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From: Warren D. <wa...@de...> - 2005-08-15 18:48:18
|
Try something like this: # Save as a .pml file load $PYMOL_PATH/test/dat/pept.pdb for st in range(2,31): \ cmd.create("pept","pept",st-1,st) \ cmd.frame(st) \ cmd.edit("4/cb","4/ca") \ cmd.torsion(5)=20 edit movie.sweep rewind mplay Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of Xavier=20 > Deupi > Sent: Monday, August 15, 2005 11:38 AM > To: pym...@li... > Subject: [PyMOL] torsion + movie >=20 > Hi, >=20 > I'm trying to create a simple movie showing the rotation around a=20 > dihedral angle. I'm sure it's an extremely easy task, but I can't=20 > figure out the way of loading each state (i.e. conformation of the=20 > dihedral > angle) into the movie object. I mean, the 'load' command (as in "load > foo1.pdb,mov") expects a pdb file as an argument, but I want to load=20 > the current state as shown in PyMOL (after modifying the torsion=20 > angle, for instance). > Any help? >=20 > Thanks in advance, >=20 > Xavier >=20 > -- > Xavier Deupi, Ph.D. > Department of Molecular and Cellular Physiology Beckman Center for=20 > Molecular and Genetic Medicine (B161) > 279 Campus Drive, Stanford University School of Medicine Stanford, CA=20 > 94305 (USA) >=20 > E-mail: Xav...@st... > Phone: +1 (650) 725-6497 > Fax : +1 (650) 725-8021 >=20 >=20 >=20 > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO=20 > September 19-22, 2005 * San Francisco, CA * Development Lifecycle=20 > Practices Agile & Plan-Driven Development * Managing Projects & Teams=20 > * Testing & QA Security * Process Improvement & Measurement *=20 > http://www.sqe.com/bsce5sf=20 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 |
From: Xavier D. <Xav...@st...> - 2005-08-15 18:25:09
|
Hi, I'm trying to create a simple movie showing the rotation around a dihedral angle. I'm sure it's an extremely easy task, but I can't figure out the way of loading each state (i.e. conformation of the dihedral angle) into the movie object. I mean, the 'load' command (as in "load foo1.pdb,mov") expects a pdb file as an argument, but I want to load the current state as shown in PyMOL (after modifying the torsion angle, for instance). Any help? Thanks in advance, Xavier -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Beckman Center for Molecular and Genetic Medicine (B161) 279 Campus Drive, Stanford University School of Medicine Stanford, CA 94305 (USA) E-mail: Xav...@st... Phone: +1 (650) 725-6497 Fax : +1 (650) 725-8021 |
From: Neema S. <nsa...@it...> - 2005-08-15 16:16:44
|
I agree with the Logitech sentiment. I have a MX 700 for my iMac, and installing the software was a bad idea when I had Panther. I haven't tried installing it on Tiger, but all the buttons (8 of them) are assignable in the System preferences menu. In addition, it's cordless, and the battery lasts a good while before it needs charging. On Aug 15, 2005, at 9:00 AM, geek theory wrote: > I have one of each of the Logitech MX 500, 510, 518 series and they > all have worked (and are still working) fine for me, albeit on windows > and linux. I don't have any experience with the cordless version, but > after a little google searching it looks like the logitech software is > buggy on macs. You might try uninstalling it and letting the OS think > its a generic 3-button mouse. > > hope it helps, > -Tzintzuni Garcia > > > On 8/12/05, Sabuj Pattanayek <sab...@va...> wrote: > > >> I use a cheap microsoft optical (or basic optical) usb mouse on >> linux, >> so it should work on your macosx. >> >> If you want something more configurable under macosx and don't >> want to >> destroy the "Appleness" of your computer with an MS mouse then this >> might work for you http://www.apple.com/mightymouse/ . I hear >> there will >> be a wireless version soon. >> >> Sarina Bromberg wrote: >> >> >>> I have a logitech MX700 Cordless Optical Mouse that claims to be >>> a 3- >>> button mouse, but I can never get it to produce the results provided >>> for 3-button viewing or editing by PyMOL. Perhaps I do not have it >>> configured correctly (I cannot find a clue in the instructions or in >>> simple experiments), or perhaps this is not the kind of 3-button >>> mouse >>> I need. Does anyone have a good solution? >>> Tx, >>> Sarina Bromberg >>> >>> >>> ------------------------------------------------------- >>> SF.Net email is Sponsored by the Better Software Conference & EXPO >>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle >>> Practices >>> Agile & Plan-Driven Development * Managing Projects & Teams * >>> Testing & QA >>> Security * Process Improvement & Measurement * http://www.sqe.com/ >>> bsce5sf >>> _______________________________________________ >>> PyMOL-users mailing list >>> PyM...@li... >>> https://lists.sourceforge.net/lists/listinfo/pymol-users >>> >>> >> >> >> >> ------------------------------------------------------- >> SF.Net email is Sponsored by the Better Software Conference & EXPO >> September 19-22, 2005 * San Francisco, CA * Development Lifecycle >> Practices >> Agile & Plan-Driven Development * Managing Projects & Teams * >> Testing & QA >> Security * Process Improvement & Measurement * http://www.sqe.com/ >> bsce5sf >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle > Practices > Agile & Plan-Driven Development * Managing Projects & Teams * > Testing & QA > Security * Process Improvement & Measurement * http://www.sqe.com/ > bsce5sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > |
From: James R. G. <jam...@ma...> - 2005-08-15 16:16:11
|
Hello Warren, Thanks for the response. That is exactly what I have done--taken structures produced with builder and brought them into GROMACS and have obtained minimized structures, but as Jim Nettles mentioned, such techniques can depend on what the initial structure is, so I was just wondering whether there were any constraints placed upon amino acids as they are placed that might mimic chemical synthesis methods. I know it's quite a reach, but thought I'd ask anyway. ;) james On Aug 15, 2005, at 12:12 PM, Warren DeLano wrote: > James, > > PyMOL's peptide & small molecular builder is no more rigorous that a > handheld plastic model. Unfortunately, DeLano Scientific doesn't have > the developer "bandwidth" right now to get into the simulations > business. Instead, we hope to facilitate and encourage integration > with > existing external packages via PyMOL wizards and simple Python glue. > > Thus, our near-term goal with the builder is to simply provide > scientists like yourself with a user interface for building molecules > and setting up *initial* poses that will then be subjected to rigorous > computations external to PyMOL. > > There are plenty of integrations options out there, from free and/or > open-source tools like GROMACS, APBS, Tinker, ArgusLab, GAMESS US, and > MMTK, to academic codes like Amber, Charmm, Dock, and Autodock, to > commercial codes like Szybki (MMFF), Fred, Glide, BatchMin, MOE, > Sybyl, > or Discover. > > Cheers, > Warren > > -- > Warren L. DeLano, Ph.D. > Principal Scientist > > . DeLano Scientific LLC > . 400 Oyster Point Blvd., Suite 213 > . South San Francisco, CA 94080 USA > . Biz:(650)-872-0942 Tech:(650)-872-0834 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:wa...@de... > > > >> -----Original Message----- >> From: pym...@li... >> [mailto:pym...@li...] On Behalf Of >> Jim Nettles >> Sent: Monday, August 15, 2005 8:56 AM >> To: James R. Graham >> Cc: pym...@li... >> Subject: Re: [PyMOL] Builder Question >> >> Hello James, >> >> There is really a lot of room for discussion regarding your >> questions. >> Considering peptide conformations is complicated business and >> there is generally not "a" structure. There is great >> conformational flexibility even for small, constrained, >> cyclic peptides. As for the MD - yes, a classical MD >> trajectory is entirely determined by the starting structure. >> One can introduce random number seeds, high temperature, etc >> ... to explore greater space, but where you start is >> definitely worthy of thoughtful consideration. >> >> I can send references and more discussion off list, if you >> are interested. >> >> Cheers, >> >> Jim N. >> ________________________________________________________ >> James Nettles, Ph. D. Computational Pharmacology >> Liotta/Snyder Group, Modeling Division, Department of >> Chemistry Emory University 1515 Pierce Dr. Atlanta, Ga. 30322 >> jn...@em... TEL: (404)966-4617 FAX: (404)728-0991 >> ________________________________________________________ >> >> On Aug 15, 2005, at 11:36 AM, James R. Graham wrote: >> >> >>> Hello All, >>> >>> How "physiological" are the structures that are produced >>> >> from builder? >> >>> Meaning, how are the angles, etc. determined? Might such a >>> >> resulting >> >>> structure mimic a chemically-synthesized peptide? >>> >>> I have taken peptides I created using builder and done some MD >>> simulations and the structures certainly change, but I >>> >> wonder whether >> >>> the changes are limited by the initial starting >>> >> structure...which is, >> >>> of course, a question for another mailing list, I suppose. ;) >>> >>> james >>> >>> >>> ------------------------------------------------------- >>> SF.Net email is Sponsored by the Better Software Conference & EXPO >>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle >>> Practices Agile & Plan-Driven Development * Managing >>> >> Projects & Teams >> >>> * Testing & QA Security * Process Improvement & Measurement * >>> http://www.sqe.com/bsce5sf >>> _______________________________________________ >>> PyMOL-users mailing list >>> PyM...@li... >>> https://lists.sourceforge.net/lists/listinfo/pymol-users >>> >> >> >> >> >> ------------------------------------------------------- >> SF.Net email is Sponsored by the Better Software Conference & >> EXPO September 19-22, 2005 * San Francisco, CA * Development >> Lifecycle Practices Agile & Plan-Driven Development * >> Managing Projects & Teams * Testing & QA Security * Process >> Improvement & Measurement * http://www.sqe.com/bsce5sf >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> >> > |
From: Warren D. <wa...@de...> - 2005-08-15 16:08:25
|
James, PyMOL's peptide & small molecular builder is no more rigorous that a handheld plastic model. Unfortunately, DeLano Scientific doesn't have the developer "bandwidth" right now to get into the simulations business. Instead, we hope to facilitate and encourage integration with existing external packages via PyMOL wizards and simple Python glue. Thus, our near-term goal with the builder is to simply provide scientists like yourself with a user interface for building molecules and setting up *initial* poses that will then be subjected to rigorous computations external to PyMOL. There are plenty of integrations options out there, from free and/or open-source tools like GROMACS, APBS, Tinker, ArgusLab, GAMESS US, and MMTK, to academic codes like Amber, Charmm, Dock, and Autodock, to commercial codes like Szybki (MMFF), Fred, Glide, BatchMin, MOE, Sybyl, or Discover. =20 Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Jim Nettles > Sent: Monday, August 15, 2005 8:56 AM > To: James R. Graham > Cc: pym...@li... > Subject: Re: [PyMOL] Builder Question >=20 > Hello James, >=20 > There is really a lot of room for discussion regarding your=20 > questions. =20 > Considering peptide conformations is complicated business and=20 > there is generally not "a" structure. There is great=20 > conformational flexibility even for small, constrained,=20 > cyclic peptides. As for the MD - yes, a classical MD=20 > trajectory is entirely determined by the starting structure.=20 > One can introduce random number seeds, high temperature, etc=20 > ... to explore greater space, but where you start is=20 > definitely worthy of thoughtful consideration. >=20 > I can send references and more discussion off list, if you=20 > are interested. >=20 > Cheers, >=20 > Jim N. > ________________________________________________________ > James Nettles, Ph. D. Computational Pharmacology=20 > Liotta/Snyder Group, Modeling Division, Department of=20 > Chemistry Emory University 1515 Pierce Dr. Atlanta, Ga. 30322=20 > jn...@em... TEL: (404)966-4617 FAX: (404)728-0991=20 > ________________________________________________________ >=20 > On Aug 15, 2005, at 11:36 AM, James R. Graham wrote: >=20 > > Hello All, > > > > How "physiological" are the structures that are produced=20 > from builder?=20 > > Meaning, how are the angles, etc. determined? Might such a=20 > resulting=20 > > structure mimic a chemically-synthesized peptide? > > > > I have taken peptides I created using builder and done some MD=20 > > simulations and the structures certainly change, but I=20 > wonder whether=20 > > the changes are limited by the initial starting=20 > structure...which is,=20 > > of course, a question for another mailing list, I suppose. ;) > > > > james > > > > > > ------------------------------------------------------- > > SF.Net email is Sponsored by the Better Software Conference & EXPO=20 > > September 19-22, 2005 * San Francisco, CA * Development Lifecycle=20 > > Practices Agile & Plan-Driven Development * Managing=20 > Projects & Teams=20 > > * Testing & QA Security * Process Improvement & Measurement *=20 > > http://www.sqe.com/bsce5sf=20 > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 >=20 > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference &=20 > EXPO September 19-22, 2005 * San Francisco, CA * Development=20 > Lifecycle Practices Agile & Plan-Driven Development *=20 > Managing Projects & Teams * Testing & QA Security * Process=20 > Improvement & Measurement * http://www.sqe.com/bsce5sf=20 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 >=20 |
From: geek t. <gee...@gm...> - 2005-08-15 16:00:47
|
I have one of each of the Logitech MX 500, 510, 518 series and they all have worked (and are still working) fine for me, albeit on windows and linux. I don't have any experience with the cordless version, but after a little google searching it looks like the logitech software is buggy on macs. You might try uninstalling it and letting the OS think its a generic 3-button mouse. hope it helps, -Tzintzuni Garcia On 8/12/05, Sabuj Pattanayek <sab...@va...> wrote: > I use a cheap microsoft optical (or basic optical) usb mouse on linux, > so it should work on your macosx. >=20 > If you want something more configurable under macosx and don't want to > destroy the "Appleness" of your computer with an MS mouse then this > might work for you http://www.apple.com/mightymouse/ . I hear there will > be a wireless version soon. >=20 > Sarina Bromberg wrote: > > I have a logitech MX700 Cordless Optical Mouse that claims to be a 3- > > button mouse, but I can never get it to produce the results provided > > for 3-button viewing or editing by PyMOL. Perhaps I do not have it > > configured correctly (I cannot find a clue in the instructions or in > > simple experiments), or perhaps this is not the kind of 3-button mouse > > I need. Does anyone have a good solution? > > Tx, > > Sarina Bromberg > > > > > > ------------------------------------------------------- > > SF.Net email is Sponsored by the Better Software Conference & EXPO > > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Pract= ices > > Agile & Plan-Driven Development * Managing Projects & Teams * Testing &= QA > > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5= sf > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practic= es > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & Q= A > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Jim N. <jn...@em...> - 2005-08-15 15:49:12
|
Hello James, There is really a lot of room for discussion regarding your questions. Considering peptide conformations is complicated business and there is generally not "a" structure. There is great conformational flexibility even for small, constrained, cyclic peptides. As for the MD - yes, a classical MD trajectory is entirely determined by the starting structure. One can introduce random number seeds, high temperature, etc ... to explore greater space, but where you start is definitely worthy of thoughtful consideration. I can send references and more discussion off list, if you are interested. Cheers, Jim N. ________________________________________________________ James Nettles, Ph. D. Computational Pharmacology Liotta/Snyder Group, Modeling Division, Department of Chemistry Emory University 1515 Pierce Dr. Atlanta, Ga. 30322 jn...@em... TEL: (404)966-4617 FAX: (404)728-0991 ________________________________________________________ On Aug 15, 2005, at 11:36 AM, James R. Graham wrote: > Hello All, > > How "physiological" are the structures that are produced from builder? > Meaning, how are the angles, etc. determined? Might such a resulting > structure mimic a chemically-synthesized peptide? > > I have taken peptides I created using builder and done some MD > simulations and the structures certainly change, but I wonder whether > the changes are limited by the initial starting structure...which is, > of course, a question for another mailing list, I suppose. ;) > > james > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle > Practices > Agile & Plan-Driven Development * Managing Projects & Teams * Testing > & QA > Security * Process Improvement & Measurement * > http://www.sqe.com/bsce5sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: James R. G. <jam...@ma...> - 2005-08-15 15:37:10
|
Hello All, How "physiological" are the structures that are produced from builder? Meaning, how are the angles, etc. determined? Might such a resulting structure mimic a chemically-synthesized peptide? I have taken peptides I created using builder and done some MD simulations and the structures certainly change, but I wonder whether the changes are limited by the initial starting structure...which is, of course, a question for another mailing list, I suppose. ;) james |
From: Michael G. L. <ml...@um...> - 2005-08-15 14:38:09
|
>> Quoting tan...@st...: >> >> # Hi everybody, >> # >> # i've just created many CGOs, which show up solid surfaces like spheres >> and >> # ellipsoids. Is it possible to set the transparency of some CGO's to >> i.e. 0.5 >> # and leave the others solid? >> # I've checked out the reference and the manual, and found something like: >> # >> # set transparency=0.5, object >> # >> # But this actually does not work for CGO's. >> # Any ideas.... >> # >> # Yusuf The last time I looked at this, it seemed like the easiest (only?) way to do this was to tweak the transparency at creation time. So, I typically have functions that look like this: def makeSphere(name,x,y,z,r,transparency=0,...): ... obj = [] ... obj.extend([cgo.ALPHA,1-transparency]) obj.extend([cgo.SPHERE,x,y,z,r]) ... cmd.load_cgo(obj,name,1) I don't know how to change it later, though. Hope that helps, -michael >> # >> # >> # -- >> # Yusuf Tanrikulu >> # Bioinformatics Diploma Student >> # Department of Biosciences >> # Johann-Wolfgang-Goethe Univerity Frankfurt >> # Siesmayerstrasse 70 >> # 60326 Frankfurt am Main >> # - Germany - >> # tan...@bi... >> # >> # |
From: <tan...@st...> - 2005-08-15 10:04:50
|
Lari, the way you've described is a nice workaround for images and presentations, which I had in mind, too. But it is not applicable while I am working with PyMOL online and want to make my CGO's transparent to see what is in them (including ability to rotate and zomm in/out the scene (which is not very doable in static pictures ;-)). I'm familiar with scripting in PyMOL. Probably I can change any transparenc= y variable while creating my triangles, which result in my CGO's? Isn't there= a implemented command in PyMOL, which does what I need? Cheers, Yusuf -- Yusuf Tanrikulu Bioinformatics Diploma Student Department of Biosciences Johann-Wolfgang-Goethe Univerity Frankfurt Siesmayerstrasse 70 60326 Frankfurt am Main - Germany - tan...@bi... Quoting Lari Lehti=F6 <lar...@he...>: > Hi, > > I've done this by rendering two images (actually 4 to get stereo). > One without > the CGOs and one with them. Then I overlaid them with photoshop and > changed the > trasnparency of the CGO containing layer. I just used triangles and it lo= oked > rather nice. > > ~Lari~ > > _______________________________________ > Lari Lehti=F6 > University of Helsinki > Institute of Biotechnology > Macromolecular X-ray crystallography > P.O.Box 65 > 00014 HY > Finland > http://www.biocenter.helsinki.fi/~lehtio/ > _______________________________________ > > > Quoting tan...@st...: > > # Hi everybody, > # > # i've just created many CGOs, which show up solid surfaces like spheres = and > # ellipsoids. Is it possible to set the transparency of some CGO's to > i.e. 0.5 > # and leave the others solid? > # I've checked out the reference and the manual, and found something like= : > # > # set transparency=3D0.5, object > # > # But this actually does not work for CGO's. > # Any ideas.... > # > # Yusuf > # > # > # -- > # Yusuf Tanrikulu > # Bioinformatics Diploma Student > # Department of Biosciences > # Johann-Wolfgang-Goethe Univerity Frankfurt > # Siesmayerstrasse 70 > # 60326 Frankfurt am Main > # - Germany - > # tan...@bi... > # > # > # ------------------------------------------------------- > # SF.Net email is Sponsored by the Better Software Conference & EXPO > # September 19-22, 2005 * San Francisco, CA * Development Lifecycle Pract= ices > # Agile & Plan-Driven Development * Managing Projects & Teams * Testing &= QA > # Security * Process Improvement & Measurement * http://www.sqe.com/bsce5= sf > # _______________________________________________ > # PyMOL-users mailing list > # PyM...@li... > # https://lists.sourceforge.net/lists/listinfo/pymol-users > # > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practic= es > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & Q= A > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Warren D. <wa...@de...> - 2005-08-14 19:26:23
|
> > I was wondering if it is possible to save a carved out section of a=20 > > map and the read it back into pymol as a separate map. > Pymol won't do it Not so, as of today (grin). =20 In 0.99beta11 and beyond, the newly implemented command to carry this out is "map_trim". (Windows build at http://delsci.com/beta or compile from source). map_trim map-name, selection-name, buffer Combined with the convenient new object-name wildcards (!!!), you could for example trim all your maps to 3 Angstroms around ligands with one commmand as follows map_trim *, organic, 3 With map size now reduced, the map_double command can come in handy to increase mesh density on your figure. map_double * Also in this new beta: Dunbrack rotamers, nucleic acid cartoons, new pop-up menus, etc. Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of Tim Fenn > Sent: Saturday, August 13, 2005 11:38 AM > To: Schubert, Carsten [PRDUS] > Cc: pym...@li... > Subject: Re: [PyMOL] Saving a carved section of a map. >=20 > On Fri, Aug 12, 2005 at 02:48:16PM -0400, Schubert, Carsten=20 > [PRDUS] wrote: > >=20 > > I was wondering if it is possible to save a carved out section of a=20 > > map and the read it back into pymol as a separate map. >=20 > Pymol won't do it, but if its something thats urgent,=20 > povscript+ saves maps in GTS format (including vertex colors): >=20 > http://gts.sf.net > http://www.stanford.edu/~fenn/povscript/gts_fileformat.html >=20 > HTH, > Tim >=20 > -- > --------------------------------------------------------- >=20 > Tim Fenn > fe...@st... > Stanford University, School of Medicine > James H. Clark Center > 318 Campus Drive, Room E300 > Stanford, CA 94305-5432 > Phone: (650) 736-1714 > FAX: (650) 736-1961 >=20 > --------------------------------------------------------- >=20 >=20 >=20 > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference &=20 > EXPO September 19-22, 2005 * San Francisco, CA * Development=20 > Lifecycle Practices Agile & Plan-Driven Development *=20 > Managing Projects & Teams * Testing & QA Security * Process=20 > Improvement & Measurement * http://www.sqe.com/bsce5sf=20 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 |
From: Tim F. <fe...@st...> - 2005-08-13 18:28:41
|
On Fri, Aug 12, 2005 at 02:48:16PM -0400, Schubert, Carsten [PRDUS] wrote: > > I was wondering if it is possible to save a carved out section of a map and > the read it back into pymol as a separate map. Pymol won't do it, but if its something thats urgent, povscript+ saves maps in GTS format (including vertex colors): http://gts.sf.net http://www.stanford.edu/~fenn/povscript/gts_fileformat.html HTH, Tim -- --------------------------------------------------------- Tim Fenn fe...@st... Stanford University, School of Medicine James H. Clark Center 318 Campus Drive, Room E300 Stanford, CA 94305-5432 Phone: (650) 736-1714 FAX: (650) 736-1961 --------------------------------------------------------- |
From: Warren D. <wa...@de...> - 2005-08-12 21:49:32
|
Xavier, PyMOL 0.99beta09 and earlier use a crude backbone-independent rotamer library. However, current development versions (PyMOL 0.99beta10 on up) now provide both the Dunbrack backbone-dependent and backbone-independent rotamers. Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Xavier Deupi > Sent: Friday, August 12, 2005 2:34 PM > To: pym...@li... > Subject: [PyMOL] conformational states in the mutagenesis wizard >=20 > Hi, >=20 > I've just realized that through the mutagenesis wizard you=20 > can view/select different conformations for a sidechain. I've=20 > been playing around, and it seems that the conformations are=20 > selected according to a backbone-independent rotamer library.=20 > Am I correct? Which library has been used? >=20 > I would also like to know if there is anybody out there using=20 > the rotamer toggle plugin. I've just installed it, and=20 > although it seems extremely useful, it makes PyMOL very slow=20 > to start. I'm running PyMOL > 0.98 for MacOSX in a PowerBook G4 1GHz with 1Gb of RAM=20 > (running MacOS X > 10.4.2) >=20 > Thanks in advance, >=20 > Xavier >=20 > -- > Xavier Deupi, Ph.D. > Department of Molecular and Cellular Physiology Beckman=20 > Center for Molecular and Genetic Medicine (B161) > 279 Campus Drive, Stanford University School of Medicine=20 > Stanford, CA 94305 (USA) >=20 > E-mail: Xav...@st... > Phone: +1 (650) 725-6497 > Fax : +1 (650) 725-8021 >=20 >=20 >=20 > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference &=20 > EXPO September 19-22, 2005 * San Francisco, CA * Development=20 > Lifecycle Practices Agile & Plan-Driven Development *=20 > Managing Projects & Teams * Testing & QA Security * Process=20 > Improvement & Measurement * http://www.sqe.com/bsce5sf=20 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 |
From: Tsjerk W. <ts...@gm...> - 2005-08-12 21:48:04
|
Hi Corinne, Sabuj, You're right with regards to the CGO. An example script (written by Gareth Stockwell) can be found at http://md.chem.rug.nl/~tsjerk/Scripts/walls.py. With regards to the raytracing, don't be fooled, I'd say this was Pymol's internal raytracer :) Hope it helps, Tsjerk On 8/12/05, Sabuj Pattanayek <sab...@va...> wrote: > It looks like a CGO (compiled graphics object) behind the molecule, then > rendered using pov-ray, probably a script floating around to do this > somewhere on the internets. >=20 > Corinne Zeitler wrote: > > Hi, > > > > I was wondering if anyone knows how to produce the type of image in > > Pymol that is on the Pymol Galleray page > > (http://pymol.sourceforge.net/pmimag.html). I would like to know > > specifically how to make the shadow of the molecule appear in the > > background. Thank you! > > > > Corinne Zeitler > > Graduate Student > > Baylor College of Medicine >=20 >=20 >=20 > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practic= es > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & Q= A > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Sabuj P. <sab...@va...> - 2005-08-12 21:41:26
|
I use a cheap microsoft optical (or basic optical) usb mouse on linux, so it should work on your macosx. If you want something more configurable under macosx and don't want to destroy the "Appleness" of your computer with an MS mouse then this might work for you http://www.apple.com/mightymouse/ . I hear there will be a wireless version soon. Sarina Bromberg wrote: > I have a logitech MX700 Cordless Optical Mouse that claims to be a 3- > button mouse, but I can never get it to produce the results provided > for 3-button viewing or editing by PyMOL. Perhaps I do not have it > configured correctly (I cannot find a clue in the instructions or in > simple experiments), or perhaps this is not the kind of 3-button mouse > I need. Does anyone have a good solution? > Tx, > Sarina Bromberg > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Sabuj P. <sab...@va...> - 2005-08-12 21:28:39
|
It looks like a CGO (compiled graphics object) behind the molecule, then rendered using pov-ray, probably a script floating around to do this somewhere on the internets. Corinne Zeitler wrote: > Hi, > > I was wondering if anyone knows how to produce the type of image in > Pymol that is on the Pymol Galleray page > (http://pymol.sourceforge.net/pmimag.html). I would like to know > specifically how to make the shadow of the molecule appear in the > background. Thank you! > > Corinne Zeitler > Graduate Student > Baylor College of Medicine |
From: Xavier D. <Xav...@st...> - 2005-08-12 21:23:20
|
Hi, I've just realized that through the mutagenesis wizard you can view/select different conformations for a sidechain. I've been playing around, and it seems that the conformations are selected according to a backbone-independent rotamer library. Am I correct? Which library has been used? I would also like to know if there is anybody out there using the rotamer toggle plugin. I've just installed it, and although it seems extremely useful, it makes PyMOL very slow to start. I'm running PyMOL 0.98 for MacOSX in a PowerBook G4 1GHz with 1Gb of RAM (running MacOS X 10.4.2) Thanks in advance, Xavier -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Beckman Center for Molecular and Genetic Medicine (B161) 279 Campus Drive, Stanford University School of Medicine Stanford, CA 94305 (USA) E-mail: Xav...@st... Phone: +1 (650) 725-6497 Fax : +1 (650) 725-8021 |
From: Michael C. <msc...@sy...> - 2005-08-12 20:13:09
|
Hi I have installed version 0.98 on my new dual processor machine running windows XP. Pymol runs fine, but when trying to load a large PDB file (~4Mb), the program crashes and I get a runtime error: "This application has requested the Runtime to terminate it in an unusual way" Does anyone have some advice? Thanks, Michael Michael S. Cosgrove, Ph.D. Assistant Professor Syracuse University Department of Biology 406D Lyman Hall 108 College Place Syracuse, NY 13244 Phone: (315) 443-2964 Fax: (315) 443-2156 Email: msc...@sy... |
From: Warren D. <wa...@de...> - 2005-08-12 19:58:03
|
Carsten, Hmm... Unfortunately, the PyMOL command language currently provide any way of expressing a newline character, so you will need to use the API form of the scene command. Note that it is perfectly legal to use that form in a ".pml" file as follows, without an intervening variable: cmd.scene("new","store","line1\nline2") Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Schubert, Carsten [PRDUS] > Sent: Friday, August 12, 2005 12:57 PM > To: pym...@li... > Subject: [PyMOL] Newline character in scene annotation message >=20 > Hi=20 >=20 > I am trying to combine a scene with annotations spanning=20 > several lines.=20 > So far something like=20 > > scene new, store, message=3D"Line1\nLine2"=20 >=20 > would produce some nice coloration effects but not a newline=20 > character.=20 >=20 > I was able to use the api function to do the trick=20 > >mesg=3D"line1\nline2"=20 > >cmd.scene("new","store",message=3Dmesg) >=20 > but I was wondering is there a way to use the non API=20 > function in the same way?=20 >=20 > Thanks=20 >=20 > Carsten=20 >=20 >=20 |
From: Schubert, C. [PRDUS] <CSC...@pr...> - 2005-08-12 19:47:15
|
Hi I am trying to combine a scene with annotations spanning several lines. So far something like > scene new, store, message="Line1\nLine2" would produce some nice coloration effects but not a newline character. I was able to use the api function to do the trick >mesg="line1\nline2" >cmd.scene("new","store",message=mesg) but I was wondering is there a way to use the non API function in the same way? Thanks Carsten |
From: Corinne Z. <cze...@gm...> - 2005-08-12 19:46:17
|
Hi, I was wondering if anyone knows how to produce the type of image in Pymol= =20 that is on the Pymol Galleray page (http://pymol.sourceforge.net/pmimag.htm= l).=20 I would like to know specifically how to make the shadow of the molecule=20 appear in the background. Thank you! Corinne Zeitler Graduate Student Baylor College of Medicine |
From: Warren D. <wa...@de...> - 2005-08-12 18:58:53
|
Hi Carsten, This isn't yet possible from within PyMOL, but it will be soon since it is a recurring request. In the meantime unforutnately, you will need to truncate the maps outside of PyMOL in order to generate smaller session files. Sorry about that! Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Schubert, Carsten [PRDUS] > Sent: Friday, August 12, 2005 11:56 AM > To: pym...@li... > Subject: [PyMOL] Saving a carved section of a map. >=20 > Hi=20 >=20 > I was wondering if it is possible to save a carved out=20 > section of a map and the read it back into pymol as a=20 > separate map. The background is that I'd like to distribute=20 > .psw files with a couple of maps, but they get rather large=20 > (>50 MB) since the map data is not compressed in pymol. I am=20 > only interested in a small portion of the map centered around=20 > a ligand and some residues, so the rest of the map would be=20 > unnecessary since it will not be shown anyway.=20 >=20 > I have tried if mapman could do the trick but apparently not.=20 > I could probably restrict the calculation of the map to be=20 > only centered around a region of interest, but was wondering=20 > if this would be possible in pymol. >=20 >=20 > Thanks=20 >=20 > Carsten=20 >=20 >=20 |
From: Schubert, C. [PRDUS] <CSC...@pr...> - 2005-08-12 18:48:33
|
Hi I was wondering if it is possible to save a carved out section of a map and the read it back into pymol as a separate map. The background is that I'd like to distribute .psw files with a couple of maps, but they get rather large (>50 MB) since the map data is not compressed in pymol. I am only interested in a small portion of the map centered around a ligand and some residues, so the rest of the map would be unnecessary since it will not be shown anyway. I have tried if mapman could do the trick but apparently not. I could probably restrict the calculation of the map to be only centered around a region of interest, but was wondering if this would be possible in pymol. Thanks Carsten |
From: Sarina B. <sa...@di...> - 2005-08-12 18:21:42
|
I have a logitech MX700 Cordless Optical Mouse that claims to be a 3- button mouse, but I can never get it to produce the results provided for 3-button viewing or editing by PyMOL. Perhaps I do not have it configured correctly (I cannot find a clue in the instructions or in simple experiments), or perhaps this is not the kind of 3-button mouse I need. Does anyone have a good solution? Tx, Sarina Bromberg |
From: Avram S. <as...@co...> - 2005-08-12 17:37:25
|
Hi, does anyone know what file type to save text as (in OS X) for a .pml file? I can't get PyMol to recognize RTF, etc... thanks Avram Slovic |