Re: [PyMOL] get translation / rotation matrix from super
Matthias, fetch 1cll 1ggz, async=0 print cmd.get_object_matrix(1cll) print cmd.get_object_matrix(1ggz) super 1cll, 1ggz print cmd.get_object_matrix(1cll) print cmd.get_object_matrix(1ggz) As you can see when an object is loaded it's transformation matrix is the identity. Then, when you call super is moves the mobile protein by the transformation matrix. Notice the matrix is a 4x4 which means it's: [ A b ] where A is the 3x3 rotation matrix, and b is the 3x1 translation vector. See also: http://pymolwiki.org/index.php/Get_object_matrix Hope this helps, -- J On Mon, Jan 18, 2010 at 5:35 AM, Matthias Haffke matze_haf...@hotmail.com wrote: Hi everybody! I was wondering if there is a way to get a translation / rotation matrix out of the super command. My problem is, that I want to superimpose 2 proteins (lets say protein B superimposed on protein A), but I also want to use the same superposition (e.g. the same translation and the rotation function / matrix) for every symmetry mate of protein B. Is there a way to extract the translation / rotation matrix out of the super command or can I use another command to align both, protein B and A and to apply the function on every symmetry mate? Both proteins don't have to be aligned perfectly, it's much more important for me to keep the symmetry operations of protein B. I already tried to use the translate function to get a sort of alignment (which could then be applied to all symmetry mates), but I wasn't very successful. Looks like the translate function works in respect of your viewing point but not in respect of the cell axis?!? Matthias Was machst Du grad bei Facebook? So erfahren es alle im Messenger -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] get translation / rotation matrix from super
Matthias Haffke said: Is there a way to extract the translation / rotation matrix out of the super command or can I use another command to align both, protein B and A and to apply the function on every symmetry mate? In addition the commands mentioned by Jason, you can look at matrix_copy http://www.pymolwiki.org/index.php/Matrix_copy You would align protein B to A, then matrix_copy protein_b, symmetry_mates Note, the second argument can have a wild card, so you only need to call the command once to move all of them if they all have a common prefix or the such. -David -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] 3D Stereo Problem
Hi All: I am unable to view 3D Stereo. The system info and error message are listed below. Pls. help. THX Deepa 1. OS: Windows 7 2. Monitor:Samsung Syncmaster 2233RZ 22in 3D Gaming LCD 3. Card: EVGA GeForce 9800 GTX+ 512MB PCIe w/Dual Link DVI 4. Glasses: NVIDIA 3D Vision Glasses Pymol message PyMOL(TM) Educational Product - Copyright (C) 2009 DeLano Scientific LLC. Free usage of this Executable Build is restricted to full-time students and their teachers while engaged in educational activities. All other uses require purchase of a PyMOL Maintenance and/or Support Subscription. Please visit http://www.pymol.org/funding.html for more information and contact sa...@delsci.com when you are ready to purchase a Subscription. This Executable Build integrates and extends Open-Source PyMOL 1.2r1. Error: The requested stereo 3D visualization mode is not available. -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] New Feature Ideas
PyMOLers, We need to move forward on PyMOL development, so I'm collecting ideas from all our users on what they most want in future versions of PyMOL. We already have a page on the PyMOL wiki for this (http://pymolwiki.org/index.php/Ideas) from 2008/2009. We can discuss the ideas here and on the wiki; this list is more for two-way communication and the wiki for one-way. If you have a specific request for an enhancement you can also email it directly to h...@schrodinger.com; please put PyMOL in the subject so I can get them easily. Each request submitted will be considered for implementation. Last, you're particularly passionate about your feature request, email me directly and we can chat about it via phone/skype. Thanks, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Feature Requests/Ideas
Jason, Here are some features that I have discussed with Warren in the in the past: 1) Vector graphics output (preferably in Adobe Illustrator format, SVG, postscript, or PDF format). I tend to make all of my posters and publication figures in Adobe illustrator (due to its scalability) and images generated from PyMOL seem to always slow me down especially when I need to go back and ray trace an image or sets of images over again since they were smaller than I had expected. I am no expert but I feel like there should be an easy way to achieve this. For example, the output for POV-RAY generated by PyMOL is essentially a list of primitive objects and how they should be drawn and I feel like it could be converted into some sort of postscript-like information which could be interpreted in programs like Adobe Illustrator or other vector-based programs. 2) In line with the first request, I stumbled across the fact that VMD now has a really cool plug-in for PDF files where you can open a PDF file that contains a figure and actually MOVE the 3D-image (or a molecule) within the PDF file! This could really change the way we interpret molecular structures in the future! More information can be found here: http://www.ks.uiuc.edu/Research/vmd/minitutorials/acrobat3d/ 3) Being a molecular dynamics guy, I've spent countless hours writing python scripts to read in MD trajectory files. Though successful, the hurdle lies within the fact that the process is extremely slow. Essentially, the python script opens the trajectory file, reads one MD frame, duplicates a state in PyMOL, copies over the coordinates from the MD frame over to the new state via the alter command (or alter_state?), and repeat for as many states as needed. The problem is really the last part of using the alter command which is extremely slow. I understand that certain versions of PyMOL contains the ability to read trajectories (which I currently use) but I also understand that not everyone has access to the same resources so it would be nice to have a faster way to access/load/modify the coordinates for different states that can be handled efficiently via python scripting (and not C). Alternatively, one may want to load several PDB files (or NMR models) into a single object if you close PyMOL (on purpose or accidentlally) then you will be forced to load the files again. This could be tedious. Instead, if you could save the states as an MD trajectory then all you would have to do next time is load the corresponding PDB file followed by the trajectory and that's it. Now, I have written the python code for this (to save states to a trajectory file) but then I run into the same issue of not being able to read in a trajectory file via python (the hard-coded method using C to read trajectories is much much faster). Thus, the ability to load trajectories is always a plus. In addition, having the ability to load trajectories not only makes loading multiple files very fast and efficient but it is more favorable than opening a movie/video generated by PyMOL since with the trajectory, you can still move the molecule while the movie is played as is without further interaction. 4) Going along the same MD theme, PyMOL seems to not be able to handle certain representations (i.e. cartoon, spheres, surface) of large biomolecules (160,000+ atoms) when a large number of states is loaded (20,000+ states). As much as I love PyMOL and as much as I've convinced other members of my lab to use it, it's hard to compete with VMD in this regard. I would be more than willing to help provide examples for this (and I had conversed with Warren about this in the past and is also where I was made aware of the defer_builds_mode setting). 5) It would be nice to have a GUI for drawing CGO objects. Hopefully, this will get the ball rolling for more ideas! Sean _ -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
