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From: Kersey B. <kb...@js...> - 2002-10-31 22:55:44
|
Hi Pymolers, Sorry for a newbie question, but here goes. I am trying to get started with movies and am having problems with the understanding the paradigm (states vs frames and how actions are associated with frames, etc). So, a couple of questions arise. 1) Perhaps I misunderstanding the utility of movies. I am thinking of using a sequence of frames that I could move through 1 by 1 as a way of moving through a presentation. [I would be doing this in PyMOL so I have slways have complete interactivity, and not as a quicktime movie.] Each frame would differ enough that I do not want to try to type in all the required pymol commands individually, nor try to do it all with the GUI on the fly. (e.g. I am thinking of something like starting by showing a protein, then show a cartoon, then go back to sticks, then zoom into the active site, etc.) Is this reasonable, or is there a better way to effectively apply "functions" containing a sequence of PyMOL commands to move through a presentation. Would it be better to do this as a bunch of individual scripts which I call from the command line? (perhaps with scirptBox, though I have not yet got it up and running on my mac -- has anyone done this?)? Any thoughts would be great. 2) I have been using the manual, the list archives, and a couple of small tutorials on the web, but remain a bit lost on movie creation. Are there examples which use movies towards the purpose I describe above which might give more hints on how to define states/frames/associated actions, etc. Most of the examples I have found go a different direction (thus, point 1)). I am using 0.84beta on OSX 10.2.1 -- it great -- thanks for all the effort in the creation of PyMOL and the port to OS X. I also have it on my SGI, if the full GUI would make any of this more obvious. 3) Where can I find the source to the "scripted animation" Demo (arginine conformations)? 4) Can transparency be applied to sticks? [saw the previous post, but could not find an answer] Thanks for any help. Kersey |
From: <wg...@ch...> - 2002-10-31 21:21:59
|
Hi Lieven: I don't have windows pymol or access currently to a windows machine, so I will have to tell you how I did it on the Mac version and then hope it is essentially identical with windows. I did this about 6 months ago in order to hyperlink quicktime to Powerpoint in XP. I am assuming hyperlinking to Pymol would work the same way, since it works the same way on a Mac. But you never know with Windows since 90% of the operating system seems to be dedicated to preventing you from using your computer. Open up powerpoint and create a new slide. In it put a word or picture or something. Then select that word or picture or whatever it is. Go to insert > hyperlink and then put in the full file hierarchy path to your pymol application Then when you are in presentation mode, you click on this and it starts pymol. On XP it seemed to embed it in situ (at least when I was using quicktime). In OS X it changes over to the pymol display. That's the basis for my claim that it works better in XP. I apologize if this doesn't. HTH, Bill Scott William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax: +1-831-4593139 (fax) |
From: DeLano, W. <wa...@su...> - 2002-10-31 17:30:57
|
Jules, Unfortunately, PyMOL molecular editing features are not really = documented yet. =20 You can move entire object independently using the "MovF" and "RotF" = mouse actions. With the normal three-button mouse configuration in = Editing Mode, that would be shift-middle-click and shift-left-click, = respectively. You can change the origin of rotation with the "Orig" = action, control-shift-middle click. By the way, Be sure that no atoms are "picked" before attempting this. = If the pick selections (pk1, pkfrag1, ...) are present, then you will = end up only moving pieces of the picked molecule. You can can first = ctrl-middle click away from any atom to unpick. Warren > -----Original Message----- > From: Jules Jacobsen [mailto:jo...@he...] > Sent: Thursday, October 31, 2002 6:39 AM > To: pym...@li... > Subject: [PyMOL] manual docking of multiple molecules and DNA=20 > fragments >=20 >=20 >=20 > Does anyone know of a way to dock (read move independantly)=20 > two or more > molecules in one window? I am aware of the rotate and=20 > translate commands > but these are really not quick or easy to use. If there isn't=20 > any way of > doing this can i then add this to a wish list of functions for future > releases. This would be especially good if it could work in=20 > conjunction > with the sculpting wizard. Also is there any way of adding=20 > DNA/RNA bases > to the fragment library? >=20 > thanks in advance >=20 > Jules >=20 >=20 >=20 > ------------------------------------------------------- > This sf.net email is sponsored by: Influence the future=20 > of Java(TM) technology. Join the Java Community=20 > Process(SM) (JCP(SM)) program now.=20 > http://ads.sourceforge.net/cgi-bin/redirect.pl?sunm0004en > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 |
From: Jules J. <jo...@he...> - 2002-10-31 14:39:14
|
Does anyone know of a way to dock (read move independantly) two or more molecules in one window? I am aware of the rotate and translate commands but these are really not quick or easy to use. If there isn't any way of doing this can i then add this to a wish list of functions for future releases. This would be especially good if it could work in conjunction with the sculpting wizard. Also is there any way of adding DNA/RNA bases to the fragment library? thanks in advance Jules |
From: Lieven B. <li...@ul...> - 2002-10-31 14:27:57
|
wg...@ch... wrote: > Also, don't overlook the fact that pymol itself is a movie player. In > powerpoint you can create what is called a hyperlink to pymol, and then > you can just load in your macro (pml script) and your movie starts > playing embedded in powerpoint. Could you provide some more details on this procedure. So far I have only managed to include an icon/object in PowerPoint that starts PyMol in an extra window (with a specified script). -- Lieven Buts Vrije Universiteit Brussel |
From: DeLano, W. <wa...@su...> - 2002-10-30 23:14:36
|
By default, PyMOL doesn't surface PDB HETATMs. To surface all atoms, set surface_mode=3D1 To surface all atoms except hydrogens, set surface_mode=3D2 Cheers, Warren > -----Original Message----- > From: Kersey Black [mailto:kb...@js...] > Sent: Wednesday, October 30, 2002 3:09 PM > To: pym...@li... > Cc: Kersey Black > Subject: [PyMOL] How to get a suurface on small molecule in=20 > active site? >=20 >=20 > Hi Pymolers, >=20 > I am trying to show a surface on a small molecule in the=20 > active site. =20 > I can create surfaces on protein residues without any problem, but I=20 > can not get a surface around the small organic structure. I=20 > have tried=20 > this on an SGI and using the 0.84beta on OS X. > I am obviously missing something. Any help out there would be great. >=20 > After loading the hapten, I try things like ... > show surface, hap > set transparency=3D0.5, hap > But I do not get a surface, with or without the transparency >=20 > Cheers, >=20 > Kersey >=20 >=20 >=20 > ------------------------------------------------------- > This sf.net email is sponsored by: Influence the future=20 > of Java(TM) technology. Join the Java Community=20 > Process(SM) (JCP(SM)) program now.=20 > http://ads.sourceforge.net/cgi-bin/redirect.pl?sunm0004en > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 |
From: Kersey B. <kb...@js...> - 2002-10-30 23:08:21
|
Hi Pymolers, I am trying to show a surface on a small molecule in the active site. I can create surfaces on protein residues without any problem, but I can not get a surface around the small organic structure. I have tried this on an SGI and using the 0.84beta on OS X. I am obviously missing something. Any help out there would be great. After loading the hapten, I try things like ... show surface, hap set transparency=0.5, hap But I do not get a surface, with or without the transparency Cheers, Kersey |
From: DeLano, W. <wa...@su...> - 2002-10-30 21:08:48
|
mset 1 x360 movie.roll 1,180,1,axis=3Dy movie.roll 181,360,1,axis=3Dx > -----Original Message----- > From: Craig Smith [mailto:boi...@ma...] > Sent: Wednesday, October 30, 2002 11:43 AM > To: pym...@li... > Subject: [PyMOL] making a two step movie in pymol >=20 >=20 > How do I create a movie in pymol in which I rotate a molecule=20 > about the=20 > y-axis 360 deg and then immediately do a 360 deg rotation about the=20 > x-axis? I couldn't figure it out from published examples. >=20 > Thanks in advance >=20 >=20 > Craig L. Smith, Ph. D. > Molecular Microbiology > Washington University School of Medicine > 660 South Euclid Box 8230 > Voice: (314) 362-9054 > Fax: (314) 362-1232 > e-mail: sm...@bo... >=20 >=20 >=20 > ------------------------------------------------------- > This sf.net email is sponsored by: Influence the future=20 > of Java(TM) technology. Join the Java Community=20 > Process(SM) (JCP(SM)) program now.=20 > http://ads.sourceforge.net/cgi-bin/redirect.pl?sunm0004en > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 |
From: DeLano, W. <wa...@su...> - 2002-10-30 21:05:33
|
This is undocumented: To get a list of settings: from pymol import setting print setting.get_name_list() To get the current value of a setting: print setting.get_setting_text("bg_rgb") print setting.get_setting_text("gamma") To get a list of names with values: print map(lambda = x:[x,setting.get_setting_text(x)],setting.get_name_list()) etc. Cheers, Warren -----Original Message----- From: Kelley Moremen [mailto:mo...@ar...] Sent: Wednesday, October 30, 2002 10:13 AM To: pym...@li... Subject: [PyMOL] Current settings list in Pymol OSX Dear Pymolers, Since the Mac OSX version of Pymol does not have a menu interface that = has a pull-down menu to view and alter the settings, is there any way to = display and alter the full set of settings from the command line? I = keep forgetting what the relevant command line syntax is for changing = the settings commands (there is only a partial list in the manual) and a = global list (as in the pull-down menu) is a great reminder, but alas the = menu interface is not yet there in the Mac OSX version. Thanks for your help. Kelley Dr. Kelley Moremen=20 Associate Professor=20 Complex Carbohydrate Research Center Department of Biochemistry and Molecular Biology=20 University of Georgia, Athens, GA 30602-7229=20 Office (706) 542-1705 Fax: (706) 542-1759 Email: mo...@ar... (send email with large attachments to: mo...@bm...) Website: http://bmbiris.bmb.uga.edu/moremen/lab/=20 |
From: Craig S. <boi...@ma...> - 2002-10-30 19:42:51
|
How do I create a movie in pymol in which I rotate a molecule about the y-axis 360 deg and then immediately do a 360 deg rotation about the x-axis? I couldn't figure it out from published examples. Thanks in advance Craig L. Smith, Ph. D. Molecular Microbiology Washington University School of Medicine 660 South Euclid Box 8230 Voice: (314) 362-9054 Fax: (314) 362-1232 e-mail: sm...@bo... |
From: Kelley M. <mo...@ar...> - 2002-10-30 18:12:54
|
Dear Pymolers, Since the Mac OSX version of Pymol does not have a menu interface that has a pull-down menu to view and alter the settings, is there any way to display and alter the full set of settings from the command line? I keep forgetting what the relevant command line syntax is for changing the settings commands (there is only a partial list in the manual) and a global list (as in the pull-down menu) is a great reminder, but alas the menu interface is not yet there in the Mac OSX version. Thanks for your help. Kelley Dr. Kelley Moremen Associate Professor Complex Carbohydrate Research Center Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602-7229 Office (706) 542-1705 Fax: (706) 542-1759 Email: mo...@ar... (send email with large attachments to: mo...@bm...) Website: http://bmbiris.bmb.uga.edu/moremen/lab/ |
From: Kersey B. <kb...@js...> - 2002-10-29 22:12:07
|
Hi all, I posted a few days ago about a screen problem I was having. In short form it was that the color map was getting screwed up when trying to drive an external monitor (though that was not specified in the original note), even with mirroring, even with all possible combinations of color profile settings, and even at relatively low resolutions. I am doing this on a 400 MHz G3 Powerbook, which has 8 (non-upgradable) MB of VRAM. I have seen a couple of flaky behaviors before which probably relate to this limitation in hardware, though for all but a couple of things, including PyMOL, driving an external display generally works fine. None the less, this problem potentially restricts my ability to use PyMOL interactively in presentations. Warren came up with a fix that seems to be working! Thus, instead of writing back to him alone with thanks for his time, I thought I would post this fix for others who may encounter the same problem, and save him having to answer this query in the future (or at least reduce that load). And I quote ... > > I have an idea: try disabling display caching > > set cache_display=0 I added this to a script and all seems to be well. I will let you know if that changes. Thanks again Cheers, Kersey ________________________________________________________ Kersey Black Joint Science Program Professor of Chemistry Claremont Colleges |
From: Luca F. <l.a...@so...> - 2002-10-29 15:47:42
|
Dear Pymolers, I've read on pymol-users mail list (http://sourceforge.net/mailarchive/message.php?msg_id=1804599) that it is now possible for pymol to read directly mol2 files. This would be really handy for me, since I'd like to use pymol to directly read GOLD output without having to convert them. I've browsed the CVS repository: - is the file I'm looking for the one called mol.py? (http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/pymol/pymol/modules/chempy/mol.py) - or is the one called importing.py? (http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/pymol/pymol/modules/pymol/importing.py)? if neither of them is, could any of you please point me to the right one? many thanks, luca -- Universities are places of knowledge. The freshman each bring a little in with them, and the seniors take none away, so knowledge accumulates. |
From: Andy C. <afc...@li...> - 2002-10-29 09:10:09
|
Making movies in MacOS X: Not to forget QuickTime Pro which can do the same from numbered .png files OR GraphicConverter the best graphics conversion program for the Mac in the entire universe from http://www.lemkesoft.com $30-35 (you can try before you buy). Converts just about any image format to just about any image format. Search on http://www.versiontracker.com for end user comments. One of the highest rated bits of software for the Mac. Makes movies too. My only connection is that I have paid my registration fee and have been a user for years and years. -- .-Dr-Andy-Calder----------. | Materials Modelling Group\ | Materials Science & Eng. \ | University of Liverpool / | UK .---------------------' |
From: <kri...@be...> - 2002-10-29 08:44:27
|
> In > powerpoint you can create what is called a hyperlink to pymol, and then > you can just load in your macro (pml script) and your movie starts > playing embedded in powerpoint. This is great news! (I've already wondered if we need something to embed Word and Powerpoint *into* PyMOL.) Kristian -- berlin.de - meine stadt im netz. Jetzt eigene eMail-adresse @berlin.de sichern! http://webmail.berlin.de |
From: Tsjerk W. <t.a...@ch...> - 2002-10-29 07:56:45
|
Hi there, For making movies there are also lots of free tools available. For instance, AVI's can be made under windows with MakeAVI: https://sourceforge.net/projects/makeavi/ Very easy to use, fast, and free. Cheers, Tsjerk -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- :) -- :) Tsjerk A. Wassenaar, M.Sc. -- :) Molecular Dynamics Group -- :) Dept. of Biophysical Chemistry -- :) University of Groningen -- :) Nijenborgh 4 -- :) 9747 AG Groningen -- :) The Netherlands -- :) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- :) -- :) Hi! I'm a .signature virus! -- :) Copy me into your ~/.signature to help me spread! -- :) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
From: Warren L. D. <wa...@su...> - 2002-10-29 04:33:33
|
Luca, For future reference, please direct technical PyMOL questions like this to the PyMOL mailing list. (See MailLists on http://www.pymol.org) Over the past couple of years, we've built up an active community of nearly 300 PyMOL users who are there to learn and to help each other get the most out of this free/open-source molecular viewer. Please join in! The answer to your question is: Launch PyMOL with a "-p" command-line argument. PyMOL will then listen for commands on standard input. Using a Perl pipe, you can then control PyMOL interactively and send commands as required in order to load new structures, change the view, color, and so on. The only trick with Perl is that you need to turn autoflush on so that commands get passed along right away. use FileHandle; open(FILE,"|pymol -p"); FILE->autoflush(1); print FILE "load \$PYMOL_PATH/test/dat/pept.pdb\n"; while(1) { sleep 0.2; print FILE "turn x,5\n"; } Please excuse my non-OOP-0Perl4-vintage example...I've been a Python addict for some time now. If you want PyMOL to be just a minimal molecular display window, then consider launching PyMOL as: pymol -qpxif 0 This will make PyMOL open a single window with no visible GUI, text, or controls. Cheers, Warren On Mon, 28 Oct 2002, Luca Fenu wrote: > Dear all, > > I need to scan and make a choice about a list of molecules. does anyone > knows how to send command to pymol through a perl or shell script? I've > read pymol's manual, and it's possible to pass pymol some scripts, from > its internal shell. but I don't know how to pass commands to it from > another program. starting the process in foreground and feeding the > command from the stdout of perl to the stdin of pymol doesn't work. I > think pymol use another filehandle for aquiring commands. how can I > avoid to restar a new pymol for every molecule? > any suggestion? many thanks > > luca > > > |
From: DeLano, W. <wa...@su...> - 2002-10-29 01:05:22
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Gordon, I fully agree with your assessment that PyMOL is currently unable to = reach its potential due to a number of factors, including poor = documentation.=20 Nevertheless, I do have a defined plan for eliminating these = deficits. It involves securing funding to hire people under contract to = document, support, and develop PyMOL on an ongoing basis. While I am = grateful for the continued assistance of PyMOL users on numerous minor = tasks, it is not reasonable to expect anyone to prepare a complete = "well-written" manual or to perform other major tasks without some form = of compensation. Also, PyMOL is still immature enough in certain areas = that a full manual really can't be constructed until the 1.0 features = are settled upon (soon hopefully!). Understanding this situation, several large pharmaceutical companies = and many smaller entities have lent support to PyMOL development through = donations and license purchases. At present the flux is low, but we are = getting to a point where some real headway can be made. The forthcoming = "Incentive PyMOL (iPyMOL)" add-on will hopefully increase the flux by = providing a specific reward to those who fund the PyMOL development = effort. =20 I know it may sound like PyMOL/iPyMOL is becoming commercial = gray-ware, but that's not it at all. I haven't devoted thousands of = hours to this project just to see it end up as yet another expensive, = lousy, inflexible, and closed-source commercial tool. PyMOL will remain = a vital open-source project, and iPyMOL will exist solely to accelerate = PyMOL's growth and guarantee its long-term health. Nurturing PyMOL and = similar efforts to fruition on such terms is central to my career vision = -- it's what I stand for in this industry. I believe that well-supported, well-documented, and well-maintained = open-source software will be a superior research product to what is = currently offered by the major scientific software vendors. My hope is = that scientists in industry and academia will eventually come to = appreciate this, and then choose to make creation of such software = economically viable through funding of balanced approaches such as the = one I am taking with PyMOL. Free software is great once it exists, but there are far too few = developers in this field to expect the kinds of dramatic successes = achieved by the Linux, GNU, and BSD communities. If = open-source/free-software is going to have a large impact on molecular = modeling, it will need direct support from users, universities, = governments, and for-profit companies. If really good open-source tools = were available and able to meet the needs of research, would you be = willing to pay reasonable amounts of money for their development, = maintenance, and support? I hope so. Thus, pharmaceutical companies like EMD/Lexigen/Merck can choose to = continue to spend millions of dollars on traditional closed-source = packages with no hope of a reprieve, or they can choose to funnel a = small fraction of that money into efforts like PyMOL. Over the long = term, open-source packages offer vendor-independence, = cost-effectiveness, flexibility, opportunities for innovation, and = support for broad sharing of information and technology. These are all = key ingredients in scientific progress, both within a single = organization and across the industry. =20 Realistically, it will take a year or more before PyMOL can fulfill = the potential you described. How soon this happens will depend in part = on whether people like yourself are content to merely gripe about the = status quo, or whether you are prepared to commit resources towards = improving it. Cheers, Warren L. DeLano, Ph.D. PyMOL Creator & Founder, DeLano Scientific -----Original Message----- From: gwe...@le... [mailto:gwe...@le...] Sent: Monday, October 28, 2002 10:33 AM To: pym...@li... Subject: [PyMOL] PyMol Manual Fellow PyMol Users=20 Although I like using PyMol, I would like to submit a gripe about the = severe lack of a decent PyMol manual.=20 A deeper description of the program's features is required if people are = seriously going to use PyMol for tricky things beyond simple = visualization (simple visualization programs are ten-a-penny and PyMol = could be so much more)=20 Particularly lacking are details of structural editing (mutation, bond = rotation, cut-and-paste etc.), interfaces (if any exist) to routines for = enegy minimization and a detailed description of the Python command line = interface with examples of scripting and how to extend PyMol's = capabilities.=20 By neglecting to adequately document what may be a really useful = program, the PyMol user community might fail to attract the kind of user = base and support that it deserves and that it needs to ensure its = success.=20 A good, clear and well-thought out manual really helps to make a case = for using a particular piece of software (and it might also lower the = odds of PyMol having to join the gray legions of commercial "payware").=20 Gordon=20 EMD Lexigen Research Center=20 |
From: <wg...@ch...> - 2002-10-28 20:47:38
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Dear Stephen Miller: Also, don't overlook the fact that pymol itself is a movie player. In powerpoint you can create what is called a hyperlink to pymol, and then you can just load in your macro (pml script) and your movie starts playing embedded in powerpoint. This is far better because you can move the molecule around while the movie plays, zoom in and out, etc. This gives a sense of immediacy in a presentation that is lost with an animated gif, or whatever movie player you might use. The hyperlink feature works better in windows powerpoint than mac powerpoint, BTW. William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax: +1-831-4593139 (fax) |
From: <wg...@ch...> - 2002-10-28 20:40:49
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There is a program called gif-builder (Mac OS 9 and 10) that is free and uses a variety of input types to make an animated gif which then is platform-independent. Sadly the link is broken http://www.macupdate.com/info.php/id/235 but if anyone needs it I can email you mine. Also if you have quicktime pro (PC version also exists) it is very simple to string together pictures to make quicktime movies. HTH William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax: +1-831-4593139 (fax) |
From: <gwe...@le...> - 2002-10-28 18:51:11
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Dear Byron Yes, it's a nice Catch-22 isn't it ... write a PyMol manual so people like myself will be able to learn PyMol well enought to be able to write the PyMol manual! Gordon Byron Delabarre <by...@SL...> 10/28/2002 01:32 PM Please respond to byron To: gwe...@le... cc: pym...@li... Subject: Re: [PyMOL] PyMol Manual So write one. gwe...@le... wrote: > > Fellow PyMol Users > > Although I like using PyMol, I would like to submit a gripe about the > severe lack of a decent PyMol manual. > > A deeper description of the program's features is required if people are > seriously going to use PyMol for tricky things beyond simple > visualization (simple visualization programs are ten-a-penny and PyMol > could be so much more) > > Particularly lacking are details of structural editing (mutation, bond > rotation, cut-and-paste etc.), interfaces (if any exist) to routines for > enegy minimization and a detailed description of the Python command line > interface with examples of scripting and how to extend PyMol's > capabilities. > > By neglecting to adequately document what may be a really useful > program, the PyMol user community might fail to attract the kind of user > base and support that it deserves and that it needs to ensure its success. > > A good, clear and well-thought out manual really helps to make a case > for using a particular piece of software (and it might also lower the > odds of PyMol having to join the gray legions of commercial "payware"). > > Gordon > EMD Lexigen Research Center -- Byron DeLaBarre Stanford University / HHMI Dept. of Molecular and Cellular Physiology P250 MSLS Building//(L)650 736 1714 (C)650 468 5677 |
From: Byron D. <by...@SL...> - 2002-10-28 18:37:48
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So write one. gwe...@le... wrote: > > Fellow PyMol Users > > Although I like using PyMol, I would like to submit a gripe about the > severe lack of a decent PyMol manual. > > A deeper description of the program's features is required if people are > seriously going to use PyMol for tricky things beyond simple > visualization (simple visualization programs are ten-a-penny and PyMol > could be so much more) > > Particularly lacking are details of structural editing (mutation, bond > rotation, cut-and-paste etc.), interfaces (if any exist) to routines for > enegy minimization and a detailed description of the Python command line > interface with examples of scripting and how to extend PyMol's > capabilities. > > By neglecting to adequately document what may be a really useful > program, the PyMol user community might fail to attract the kind of user > base and support that it deserves and that it needs to ensure its success. > > A good, clear and well-thought out manual really helps to make a case > for using a particular piece of software (and it might also lower the > odds of PyMol having to join the gray legions of commercial "payware"). > > Gordon > EMD Lexigen Research Center -- Byron DeLaBarre Stanford University / HHMI Dept. of Molecular and Cellular Physiology P250 MSLS Building//(L)650 736 1714 (C)650 468 5677 |
From: <gwe...@le...> - 2002-10-28 18:32:55
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Fellow PyMol Users Although I like using PyMol, I would like to submit a gripe about the severe lack of a decent PyMol manual. A deeper description of the program's features is required if people are seriously going to use PyMol for tricky things beyond simple visualization (simple visualization programs are ten-a-penny and PyMol could be so much more) Particularly lacking are details of structural editing (mutation, bond rotation, cut-and-paste etc.), interfaces (if any exist) to routines for enegy minimization and a detailed description of the Python command line interface with examples of scripting and how to extend PyMol's capabilities. By neglecting to adequately document what may be a really useful program, the PyMol user community might fail to attract the kind of user base and support that it deserves and that it needs to ensure its success. A good, clear and well-thought out manual really helps to make a case for using a particular piece of software (and it might also lower the odds of PyMol having to join the gray legions of commercial "payware"). Gordon EMD Lexigen Research Center |
From: Luca J. <luc...@ma...> - 2002-10-28 17:12:07
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An even cheaper alternative to Premiere, if you are using Mac OSX, is a $20 shareware program called QuickMovie: http://www.chaoticsoftware.com/ProductPages/QuickMovie.html I have recently tested it to generate a QuickTime movie from PyMOL PNG frames, and it worked just fine; it supports various formats and allows you to specify output dimensions, as well as frame rate. Note that I am note associated in any way to the company who makes this software, just thought other Mac PyMOL users might find this information useful... -Luca -------------------------------------------------------- Luca Jovine, Ph.D. Department of Molecular, Cell & Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18 One Gustave L. Levy Place, New York, NY 10029-6574, USA Voice: +1.212.241-8620 FAX: +1.509.356-2832 E-Mail: luc...@ma... W3: http://www.mssm.edu/students/jovinl02 -------------------------------------------------------- |
From: Kelley M. <mo...@ar...> - 2002-10-28 17:06:22
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Dear Pymolers, I am trying to create a carved electron density around a ligand for a publication figure and I have come up with a question: what is the relationship between the level number in an isomesh command line versus a sigma level for a display of the density map in an application such as Xtalview. It does not appear that a value of 1.0 for level in Pymol yields a similar level of density in a map representation as a 1.0 sigma value in Xtalview. The relationship appears to be approximately 0.5 level in Pymol = 1.0 sigma in Xtalview. Is there a defined set of units or conversions for the Pymol level value? Are these the units even comparable? Thanks for your assistance. Kelley Dr. Kelley Moremen Associate Professor Complex Carbohydrate Research Center Department of Biochemistry and Molecular Biology University of Georgia, Athens, GA 30602-7229 Office (706) 542-1705 Fax: (706) 542-1759 Email: mo...@ar... (send email with large attachments to: mo...@bm...) Website: http://bmbiris.bmb.uga.edu/moremen/lab/ |