[PyMOL] More on A Few Good MacPyMOL OS X Beta Testers
Sorry, a bit of confusion seems to have arisen over the MacPyMOL beta test. What is MacPyMOL? See below. Subject: [PyMOL] A Few Good Mac PyMOL OS X Beta Testers Mac Users: I have something new in the works for OS X/Aqua and need some beta testers for the next couple of months. Specifically, I am looking for users who: 1) have experience with full PyMOL (under Fink, X11, or Windows). 2) are current PyMOL sponsors/subscribers. 2) Means: You voluntarily purchased a PyMOL license or support subscription within the last 12 months. (This has nothing to do with mailing list subscriptions). 3) are running OS X 10.2.8 or 10.3.x 4) have QuickTime 6.4 installed. 5) would value a Mac-enhanced PyMOL derivative. 6) don't mind closed-source software. 6) Means: You're willing to use a closed-source variant to get the job done when the open-source version falls short of the mark, as has been the case with cross-platform PyMOL on the Mac due to OS X's continuing inability to deliver usable Tcl/Tk under Python (without X11, Fink, or other complicating dependencies). If you meet all of these qualifications, please email me. If you don't, then please sit tight for now -- more information will be forthcoming in January. (or now...) Just to quell any potential anxiety, I do want to reassure everyone that Open-Source PyMOL is alive and well and remains a central focus of DeLano Scientific LLC. We are committed to providing commercial-grade solutions on top of OPEN SOURCE FOUNDATIONS that are themselves useful in isolation and are accessible to virtually everyone. Our business model is to deliver valuable products and services at a fair price while simultaneously generating useful free tools and open-source code for the scientific community. We can do that because we answer only to our customers and ourselves -- no venture capitalists, no outside shareholders, and no fiduciary obligation to maximize profits. This is not your typical American business, but we are succeeding nonetheless thanks to you, our sponsors. Over the past year or so, I have made no secret of our plans to deliver extra rewards (Incentive Products) to PyMOL sponsors in order to generate robust recurring funding for the project. Thus you should expect a variety of new benefits to appear for sponsors over coming years in addition to steady progress on the open-source front. Besides improved documentation and training materials, sponsorship incentives may include enhanced versions of PyMOL which: - work inside of Internet Explorer and PowerPoint (ala Chime)... - have protein sequence display and alignment (ala MOE)... - provide simple user interfaces (ala WebLab/DSViewer)... - include 2D chemical structure display (ala VIDA/ChemDraw)... - have built-in energy minimization (ala MacroModel)... - include better building tools (ala O/Quanta/MODELER)... - provide live built-in tutorials (ala ???)... - use platform-dependent tools (ala QuickTime/Clipboard/COM/AVI)... - support molecular morphing (ala RigiMOL)... - perform property analyses (ala Grasp/SiteFinder/HotPatch)... Quite a list, but some things will take many person-years to complete. What happens first depends on who provides what resources, when they do so, and with what prioritization. When the PyMOL vision is realized, hopefully all of the above and more will be accessible from within the suite, and as many of these components as possible will be Open-Source and reusable. Every day, we do what we can given our current resources, given the state of the code and documentation, and given the various platforms that we have to work with. So long as we keep making steady progress, with your help, we will eventually reach many of these goals. With that important background, I am pleased to announce that MacPyMOL is an Aqua-Based version of PyMOL for OS X that will be released publicly in late January as our first software Incentive Product. It contains the complete PyMOL GUI and Menu Set along with a couple features found nowhere else. MacPyMOL is currently being beta tested by a small group of PyMOL sponsors in order to work out the remaining glitches. Here are some details on it: MacPyMOL outputs QuickTime movies straight away. MacPyMOL allows you to Copy and Paste images directly. MacPyMOL is fully compatible with Open-Source PyMOL. MacPyMOL usage incurs no additional cost for current PyMOL sponsors. MacPyMOL usage will be free for full-time students. MacPyMOL usage will be free for teaching. MacPyMOL usage will be free for use with public/published data (only). MacPyMOL is not open-source because it is an Incentive Product. MacPyMOL was specifically requested by several major PyMOL sponsors. By the way, MacPyMOL has no significant implications for Open-Source PyMOL on the Mac, which continues to be free and unrestricted open-source software. Because MacPyMOL is built on the Open-Source PyMOL foundation, it will continue to evolve
RE: [PyMOL] Object orientation matrices
Laurence, Sort of. Right now PyMOL doesn't fully support translations of individual objects by independent matrices, but you can translate their representations by a matrix for animation purposes using translate and rotate with the object argument. However, you can cleanly transform the atoms in an object. See print cmd.transform_selection.__doc__ for details on the matrix used for that. The object matrix system is just about due for an overhaul -- we need more flexibility than is currently provided... 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 Laurence Pearl Sent: Tuesday, December 02, 2003 5:47 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Object orientation matrices Is there any way of accessing the matrices that define the orientation and position of an individual object relative to the world in PyMol in the same way that get_view and set_view do for the overall view matrix ? -- Laurence H. Pearl Section of Structural Biology, Institute of Cancer Research Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK Phone +44-207-970 6045 : Secretary +44-207-970 6046 FAX +44-207-970 6051 : E-Mail laurence.pe...@icr.ac.uk -- Live Simply and do Serious Things .. - Dorothy Crowfoot Hodgkin -- --- 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/pymol-users
[PyMOL] cannot 'fit' a particular pdb file
Hi, I have loaded 3 pdb files of homologous forms of an enzyme. The 'fit' command works for superimposing/aligning two of them, but the third file always gives a No Atoms Selected error. Is there something in the pdb file I can fix? As a general rule now, I Hide Everything at first and then Show Lines as I begin with a new PyMOL session. I can see all three molecules, just can't align the third one (EcHRSade) with the first two (TtHisRS and SaHRS). PyMOLfit TtHisRS, SaHRS Executive: RMS =4.222 (718 to 718 atoms) PyMOLfit TtHisRS, EcHRSade ExecutiveRMS-Error: No atoms selected. PyMOLfit EcHRSade, TtHisRS ExecutiveRMS-Error: No atoms selected. PyMOLfit EcHRSade, SaHRS ExecutiveRMS-Error: No atoms selected. Thanks, --Michael
RE: [PyMOL] cannot 'fit' a particular pdb file
Michael, Try align... Fit only works when all of the atom identifiers match. Align matches atoms through a 1D alignment and then performs some optimization: align TtHisRSca, EcHRSadeca align SaHRSca, EcHRSadeca 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 Michael Bovee Sent: Tuesday, December 02, 2003 11:17 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] cannot 'fit' a particular pdb file Hi, I have loaded 3 pdb files of homologous forms of an enzyme. The 'fit' command works for superimposing/aligning two of them, but the third file always gives a No Atoms Selected error. Is there something in the pdb file I can fix? As a general rule now, I Hide Everything at first and then Show Lines as I begin with a new PyMOL session. I can see all three molecules, just can't align the third one (EcHRSade) with the first two (TtHisRS and SaHRS). PyMOLfit TtHisRS, SaHRS Executive: RMS =4.222 (718 to 718 atoms) PyMOLfit TtHisRS, EcHRSade ExecutiveRMS-Error: No atoms selected. PyMOLfit EcHRSade, TtHisRS ExecutiveRMS-Error: No atoms selected. PyMOLfit EcHRSade, SaHRS ExecutiveRMS-Error: No atoms selected. Thanks, --Michael --- 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/pymol-users
[PyMOL] Clarification on A Few Good MacPyMOL OS X Beta Testers
Sorry, a bit of confusion seems to have arisen over the MacPyMOL beta test. What is MacPyMOL? See below. Subject: [PyMOL] A Few Good Mac PyMOL OS X Beta Testers Mac Users: I have something new in the works for OS X/Aqua and need some beta testers for the next couple of months. Specifically, I am looking for users who: 1) have experience with full PyMOL (under Fink, X11, or Windows). 2) are current PyMOL sponsors/subscribers. 2) Means: You voluntarily purchased a PyMOL license or support subscription within the last 12 months. (This has nothing to do with mailing list subscriptions). 3) are running OS X 10.2.8 or 10.3.x 4) have QuickTime 6.4 installed. 5) would value a Mac-enhanced PyMOL derivative. 6) don't mind closed-source software. 6) Means: You're willing to use a closed-source variant to get the job done when the open-source version falls short of the mark, as has been the case with cross-platform PyMOL on the Mac due to OS X's continuing inability to deliver a usable Tcl/Tk under Python (without X11 or Fink). If you meet all of these qualifications, please email me. If you don't, then please sit tight for now -- more information will be forthcoming in January. (or now...) Just to quell any potential anxiety, I do want to reassure everyone that Open-Source PyMOL is alive and well and remains a central focus of DeLano Scientific LLC. We are committed to providing commercial-grade solutions on top of OPEN SOURCE FOUNDATIONS that are themselves useful in isolation and are accessible to virtually everyone. Our business model is to deliver valuable products and services at a fair price while simultaneously generating useful free tools and open-source code for the scientific community. We can do that because we answer only to our customers and ourselves -- no venture capitalists, no outside shareholders, and no fiduciary obligation to maximize profits. This is not your typical American business, but we are succeeding nonetheless thanks to you, our sponsors. Over the past year or so, I have made no secret of our plans to deliver extra rewards (Incentive Products) to PyMOL sponsors in order to generate robust recurring funding for the project. Thus you should expect a variety of new benefits to appear for sponsors over coming years in addition to steady progress on the open-source front. Besides improved documentation and training materials, incentives may include enhanced versions of PyMOL which: - work inside of Internet Explorer and PowerPoint (ala Chime)... - have protein sequence display and alignment (ala MOE)... - provide simple user interfaces (ala WebLab/DSViewer)... - include 2D chemical structure display (ala VIDA/ChemDraw)... - have built-in energy minimization (ala MacroModel)... - include better building tools (ala O/Quanta/MODELER)... - provide live built-in tutorials (ala ???)... - use platform-dependent tools (ala QuickTime/Clipboard/COM/AVI)... - support molecular morphing (ala RigiMOL)... - perform property analyses (ala Grasp/SiteFinder/HotPatch)... Quite a list, but some things will take many person-years to complete. What happens first depends on who provide resources, when they do so, to what extent, and with what prioritization. When the PyMOL vision is realized, hopefully all of the above and more will be accessible from within the suite, and as many of these components as possible will be Open-Source and reusable. Every day, we do what we can given our current resources, given the state of the code and documentation, and given the various platforms that we have to work with. So long as we keep making steady progress, with your help, we will eventually reach many of these goals. With that important background, I am pleased to announce that MacPyMOL is an Aqua-Based version of PyMOL for OS X that will be released publicly in late January as our first software Incentive Product. It contains the complete PyMOL GUI and Menu Set along with a couple features found nowhere else. MacPyMOL is currently being beta tested by a small group of PyMOL sponsors in order to work out the remaining glitches. Here are some details on it: MacPyMOL outputs QuickTime movies straight away. MacPyMOL allows you to Copy and Paste images directly. MacPyMOL is fully compatible with Open-Source PyMOL. MacPyMOL usage incurs no additional cost for current PyMOL sponsors. MacPyMOL usage will be free for full-time students. MacPyMOL usage will be free for teaching. MacPyMOL usage will be free for use with public/published data (only). MacPyMOL is not open-source because it is an Incentive Product. MacPyMOL was specifically requested by several major PyMOL sponsors. By the way, MacPyMOL has no significant implications for Open-Source PyMOL on the Mac, which continues to be free and unrestricted open-source software. Because MacPyMOL is built on the Open-Source PyMOL foundation, it will continue to evolve and improve in synchronization with
[PyMOL] Viewing homotetramers with PyMol
Hi everyone, I am quite new to PyMol and structural biology as well, since I am still a student. I installed PyMol via Fink on my iBook running Panther 10.3.1. I want to view the homotetramer of the TTR-protein. I got it from the PDB (PDB-id: 1f41). The asymmetric unit is a dimer. But the assumed biological molecule is the tetramer. One can download the coordinates of this molecule. But when I try to load it in Pymol, only the dimer shows up. I am quite sure that this file should contain the right coordinates, because the origin of rotation differs between the tetramer file and the dimer file. How can display the other dimer? This is necessary in particular, because i am supposed to examine the loops which mediates the dimer-dimer-interaction. Do you want me to send the coordinates file to the list? Thanks in advance and please apologize my bad english, René Wuttke
RE: [PyMOL] Viewing homotetramers with PyMol
Rene, The problem is that each biological unit copy in the PDB is handled as a separate molecular state (i.e. a movie), which then become distinct states in PyMOL. Hit play to see what I mean. To solve this, the most recent versions of PyMOL can split multi-state objects into multiple single-state objects automatically: load 1f41_tetra.pdb split_states 1f41_tetra dele 1f41_tetra With older versions, you'll need to create the new objects manually load 1f41_tetra.pdb create 1f41_tetra_1, 1f41_tetra, source_state=1, target_state=1 create 1f41_tetra_2, 1f41_tetra, source_state=2, target_state=1 dele 1f41_tetra 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 René Wuttke Sent: Tuesday, December 02, 2003 1:08 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Viewing homotetramers with PyMol Hi everyone, I am quite new to PyMol and structural biology as well, since I am still a student. I installed PyMol via Fink on my iBook running Panther 10.3.1. I want to view the homotetramer of the TTR-protein. I got it from the PDB (PDB-id: 1f41). The asymmetric unit is a dimer. But the assumed biological molecule is the tetramer. One can download the coordinates of this molecule. But when I try to load it in Pymol, only the dimer shows up. I am quite sure that this file should contain the right coordinates, because the origin of rotation differs between the tetramer file and the dimer file. How can display the other dimer? This is necessary in particular, because i am supposed to examine the loops which mediates the dimer-dimer-interaction. Do you want me to send the coordinates file to the list? Thanks in advance and please apologize my bad english, René Wuttke --- 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/pymol-users
RE: [PyMOL] residues deviate from protein secondary catoon representation
(becoming an FAQ) For starters, set cartoon_smooth_loops, off set cartoon_flat_sheets, off If that doesn't meet your needs, then you'll need to split your object into separate objects to get the desired effect of mixing smoothed and non-smoothed cartoons. Thankfully, the next version will provide an easier workaround for this... 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 Yunfeng Hu Sent: Tuesday, December 02, 2003 1:57 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] residues deviate from protein secondary catoon representation Dear pymol users, I am trying to show some residues in sticks while the whole protein is in cartton representation. However I find that some residues do not attach to the cartoon at all. I understand that the secondary cartoon is an approximation along the backbone. Is there a way that I can show at least those residues are anchored in the cartoon? Thanks. Yunfeng --- 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/pymol-users
