[PyMOL] surface/grid questions
Dear all, My name is Marcelo and I am a basic-level pymol user. I work with docking programs and I am trying to make pymol our default program for analysing docking results...this brings me to some questions: Is it possible to colour protein surface according to Hydrogen donor/acceptor properties in pymol ? Does Pymol computes a ligand-protein interface (for example just the contact area between the ligand and the protein)? is it possible to see just this surface area according to the previous question schema ? Does pymol read grid (Goodford's grids) ? in case not, how can I convert GRID maps into something pymol can read ? Thanks a lot Marcelo
Re: [PyMOL] raytraced labels
What I did so that I could use the labels command was read the coordinates in twice. One copy was used for display, the second copy had no atoms/representations displays, but instead I attatched labels to the atoms on the second copy and then moved these atoms around (and thusly the labels) till the label were visible and well oriented. I have to admit though, once you raytrace the labels become almost unreadable and I think I will end up using them only to help me to position the final labels in a picture editing program... Robert PS: Here is an example of what I mean: #read in PDB file with dummy name to move around atom-labels set label_color,black load a.pdb, label (///A/GLN`112/CA) ," %s-%s" % (resn,resi) translate [-1,0,0],///A/GLN`112/CA Ingo P. Korndoerfer: > >hello everybody, > >shouldn't it be possible to extract the proper rotation for the cgo >labels >from the view matrix ? > >i have been trying arount a few things, but was not so succesful so far. > >my idea was, to > >- extract the coordinates of the atom i want from the pdb file. either >from within pymol or in an external python script. >- put a label at those positions >- move the label to the origin. >- apply the inverse of the rotational part of the view matrix >- move the label back to were it came from >- and then adjust the wee little offsets for better image clarity >manually (try and error, as in molscript). > >or is that not possible ? > >from what i have seen, i can not apply a matrix directly to the cgo >objects, >but would have to convert the matrix to three succesive rotations around >x, y and z. > >also, moving the label to the origin, rotating and moving it back >afterwards >did not have quite the effect i was anticipating. i.e., it looked the >same, as rotating in place. >in particular, the label got moved a significant way off ... > >would anybody have any insights he would like to share ... > >putting in the labess in illustrator or gimp afterwards is way too >cumbersome ... > >1000 thanks for your help > >ingo ___ Robert Lucas rlu...@alumni.uci.edu Department of BiochemistryPhone: (206) 616-4510 HHMI & Univ. of WashingtonFax: (206) 685-7002 Health Science Bldg., Room K-428 Box 357742, Seattle, WA 98195 ___
Re: [PyMOL] rms commands
Hi, I could be wrong about this, but there are a couple of very picky alignment/fitting commands in PyMOL, and I think this is one of them. If it's one of the picky ones, it'll only work if everything about the two selections looks the same. In this case, your residue ids don't match up. Can you try alter object1, resi=int(resi)+10 rms_cur (object1 and i. 30:39 and (name c,o,n,ca)), (object2 and i. 30:39 and (name c,o,n,ca)) to make sure that the residue ids match first? -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich On Mon, 23 Aug 2004, Andreas [ISO-8859-1] Förster wrote: > Hey all, > > just the other day I discovered a nifty command in pymol. >rms_cur selection1, selection2 > determines the deviation between two (previously aligned) selections > without doing a fit. Here's what I do: >rms_cur (object1 and i. 20:29 and (name c,o,n,ca)), (object2 and i. > 30:39 and (name c,o,n,ca)) > > Hmmm, doesn't work. Error: >ExecutiveRMS-Error: No atoms selected. > > OK, differnt try (debugging for beginners): >select selection1, (object1 and i. 20:29 and (name c,o,n,ca)) > > So far so good. Feedback: >Selector: selection "selection1" defined with 40 atoms. > > And again: >select selection2, (object2 and i. 30:39 and (name c,o,n,ca)) > > Good again. Feedback: >Selector: selection "selection1" defined with 40 atoms. > > Now I go for gold: >rms_cur selection1, selection2 > > Arrgh, bummer: >ExecutiveRMS-Error: No atoms selected. > > > What am I doing wrong?? I'm using pymol 0.95 under WinXPpro and pymol > 0.95rh9 under linux/FC2. > > > Andreas > > > -- > Andreas Förster > Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg. > Salt Lake City, UT 84132, phone: 001.801.585.3919 > home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529 > http://www.biochem.utah.edu/~andreas > > > > --- > SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media > 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33 > Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift. > http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285 > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > >
[PyMOL] rms commands
Hey all, just the other day I discovered a nifty command in pymol. rms_cur selection1, selection2 determines the deviation between two (previously aligned) selections without doing a fit. Here's what I do: rms_cur (object1 and i. 20:29 and (name c,o,n,ca)), (object2 and i. 30:39 and (name c,o,n,ca)) Hmmm, doesn't work. Error: ExecutiveRMS-Error: No atoms selected. OK, differnt try (debugging for beginners): select selection1, (object1 and i. 20:29 and (name c,o,n,ca)) So far so good. Feedback: Selector: selection "selection1" defined with 40 atoms. And again: select selection2, (object2 and i. 30:39 and (name c,o,n,ca)) Good again. Feedback: Selector: selection "selection1" defined with 40 atoms. Now I go for gold: rms_cur selection1, selection2 Arrgh, bummer: ExecutiveRMS-Error: No atoms selected. What am I doing wrong?? I'm using pymol 0.95 under WinXPpro and pymol 0.95rh9 under linux/FC2. Andreas -- Andreas Förster Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg. Salt Lake City, UT 84132, phone: 001.801.585.3919 home: 465 3rd Av, SLC, UT 84103, 001.801.364.0529 http://www.biochem.utah.edu/~andreas
[PyMOL] raytraced labels
hello everybody, shouldn't it be possible to extract the proper rotation for the cgo labels from the view matrix ? i have been trying arount a few things, but was not so succesful so far. my idea was, to - extract the coordinates of the atom i want from the pdb file. either from within pymol or in an external python script. - put a label at those positions - move the label to the origin. - apply the inverse of the rotational part of the view matrix - move the label back to were it came from - and then adjust the wee little offsets for better image clarity manually (try and error, as in molscript). or is that not possible ? from what i have seen, i can not apply a matrix directly to the cgo objects, but would have to convert the matrix to three succesive rotations around x, y and z. also, moving the label to the origin, rotating and moving it back afterwards did not have quite the effect i was anticipating. i.e., it looked the same, as rotating in place. in particular, the label got moved a significant way off ... would anybody have any insights he would like to share ... putting in the labess in illustrator or gimp afterwards is way too cumbersome ... 1000 thanks for your help ingo
[PyMOL] Fast Coloring
I am working on a plugin that entails coloring residues based on a value. Right now creating a new color for each residue and setting the color corresponding works, BUT it is very inefficient and takes more than a tolerable amount of time to display. Is there a better approach? It is possible to assign a procedural color to the protein? Thanks, Charlie
Re: [PyMOL] PyMOL tutorial (moved and slightly updated)
On Fri, Aug 20, 2004 at 09:37:00AM -0700, chuit...@interchange.ubc.ca wrote: > >In any case, you ask a useful question: I too would like to know > >what license, if any, is granted by the tutorial's authors. If > >released under an appropriate license, it could be modified for > >Linux/Unix/MacOSX users, and used in course material, distributed > >with PyMOL, etc. > > I haven't really thought about licenses for releasing the tutorial > under, I'm not familiar with the different types of licenses. I would > like to see the tutorial treated as the program Having it under the same copyright license as pymol seems like a good idea to me. > where you can't sell it or claim you created it. Why do you think pymol cannot be sold? The copyright license does not seem to imply this[1], and such a restriction would render pymol not Open Source. Warren, can you tell us what you think on this? Michael [1] "Permission to use, copy, modify, distribute, and distribute modified versions of this software and its documentation for any purpose and without fee is hereby granted [...]"
