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From: Andrew D. F. <fa...@po...> - 2007-08-31 21:55:01
|
Is there an easy way to refer to/select a portion of a molecular surface that is within a given distance of another molecule's surface? I'm trying to generate some graphics for a presentation on a signaling pathway, and I want to show just the part of each peptide's solvent accessible surface that is making contact with the binding site. Ideally, I would like to be able to color this, at least in a contrasting color to the structures of the components, but preferably tied to electrostatic potential or hydrophobicity. Has anyone ever done this, and if so, can you spare any advice? Thanks, Andy |
From: DeLano S. <de...@de...> - 2007-08-31 04:40:53
|
Roger, This isn't so much a PyMOL bug as a flaky characteristic of OpenGL under Windows XP, which eventually stops updating the screen when an application like PyMOL attempts to draw continuously for a long period of time without relinquishing control back to the operating system event loop. PyMOL isn't actually frozen when this happens -- it continues to render and write out images. Windows simply isn't updating the screen. The problem doesn't exist on Windows 2k or Linux, but a very similar behavior occurs with MacPYMOL (but which can be worked around by dragging the MacPyMOL window). Eventually we'll rearchitect PyMOL's event loop so as to eliminate this annoyance. Cheers, Warren > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf > Of Roger Rowlett > Sent: Thursday, August 30, 2007 9:15 PM > To: pym...@li... > Subject: [PyMOL] Pymol 1.0 graphics bug > > In Pymol 1.0, the pymol viewer freezes during an mpng command > in progress if the mouse pointer is moved. (Windows XP XP2 > only, using Intel chips and motherboard, Nvidia graphics card > and driver) PNG files are written out properly, and viewer > window becomes live again after completion of the mpng > command. I have verified this on two different systems, one > with an Intel DG945CC board and Pentium D 805 with Nvidia > GeForce 7300S and another with an Intel DQ965FE board and > Core Duo 2 E6600 with XFX GeForce 8600 GT graphics. Both > machines have 2 Gbyte of RAM and the latest Nvidia drivers. > This behavior cannot be duplicated in Linux FC6 using a > Quadro 980XGL and a single core Pentium 4, also with 2 Gbyte of RAM. > > Anybody else notice this? > > Cheers, > > > -------------------------------------------------------------- > ----------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and > a browser. > Download your FREE copy of Splunk now >> > http://get.splunk.com/ _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Roger R. <rro...@ma...> - 2007-08-31 04:15:06
|
In Pymol 1.0, the pymol viewer freezes during an mpng command in progress if the mouse pointer is moved. (Windows XP XP2 only, using Intel chips and motherboard, Nvidia graphics card and driver) PNG files are written out properly, and viewer window becomes live again after completion of the mpng command. I have verified this on two different systems, one with an Intel DG945CC board and Pentium D 805 with Nvidia GeForce 7300S and another with an Intel DQ965FE board and Core Duo 2 E6600 with XFX GeForce 8600 GT graphics. Both machines have 2 Gbyte of RAM and the latest Nvidia drivers. This behavior cannot be duplicated in Linux FC6 using a Quadro 980XGL and a single core Pentium 4, also with 2 Gbyte of RAM. Anybody else notice this? Cheers, |
From: EFFICIENT E. A. E. F. P. OF K. I. O. A. <b1...@ma...> - 2007-08-31 01:17:19
|
Dear all, I have a structure of a monomer and want to view the dimer. I try split_states following the PymolWiki: http://pymolwiki.org/index.php/Split_States, but it still give me a monomer. any suggestion will be greatly appreciated. best wishes, Rong ------------------------------------------------- This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk |
From: Andrew W. <sen...@gm...> - 2007-08-29 23:02:42
|
Does anyone have any idea how to render the interior of a protein like this example: http://skuld.bmsc.washington.edu/raster3d/examples/slice.png While I can do it for the entire scene, I'd like a solid slab of the protein but be able to see sidechains in front of the solid slab. Any ideas? Cheers, Andrew Wollacott University of Washington |
From: Abhinav V. <abh...@gm...> - 2007-08-29 18:46:40
|
hi one of doing this would be, to load ur file and then type the follwing for i in range(200): cmd.mset(str(i),str(i)) cmd.mdo(1, "color yellow") cmd.mdo(101, "color red") mplay cheers, Abhi Abhinav Verma Postdoc, University of Washington, Seattle WA On 8/29/07, Nicola Giacch=E8 <ni...@ch...> wrote: > > Hi, > it is possible to have frames with different colors of pdb structure? > for example from 1 to 100 frames the structure must be yellow whereas > from 101 to 200 the structure must be red... > thanks, > Nicola > > -- > Nicola Giacch=E8, > > PhD Student > Bachelor Degree in Medicinal Chemistry and Technology of Drugs > > University of Perugia > Department of Medicinal Chemistry and Technology of Drugs > Via del Liceo, 1 - 06123 Perugia (Italy) > Tel ++39 075 585 5169/5156 > E-mail: ni...@ch... > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Stuart Endo-S. <stu...@du...> - 2007-08-29 18:33:27
|
> unbond selection1, selection2 On Wednesday 29 August 2007 18:16, th...@br... wrote: > Hi, > > I am modeling both an ADP and an AMP molecules in the same binding > site for my enzyme; occupancy at 50%. I am trying to represent both > molecules as sticks however pymol connects the atoms that ADP atoms to > the AMP atoms in addition to the correct intramolecular bonds. Is > there a way to prevent this from happening? > > I have tried renumbering the two molecules but that doesn't seem to > work either. > > Thanks in advance for any assistance. > Vu > > Here is the pdb for the ligand: > > ATOM 3317 O2A ADP C 300 -12.891 -31.977 0.219 0.50 13.89 > O ATOM 3318 PA ADP C 300 -11.985 -31.320 -0.791 0.50 11.99 > P ATOM 3319 O1A ADP C 300 -11.373 -29.973 -0.515 0.50 13.45 > O ATOM 3320 O3A ADP C 300 -12.595 -31.241 -2.295 0.50 15.19 > O ATOM 3321 PB ADP C 300 -14.063 -31.588 -2.912 0.50 > 15.05 P ATOM 3322 O3B ADP C 300 -14.089 -33.099 -2.944 > 0.50 17.83 O ATOM 3323 O2B ADP C 300 -15.064 -31.025 > -1.914 0.50 18.59 O ATOM 3324 O1B ADP C 300 -14.162 > -30.895 -4.245 0.50 19.02 O ATOM 3325 O5* ADP C 300 > -10.845 -32.409 -1.042 0.50 9.81 O ATOM 3326 C5* ADP C 300 > -9.842 -32.119 -2.001 0.50 10.91 C ATOM 3327 C4* ADP C > 300 -8.684 -33.087 -1.844 0.50 9.33 C ATOM 3328 C3* > ADP C 300 -9.032 -34.573 -1.896 0.50 9.63 C ATOM 3329 > O3* ADP C 300 -9.242 -35.052 -3.249 0.50 8.90 O ATOM > 3330 C2* ADP C 300 -7.855 -35.160 -1.134 0.50 8.90 C > ATOM 3331 O2* ADP C 300 -6.678 -35.178 -1.953 0.50 9.51 > O ATOM 3332 C1* ADP C 300 -7.612 -34.116 -0.038 0.50 8.69 > C ATOM 3333 O4* ADP C 300 -8.058 -32.876 -0.567 0.50 10.93 > O ATOM 3334 N9 ADP C 300 -8.485 -34.447 1.112 0.50 8.22 > N ATOM 3335 C4 ADP C 300 -8.437 -35.592 1.790 0.50 > 8.39 C ATOM 3336 C5 ADP C 300 -9.471 -35.475 2.807 > 0.50 8.12 C ATOM 3337 N7 ADP C 300 -10.034 -34.267 > 2.665 0.50 7.40 N ATOM 3338 C8 ADP C 300 -9.438 > -33.647 1.622 0.50 8.88 C ATOM 3339 N3 ADP C 300 > -7.686 -36.716 1.682 0.50 7.55 N ATOM 3340 C2 ADP C 300 > -7.900 -37.723 2.547 0.50 7.99 C ATOM 3341 N1 ADP C > 300 -8.847 -37.696 3.503 0.50 7.64 N ATOM 3342 C6 > ADP C 300 -9.652 -36.630 3.682 0.50 8.15 C ATOM 3343 > N6 ADP C 300 -10.592 -36.602 4.662 0.50 6.97 N ATOM > 3344 O3P AMP C 300 -12.386 -32.366 -2.017 0.50 15.02 O > ATOM 3345 P AMP C 300 -11.925 -31.677 -0.753 0.50 10.92 > P ATOM 3346 O1P AMP C 300 -11.847 -30.186 -0.880 0.50 11.64 > O ATOM 3347 O2P AMP C 300 -12.551 -32.108 0.554 0.50 9.93 > O ATOM 3348 O5* AMP C 300 -10.360 -32.000 -0.546 0.50 11.26 > O ATOM 3349 C5* AMP C 300 -9.423 -31.767 -1.590 0.50 > 10.64 C ATOM 3350 C4* AMP C 300 -8.421 -32.915 -1.587 > 0.50 11.52 C ATOM 3351 C3* AMP C 300 -9.037 -34.271 > -1.900 0.50 11.54 C ATOM 3352 O3* AMP C 300 -9.264 > -34.467 -3.299 0.50 13.20 O ATOM 3353 C2* AMP C 300 > -8.024 -35.226 -1.313 0.50 10.05 C ATOM 3354 O2* AMP C 300 > -6.891 -35.236 -2.197 0.50 11.30 O ATOM 3355 C1* AMP C > 300 -7.642 -34.492 -0.031 0.50 10.00 C ATOM 3356 O4* > AMP C 300 -7.815 -33.102 -0.294 0.50 9.81 O ATOM 3357 > N9 AMP C 300 -8.539 -34.824 1.112 0.50 8.85 N ATOM > 3358 C4 AMP C 300 -8.487 -35.983 1.773 0.50 8.44 C > ATOM 3359 C5 AMP C 300 -9.484 -35.904 2.839 0.50 7.99 > C ATOM 3360 N7 AMP C 300 -10.054 -34.689 2.756 0.50 8.54 > N ATOM 3361 C8 AMP C 300 -9.465 -34.047 1.707 0.50 10.10 > C ATOM 3362 N3 AMP C 300 -7.745 -37.107 1.621 0.50 9.33 > N ATOM 3363 C2 AMP C 300 -7.922 -38.163 2.444 0.50 > 10.24 C ATOM 3364 N1 AMP C 300 -8.841 -38.161 3.428 > 0.50 9.63 N ATOM 3365 C6 AMP C 300 -9.634 -37.099 > 3.677 0.50 9.56 C ATOM 3366 N6 AMP C 300 -10.544 > -37.126 4.684 0.50 8.49 C > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users -- ______________________________________ Stuart T. Endo-Streeter Structural Biology and Biophysics Dept. Biochemistry LSRC C266 Duke University 919-681-1668 stu...@du... |
From: <th...@br...> - 2007-08-29 18:16:30
|
Hi, I am modeling both an ADP and an AMP molecules in the same binding =20 site for my enzyme; occupancy at 50%. I am trying to represent both =20 molecules as sticks however pymol connects the atoms that ADP atoms to =20 the AMP atoms in addition to the correct intramolecular bonds. Is =20 there a way to prevent this from happening? I have tried renumbering the two molecules but that doesn't seem to =20 work either. Thanks in advance for any assistance. Vu Here is the pdb for the ligand: ATOM 3317 O2A ADP C 300 -12.891 -31.977 0.219 0.50 13.89 = O ATOM 3318 PA ADP C 300 -11.985 -31.320 -0.791 0.50 11.99 = P ATOM 3319 O1A ADP C 300 -11.373 -29.973 -0.515 0.50 13.45 = O ATOM 3320 O3A ADP C 300 -12.595 -31.241 -2.295 0.50 15.19 = O ATOM 3321 PB ADP C 300 -14.063 -31.588 -2.912 0.50 15.05 = P ATOM 3322 O3B ADP C 300 -14.089 -33.099 -2.944 0.50 17.83 = O ATOM 3323 O2B ADP C 300 -15.064 -31.025 -1.914 0.50 18.59 = O ATOM 3324 O1B ADP C 300 -14.162 -30.895 -4.245 0.50 19.02 = O ATOM 3325 O5* ADP C 300 -10.845 -32.409 -1.042 0.50 9.81 = O ATOM 3326 C5* ADP C 300 -9.842 -32.119 -2.001 0.50 10.91 = C ATOM 3327 C4* ADP C 300 -8.684 -33.087 -1.844 0.50 9.33 = C ATOM 3328 C3* ADP C 300 -9.032 -34.573 -1.896 0.50 9.63 = C ATOM 3329 O3* ADP C 300 -9.242 -35.052 -3.249 0.50 8.90 = O ATOM 3330 C2* ADP C 300 -7.855 -35.160 -1.134 0.50 8.90 = C ATOM 3331 O2* ADP C 300 -6.678 -35.178 -1.953 0.50 9.51 = O ATOM 3332 C1* ADP C 300 -7.612 -34.116 -0.038 0.50 8.69 = C ATOM 3333 O4* ADP C 300 -8.058 -32.876 -0.567 0.50 10.93 = O ATOM 3334 N9 ADP C 300 -8.485 -34.447 1.112 0.50 8.22 = N ATOM 3335 C4 ADP C 300 -8.437 -35.592 1.790 0.50 8.39 = C ATOM 3336 C5 ADP C 300 -9.471 -35.475 2.807 0.50 8.12 = C ATOM 3337 N7 ADP C 300 -10.034 -34.267 2.665 0.50 7.40 = N ATOM 3338 C8 ADP C 300 -9.438 -33.647 1.622 0.50 8.88 = C ATOM 3339 N3 ADP C 300 -7.686 -36.716 1.682 0.50 7.55 = N ATOM 3340 C2 ADP C 300 -7.900 -37.723 2.547 0.50 7.99 = C ATOM 3341 N1 ADP C 300 -8.847 -37.696 3.503 0.50 7.64 = N ATOM 3342 C6 ADP C 300 -9.652 -36.630 3.682 0.50 8.15 = C ATOM 3343 N6 ADP C 300 -10.592 -36.602 4.662 0.50 6.97 = N ATOM 3344 O3P AMP C 300 -12.386 -32.366 -2.017 0.50 15.02 = O ATOM 3345 P AMP C 300 -11.925 -31.677 -0.753 0.50 10.92 = P ATOM 3346 O1P AMP C 300 -11.847 -30.186 -0.880 0.50 11.64 = O ATOM 3347 O2P AMP C 300 -12.551 -32.108 0.554 0.50 9.93 = O ATOM 3348 O5* AMP C 300 -10.360 -32.000 -0.546 0.50 11.26 = O ATOM 3349 C5* AMP C 300 -9.423 -31.767 -1.590 0.50 10.64 = C ATOM 3350 C4* AMP C 300 -8.421 -32.915 -1.587 0.50 11.52 = C ATOM 3351 C3* AMP C 300 -9.037 -34.271 -1.900 0.50 11.54 = C ATOM 3352 O3* AMP C 300 -9.264 -34.467 -3.299 0.50 13.20 = O ATOM 3353 C2* AMP C 300 -8.024 -35.226 -1.313 0.50 10.05 = C ATOM 3354 O2* AMP C 300 -6.891 -35.236 -2.197 0.50 11.30 = O ATOM 3355 C1* AMP C 300 -7.642 -34.492 -0.031 0.50 10.00 = C ATOM 3356 O4* AMP C 300 -7.815 -33.102 -0.294 0.50 9.81 = O ATOM 3357 N9 AMP C 300 -8.539 -34.824 1.112 0.50 8.85 = N ATOM 3358 C4 AMP C 300 -8.487 -35.983 1.773 0.50 8.44 = C ATOM 3359 C5 AMP C 300 -9.484 -35.904 2.839 0.50 7.99 = C ATOM 3360 N7 AMP C 300 -10.054 -34.689 2.756 0.50 8.54 = N ATOM 3361 C8 AMP C 300 -9.465 -34.047 1.707 0.50 10.10 = C ATOM 3362 N3 AMP C 300 -7.745 -37.107 1.621 0.50 9.33 = N ATOM 3363 C2 AMP C 300 -7.922 -38.163 2.444 0.50 10.24 = C ATOM 3364 N1 AMP C 300 -8.841 -38.161 3.428 0.50 9.63 = N ATOM 3365 C6 AMP C 300 -9.634 -37.099 3.677 0.50 9.56 = C ATOM 3366 N6 AMP C 300 -10.544 -37.126 4.684 0.50 8.49 = C |
From: <ni...@ch...> - 2007-08-29 14:26:49
|
Hi, it is possible to have frames with different colors of pdb structure? for example from 1 to 100 frames the structure must be yellow whereas from 101 to 200 the structure must be red... thanks, Nicola -- Nicola Giacchè, PhD Student Bachelor Degree in Medicinal Chemistry and Technology of Drugs University of Perugia Department of Medicinal Chemistry and Technology of Drugs Via del Liceo, 1 - 06123 Perugia (Italy) Tel ++39 075 585 5169/5156 E-mail: ni...@ch... |
From: Christian S. <ade...@go...> - 2007-08-29 12:21:52
|
Dear all, I was wondering whether Pymol could manage to generate bounding planes like Raster3D does, e.g. at http://skuld.bmsc.washington.edu/raster3d/html/r3d_hints.html It would be great for visualizing intramolecular channels! Thanks, christian -- Christian Stegmann Max-Planck Institute for Biophysical Chemistry Dept. Cellular Biochemistry / X-ray Crystallography Am Fassberg 11 37077 Goettingen, Germany Phone: +49-551-201-1068 Fax: +49-551-201-1197 |
From: aaron b. <br...@wi...> - 2007-08-28 20:13:56
|
normals appear to be still broken in VRML export. I have attached a simple test case that demonstrates this. The pdb file attached contains 1 atom at the origin. To reproduce the wrl file that I have attached, set the quality to best performance, turn on surface rendering of the molecule and export the wrl file. The resulting wrl file clearly has wrong normals both looking at it by hand an opening it up in deep exploration version 5 and looking at the normals. This is with the latest incentive build on OS X. aaron |
From: DeLano S. <de...@de...> - 2007-08-27 19:27:45
|
Patrick, To accomplish this, you must launch the program via command line with -X and -Y options specifying the cartesian coordinates of the window on the CRT. For example, if the CRT is off to the left, use something like: /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 -Y 100 Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:de...@de... _____ From: pym...@li... [mailto:pym...@li...] On Behalf Of Patrick Loll Sent: Monday, August 27, 2007 12:05 PM To: pym...@li... Subject: [PyMOL] More MacPro questions Thanks to all who offered help when I was trying to get hardware stereo working on my new MacPro. It appears that the two critical steps were 1) making certain that the refresh rate on the CRT was set to an appropriate value (default was too low) and 2) putting the Dock in the CRT window (when the Dock lives on the LCD I can only get . Now I have two more questions: 1) Does anyone know of a way to get the stereo to work when the Dock resides on the LCD? (This would seem to involve forcing the application to open on the CRT). After years of looking at nice LCDs, I hate to spend a lot of time looking at the CRT (unless I'm gazing at some beautiful molecule in stereo). 2) Is there some way to drag molecules when using the Mighty Mouse? Whenever I press the middle mouse button (scroll ball), the LH button is also depressed, and so I rotate instead of drag. Thanks, Pat ---------------------------------------------------------------------------- ----------- Patrick J. Loll, Ph. D. (215) 762-7706 Associate Professor FAX: (215) 762-4452 Department of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA pat...@dr... |
From: Patrick L. <pat...@dr...> - 2007-08-27 19:05:30
|
Thanks to all who offered help when I was trying to get hardware stereo working on my new MacPro. It appears that the two critical steps were 1) making certain that the refresh rate on the CRT was set to an appropriate value (default was too low) and 2) putting the Dock in the CRT window (when the Dock lives on the LCD I can only get . Now I have two more questions: 1) Does anyone know of a way to get the stereo to work when the Dock resides on the LCD? (This would seem to involve forcing the application to open on the CRT). After years of looking at nice LCDs, I hate to spend a lot of time looking at the CRT (unless I'm gazing at some beautiful molecule in stereo). 2) Is there some way to drag molecules when using the Mighty Mouse? Whenever I press the middle mouse button (scroll ball), the LH button is also depressed, and so I rotate instead of drag. Thanks, Pat ------------------------------------------------------------------------ --------------- Patrick J. Loll, Ph. D. (215) 762-7706 Associate Professor FAX: (215) 762-4452 Department of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA pat...@dr... |
From: DeLano S. <de...@de...> - 2007-08-25 00:34:59
|
Patrick, Please use the Display panel in System Preferences to confirm that the CRT monitor is configured for a high refresh rate (100 Hz or better). By default, MacPyMOL won't open a stereo context if the refresh rate is too low. However, you can indeed force use of a stereo context with the -S option (hypen capital S). Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:de...@de... "Not yet a PyMOL Subscriber, but want to support the project? Email sa...@de... to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor!" -WLD _____ From: pym...@li... [mailto:pym...@li...] On Behalf Of Patrick Loll Sent: Friday, August 24, 2007 3:01 PM To: pym...@li... Subject: [PyMOL] stereo on MacPro, part deux OK, so I AM stupid, and /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL IS the path to an executable. It still remains that I don't get stereo... ---------------------------------------------------------------------------- ----------- Patrick J. Loll, Ph. D. (215) 762-7706 Associate Professor FAX: (215) 762-4452 Department of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA pat...@dr... |
From: Patrick L. <pat...@dr...> - 2007-08-24 22:01:09
|
OK, so I AM stupid, and /Applications/MacPyMOL.app/Contents/MacOS/ MacPyMOL IS the path to an executable. It still remains that I don't get stereo... ------------------------------------------------------------------------ --------------- Patrick J. Loll, Ph. D. (215) 762-7706 Associate Professor FAX: (215) 762-4452 Department of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA pat...@dr... |
From: Patrick L. <pat...@dr...> - 2007-08-24 21:55:41
|
OK, I've got my spanking new Mac Pro with the (very expensive) NVIDIA Quadro FX 4500 and I bought a shiny new ViewSonic G225f to augment my LCD display. I plug in the Stereographics E2 emitter...and now what? I'm not getting hardware stereo (which isn't surprising, it surely couldn't be that easy), but I'm not finding a lot of guidance about what it is I need to do. One question is whether I have the appropriate build. This is what comes up in the text window when I launch: This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6 I do find this comment on the Wiki: "The trick to getting MacPyMOL to work in stereo on the second monitor is to force it to initially open on that display by providing an appropriate "-X #" (and perhaps -Y #) option on launch. That way the OpenGL context will be created with stereo support. ./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 ./MacPyMOL.app/Contents/MacOS/MacPyMOL -X -1000 -Y 100" But I don't understand the syntax. This is invoked from the command line, I assume, but ./something.app/somethingelse doesn't look like the path to an executable to me...If I simply try ./ MacPyMOL.app -X 1000, I get back "Permission denied." My apologies if I'm being unusually stupid. The emitter worked when last tested (a month or so ago, on an SGI). Pat ------------------------------------------------------------------------ --------------- Patrick J. Loll, Ph. D. (215) 762-7706 Associate Professor FAX: (215) 762-4452 Department of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA pat...@dr... |
From: Robert C. <rob...@qu...> - 2007-08-23 20:46:52
|
Hi Abhi, On Thu, 23 Aug 2007 12:51:10 -0700, Abhinav Verma <abh...@gm...> wrote: > I want to align different models of a multimodel pdb file. > > How can I do that without extracting models as identical pdb. > > cheers, > Abhi Try the intra_fit command. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |
From: Abhinav V. <abh...@gm...> - 2007-08-23 19:51:09
|
I want to align different models of a multimodel pdb file. How can I do that without extracting models as identical pdb. cheers, Abhi |
From: Gianluigi C. <chi...@ya...> - 2007-08-23 10:06:20
|
What about the possibility to show the surfaces of just a selection of resi= dues?=0AThank You,=0A=0AGianluigi Caltabiano, Ph.D.=0ALab of Computational = Medicine=0AAutonomic University of Barcelona=0ASpain=0A=0A----- Messaggio o= riginale -----=0ADa: Michael Lerner <mgl...@gm...>=0AA: pymol-users@l= ists.sourceforge.net=0AInviato: Gioved=EC 9 agosto 2007, 23:23:39=0AOggetto= : [PyMOL] Are there any feature requests for the PyMOL-APBS plugin?=0A=0AHi= ,=0A=0AI'm working on an update to the PyMOL-APBS plugin. Are there any=0Af= eatures that you would like to see included? As an example, I'm=0Aincluding= the ability to use PDB2PQR to generate PQR files in the next=0Aversion. Pl= ease request anything you'd like, no matter how=0Atrivial/difficult you thi= nk it might be to implement (that's not a=0Apromise that I'll implement it = .. just that I'll consider it :) ).=0A=0AThanks,=0A=0A-Michael Lerner=0A=0A= -- =0ABiophysics Graduate Student=0ACarlson Lab, University of Michigan=0Ah= ttp://www.umich.edu/~mlerner=0A=0A-----------------------------------------= --------------------------------=0AThis SF.net email is sponsored by: Splun= k Inc.=0AStill grepping through log files to find problems? Stop.=0ANow Se= arch log events and configuration files using AJAX and a browser.=0ADownloa= d your FREE copy of Splunk now >> http://get.splunk.com/=0A_______________= ________________________________=0APyMOL-users mailing list=0APyMOL-users@l= ists.sourceforge.net=0Ahttps://lists.sourceforge.net/lists/listinfo/pymol-u= sers=0A=0A=0A=0A=0A=0A=0A=0A ___________________________________ =0AL'= email della prossima generazione? Puoi averla con la nuova Yahoo! Mail: htt= p://it.docs.yahoo.com/nowyoucan.html |
From: shivesh k. <shi...@ya...> - 2007-08-17 16:15:21
|
Dear all, I have to show the electron density at two different positions in the structure, wheree two residues are interacting.I have made the object.I load the 2fofc.xplor.and given the isomesh m1,map1,1.0,(A.......),carve=2.0.I can select either the whole chainA or a particular residue,it shows the Electron density map.But,how can I get the density at two different residues which are apart from each other coming closer in 3D structure,and interacting. All suggestions are welcome.Thanx in advance. Shivesh Kumar shivesh --------------------------------- Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase. |
From: DeLano S. <de...@de...> - 2007-08-17 01:30:21
|
> The goal is > to produce a Pymol that uses native Windows graphics, not one > that requires X11. David, Please note that the goal behind Open-Source PyMOL (as maintained by DeLano Scientific LLC) is to enable compilation under open-source operating systems, and primarily, Linux with X11/GLUT. It not our current intent to support, assist, or encourage native compilation of PyMOL open-source code on closed-source operating systems, despite the fact that such compilation is deliberately permitted under the unrestrictive open-source license terms. An open-source version targeting native Windows (via any means) would necessarily comprise a fork of the project. Since such a fork would provide a realistic alternative to DeLano Scientific LLC's precompiled incentive builds for Windows, it could jeopardize our ability to continue funding development of the open-source code. If PyMOL revenues were imperiled, then to make ends meet, DeLano Scientific LLC would have no choice but to redirect development efforts into proprietary assets, significantly curtailing participation in the unrestricted open-source project. At the very least, our unrestrictive open-source license would have to be restricted in future versions, thus defeating one of the primary aims of the project. We don't want that... do you? If not, then proceed down this path only with due care and consideration of the possible consequences. Given enough effort, native compilation is certainly do-able, but it is not intended to be easy... nor commonplace. To the extent that you achieve your goal, please do think twice before publicly sharing the fruits and/or details of that success. We would naturally prefer that such accomplishments remain private, since the future of PyMOL could well depend upon it. With great freedom comes great responsibility! ;) Warren L. DeLano DeLano Scientific LLC > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf > Of David Mathog > Sent: Thursday, August 16, 2007 12:14 PM > To: pym...@li... > Subject: [PyMOL] Building pymol on Windows? > > Since building under Mingw is turning out to be nontrivial, > let me broaden the question slightly. How does one build > PyMol from source (via subversion) on Windows? The goal is > to produce a Pymol that uses native Windows graphics, not one > that requires X11. > > Other than Warren, has anybody successfully built PyMol on Windows? > If so, please let us know how it was done. > > Thanks, > > David Mathog > ma...@ca... > Manager, Sequence Analysis Facility, Biology Division, Caltech |
From: David M. <ma...@ca...> - 2007-08-16 22:24:15
|
For some reason or other it blows up at "import pymol" in __init__.py. Or maybe I'm using IDLE wrong? Anyway, after observing that all pymol.bat did was: "c:\progs\python25\python.exe" "c:\progs\python25\lib\site-packages\pymol\__init__.py" %1 %2 %3 %4 %5 %6 %7 %8 %9 I tried: run -> programs -> python -> idle Then used the path browser to find the __init__.py file above, Then used the debugger to step along until it messed up, which took place at line 157, which is the last line of this section if try_again: try: sys.exc_clear() sys.path.insert(0,os.path.dirname(os.path.dirname(__file__))) except: pass import pymol Any ideas? The files on the linux system here: /usr/lib/python2.5/site-packages/pymol seem to be 1:1 with the ones on the Windows system here: /c/progs/python25/lib/site-packages/pymol That is, same number of files, and the names are all the same except .so on linux became .pyd on Windows. I also tried just loading __init__.py in idle then running it without the debugger. That does this instead: Traceback (most recent call last): File "C:\progs\Python25\lib\site-packages\pymol\__init__.py", line 167, in <module> import pymol File "C:\progs\Python25\lib\site-packages\pymol\__init__.py", line 396, in <module> import _cmd ImportError: DLL load failed: The specified module could not be found. >>> Which is a similar sort of message, albeit with a different line number. This one looks like pymol won't import because _cmd wouldn't import, because it couldn't be found. But there is a _cmd.pyd (as there is a _cmd.so on linux), yet it isn't found for some reason. The latter is a lot bigger though, at 11.1Mb whereas the former is only 2.0 Mb. I tried copying _cmd.pyd to the python DLLs directory, but that didn't help. Any ideas? So close, and yet, so far... Thanks, David Mathog ma...@ca... Manager, Sequence Analysis Facility, Biology Division, Caltech |
From: David M. <ma...@ca...> - 2007-08-16 19:14:17
|
Since building under Mingw is turning out to be nontrivial, let me broaden the question slightly. How does one build PyMol from source (via subversion) on Windows? The goal is to produce a Pymol that uses native Windows graphics, not one that requires X11. Other than Warren, has anybody successfully built PyMol on Windows? If so, please let us know how it was done. Thanks, David Mathog ma...@ca... Manager, Sequence Analysis Facility, Biology Division, Caltech |
From: David M. <ma...@ca...> - 2007-08-16 19:06:21
|
I'm working on the same thing, without getting to a working pymol yet though. Here's what I've done so far: 1. installed mingw and msys, also 4.2.1 gcc 2. made /mingw/bin/gcc.exe the 4.2.1 gcc 3. built and installed zlib, using ./configure --prefix=/mingw 4. built and installed pnglib, using ./configure --prefix=/mingw 5. Obtained the current branch of pymol on a linux system with subversion with: svn co \ https://pymol.svn.sourceforge.net/svnroot/pymol/branches/b10 \ pymol made a .tar.gz and transferred it to the mingw environment. 6. cd pymol* 7. modified setup.py. It thinks this is a "win32" system, which is a problem, since it keeps making Visual C specific assumptions even when "-c mingw32" is used. Anyway, changed the win32 section of setup.py to this: if sys.platform=='win32': inc_dirs=["ov/src", "layer0","layer1","layer2", "layer3","layer4","layer5", "others"] libs=["opengl32","glu32","png","z"] pyogl_libs = ["opengl32","glu32"] lib_dirs=["/mingw/lib"] def_macros=[("_PYMOL_MODULE",None), ("WIN32",None), ("_HAVE_LIBPNG",None), ("_STDCALL_SUPPORTED",None), ("_M_IX86",None) ] ext_comp_args=[] ext_link_args=["glut32.lib"] 8. Removed the include of winappc.h from layer1/P.c. That is a VisualC++ include. Since we aren't using VisualC, the include is not needed. 9. Put glut.h in /pymol/others/GL/glut.h 10. put glut32.lib and glut32.dll in /pymol. (Note, see: http://www.mingw.org/MinGWiki/index.php/Glut I have a positive control with the pulsar.c program that this glut works within mingw to produce programs capable of showing stereo, ie gcc -D_STDCALL_SUPPORTED -D_M_IX86 -I. -o pulsar.exe pulsar.c glut32.lib -lopengl32 -lglu32 where pulsar.c is from http://local.wasp.uwa.edu.au/~pbourke/projection/stereorender/pulsar.c ) 11. export PATH=$PATH:/c/progs/python25 (wherever you have python installed. This is the WINDOWS version of python that installs with an .msi, from www.python.org). Your path will probably differ. 12. Create a pydistutils.cfg, otherwise the "install" step won't work, as Python was built with VisualC++ and install won't accept a "-c mingw32" modifier: cd ~ cat >pydistutils.cfg <<EOD [build] compiler=mingw32 EOD 13. Now in an MSYS window try to build: cd pymol* python setup.py build 2>xpbuild_stderr_step1_phase1.log | tee xpbuild_step1_phase1.log which will run along fine until it tries to build _glut.pyd. The problem is that it needs to include glut32.def but the Python build mechanism doesn't recognize this as a link step, so it ignores the ext_link_args value in setup.py. I could not find a workaround. So I opened a DOS window, changed directory to the top of pymol, cut the command from the MSYS window, pasted it into the DOS window, added glut32.def on the end, and ran it. As expected, it completed correctly. Then resumed building with: python setup.py build 2>xpbuild_stderr_step1_phase2.log | tee xpbuild_step1_phase2.log and it went to the end. There are a LOT of warnings in there though. Most involve ignored pragmas and variables declared but not used in glut.h, such as: xpbuild_stderr_step1_phase1_try1.log:others/GL/glut.h:503: warning: 'glutCreateWindow_ATEXIT_HACK' defined but not used However, there were 33 uninitialized variable warnings, and some incompatible pointer types. I'll have to look at those regions of the code. 14. Next do the installation steps: python setup.py install 2>xpbuild_stderr_step2.log | tee xpbuild_step2.log python setup2.py build 2>xpbuild_stderr_step3.log | tee xpbuild_step3.log And voila! A nonworking pymol :-( Double clicking on pymol.bat resulted in a "This application has failed to start because libpng-3.dll was not found." Well libpng-3.dll was in /mingw/bin, so it was copied to /c/progs/python25/DLLs and /mingw/lib Neither of which helped. Finally, it was copied to the same directory as pymol.bat. Now when it starts (double click on pymol.bat) it comes up a bit farther. It: 1. puts up the copyright notice, and gets down to the PyMol>_ prompt. 2. The rest of the first window (the right side, with what looks like sound player control buttons along the bottom) comes up. However the Tcl/Tk GUI part never starts. Python 2.5.1 definitely includes both of those, and Pmw is installed. I built the same version (rev 3028 from subversion) on linux and it had many fewer warnings and of course ran without problems. It was the same version of Python on both platforms, but gcc 4.1.2 on Linux and 4.2.1-sjlj on Mingw. I suspect platform specific changes in types, as caught by the various warning messages noted above. Anybody know a way to force pymol to run in a mode that will give some hint as to where this is going wrong? How does one start pymol up within Idle? Thanks, David Mathog ma...@ca... Manager, Sequence Analysis Facility, Biology Division, Caltech |
From: Julien M. <jul...@ya...> - 2007-08-16 14:25:35
|
Hi there,=0A=0AI have trouble to have a correct display with pymol under Ub= untu Feisty Fawn with fresh Compiz-Fusion install. =0A=0AWhen I launch pymo= l, the gui is ok, but the pymol viewer window has no decoration, and cannot= be moved or resized, and the display disapear when it has not the focus ! = Everything is ok under metacity window manager. Does anyone have the same p= roblem ?=0A=0Athanks in advance.=0A=0ABest regards.=0A=0APymol version: 0.9= 9rc6=0ASystem Ubuntu Linux Feisty Fawn=0A =0A--=0AJulien Maupetit >> http:/= /www.galadalfos.org <<=0A=0A=0A=0A=0A ________________________________= _____________________________________________ =0ANe gardez plus qu'une seul= e adresse mail ! Copiez vos mails vers Yahoo! Mail |