Warren > > -- > mailto:war...@delanoscientific.com > Warren L. DeLano, Ph.D. > Principal Scientist > DeLano Scientific LLC > Voice (650)-346-1154 > Fax (650)-593-4020 > > > -Original Message- > > From: pymol-users-ad...@lists.sourceforge.net > > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Ben Hitz > > Sent: Monday, November 03, 2003 8:28 AM > > To: pymol-users@lists.sourceforge.net > > Subject: [PyMOL] DSSP > > > > > > Warren - > > The advantage of using DSSP over another heuristic method, is > > that it is a standard. A DSSP helix is a DSSP helix > > everywhere, even if a crystallographer might extend the end a bit. > > > > Ben > > -- > > Ben HitzExelixis > > Computational Biology and Informatics > > bh...@exelixis.com 650-837-8137 > > > > > > > > --- > > This SF.net email is sponsored by: SF.net Giveback Program. > > Does SourceForge.net help you be more productive? Does it > > help you create better code? SHARE THE LOVE, and help us help > > YOU! Click Here: http://sourceforge.net/donate/ > > ___ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/p> ymol-users > > >
RE: [PyMOL] DSSP
Ben, Granted -- and there are certain times when it makes sense for everyone to be "wrong" in order to be consistent. But is this one such case? I think not. If DSSP "helices" aren't actually helices, then of what use is the standard? Neither the resulting statistics nor the cartoon figures will be correct. I've put up one particularly egregious DSSP example on the web at http://www.pymol.org/not_helix for inspection. If you are comfortable with obvious turn regions (such as this one) being assigned as helix, then by all means, go right ahead and continue using DSSP via rTools or the PDB. But for me, I am not going to lose sleep over deviating from an existing standard in PyMOL. As I said before, the DSSP paper wasn't even written in such a way as to enable exact reproduction of their research other than by running their proprietary (1000 EURO) software program or by analyzing their source code. PyMOL's new "dss" algorithm is nowhere near validated enough to become a standard, but I do think that if we are going to agree upon a standard for secondary structure assignment, that the standard should reflect common notions of secondary structure, be exactly described, be reproducible, and be available in an open-source reference implementation. Does DSSP meet these criteria? No, but STRIDE might (if one could find it), and "dss" probably could in time. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Ben Hitz > Sent: Monday, November 03, 2003 8:28 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] DSSP > > > Warren - > The advantage of using DSSP over another heuristic method, is > that it is a standard. A DSSP helix is a DSSP helix > everywhere, even if a crystallographer might extend the end a bit. > > Ben > -- > Ben HitzExelixis > Computational Biology and Informatics > bh...@exelixis.com 650-837-8137 > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/p> ymol-users >
[PyMOL] DSSP
Warren - The advantage of using DSSP over another heuristic method, is that it is a standard. A DSSP helix is a DSSP helix everywhere, even if a crystallographer might extend the end a bit. Ben -- Ben HitzExelixis Computational Biology and Informatics bh...@exelixis.com 650-837-8137
[PyMOL] Mac questions
Hi, Several questions regarding pymol on macs. 1)I'm using a G3. will version 0.93 work on it as the 0.90 version does? 2)The interface for mac is .. well.. very uncomfortable. Is there a chance of improvement soon? 3)In fink there is only version 0.86 of pymol. At least as much as I can see. Is there a more recent version? Thanks, Einat. Einat Sitbon Department of Molecular Genetics Weizmann Institute of Science _ Protect your PC - get McAfee.com VirusScan Online http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963
[PyMOL] Re: 3 button editing and viewing, modifier button clicking not working
Hi Warren, I spotted this a while ago but thought I was just doing it wrong On my system, RHL8.0 with with commercial xig.com summit Xserver for hardware stereo, when I try to do what is described below, in 3 button editing, ctrl middle click on an atom, no white sphere appears on the atom so I cant move that molecule. The three buttons on my logitech ps2 scroll wheel mouse work fine on their own for rotate, zoom and translate, but don't seem to work with modifier keys in pymol... shift left click works in another application, MayaVi (uses tkinter) any ideas? Dan On Monday, November 3, 2003, at 06:15 AM, pymol-users-requ...@lists.sourceforge.net wrote: Send PyMOL-users mailing list submissions to pymol-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/pymol-users or, via email, send a message with subject or body 'help' to pymol-users-requ...@lists.sourceforge.net You can reach the person managing the list at pymol-users-ad...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of PyMOL-users digest..." Today's Topics: 1. RE: a couple of newbie questions (Warren L. DeLano) --__--__-- Message: 1 From: "Warren L. DeLano" To: "'Andrew Fant'" , Subject: RE: [PyMOL] a couple of newbie questions Date: Sat, 1 Nov 2003 20:33:20 -0800 Hello all. I am relatively new to pymol, so please excuse me if these questions are too simple for the list as a whole. I am running 0.90 on a Linux system by way of introduction. 1) What is the easiest way to select one molecule out of several on the screen and translate it independently from everything else? I try selecting it. but moving the mouse while holding the mov button still translates everything. Select "3 Button Editing Mode" from the mouse menu (or click on the mouse matrix, or simply type "edit_mode"). Ctrl-middle click on one atom in the molecule you wish to translate. A white ball should appear on that atom. Then shift-middle-click on that same atom to translate the molecule, or shift-left-click to rotate it. (If you click on other atoms in the molecule, only that fragment, relative to the ball will be translated) When done, click the Unpick button, or type "unpick", or ctrl-middle click away from any atoms to clear the picked selection. 2) Is there an easy way to superimpose many molecules independently? I know that I can do individual pairwise alignments, but that seems like a good way to let more errors creep into the process. Not really. "fit" and "align" give you pairwise alignments -- there isn't any multiple-sequence-alignment capability in PyMOL yet. 3) Is there an automated way to take HET groups in a structure read from a PDB file and make independent molecules out of them? The following commands will move the heteroatoms into a separate object: create hetobj, hetatm remove hetatm and not hetobj Cheers, Warren --__--__-- ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users End of PyMOL-users Digest Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 (0)14 260 4183 (work) +358 (0)414740463 (mob) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
