Re: [PyMOL] Trying to plug APBS into PyMOL for electrostatics (almost working)
> > What's the problem? Both PyMOL and APBS are licensed under the GPL so I > > see no problems there. > > Well, pymol isn't obviously. Note to self: Don't post about licensing > stuff after an evening of mulled wine. I've had an evening of nice port .. we'll see how a port-influenced evening compares to a mulled-wine-influenced evening :). > Still, as long as the pymol license is GPL-compatible (which I believe > it is, but I'm no lawyer), and the additional code is licensed under the > same license, it should be alright, as I understand it. The potential problem is this: once I get this working, I want to give it to PyMOL. That way, I don't have to care about maintainance :). If I'm going to give it to PyMOL, I think it needs to use the PyMOL license, not the GPL. The license thing is probably not a big deal anyway. On the one hand, I'm not sure that anything I've done is actually forced to be GPL'd. On the other hand, it would probably take Warren all of an hour to re-create everything I've done. It took me a while because in addition to writing something that parses DX files, I had to figure out some of the PyMOL internals. And I'm slow :). Playing around with PyMOL is definately fun, though. -michael
Re: [PyMOL] Trying to plug APBS into PyMOL for electrostatics (almost working)
On Thu, Dec 18, 2003 at 12:26:48AM +0100, Michael Banck wrote: > On Wed, Dec 17, 2003 at 06:00:44PM -0500, Michael George Lerner wrote: > > I've gotten the code much closer to working. Also, I think it's factored > > well enough that most of it should be non-GPL-contaminated. After I > > actually get it working completely, I'll email the APBS folks to see if > > they care about licensing issues. > > What's the problem? Both PyMOL and APBS are licensed under the GPL so I > see no problems there. Well, pymol isn't obviously. Note to self: Don't post about licensing stuff after an evening of mulled wine. Still, as long as the pymol license is GPL-compatible (which I believe it is, but I'm no lawyer), and the additional code is licensed under the same license, it should be alright, as I understand it. sorry, Michael
Re: [PyMOL] Trying to plug APBS into PyMOL for electrostatics (almost working)
On Wed, Dec 17, 2003 at 06:00:44PM -0500, Michael George Lerner wrote: > I've gotten the code much closer to working. Also, I think it's factored > well enough that most of it should be non-GPL-contaminated. After I > actually get it working completely, I'll email the APBS folks to see if > they care about licensing issues. What's the problem? Both PyMOL and APBS are licensed under the GPL so I see no problems there. Do you imply that you want to license your own code under a non-GPL-compatible license? Why? Michael
RE: [PyMOL] Trying to plug APBS into PyMOL for electrostatics (almost working)
Hi again,
I've gotten the code much closer to working. Also, I think it's factored
well enough that most of it should be non-GPL-contaminated. After I
actually get it working completely, I'll email the APBS folks to see if
they care about licensing issues.
Right now, I can generate isomeshes and isosurfaces for methanol that look
reasonable (yay!). But I can't get the surface coloring to work. If I do
this:
load methanol.pdb
show surface, methanol
run cleanerDxMap.py # loads up my APBS-generated map
ramp_new e_lvl, map, [-10,0.00,10]
set surface_color, e_lvl, methanol
isosurf surfneg, map, -0.1
isomesh meshpos, map, 0.1
color red, surfneg
color blue, meshpos
I get a good looking mesh, a good looking isosurface, and a completely
white surface around methanol. dragging the limits on the map around to
really small things or really large things doesn't seem to help either.
Any quick guesses?
In case you have a little bit of spare time, I have two dumb sounding
questions:
1) What exactly is supposed to go into ObjectMapState->Dim?
At first, I thought it was just a list of three integers giving the map
dimensions (in grid points), but that doesn't seem to be the answer. When
I take a map that PyMOL generates for me (e.g. with
cmd.map_new("map","gaussian","0.1","methanol")) and print it out as a
Python list (using ObjectMapAsPyList, etc.), I get different results each
time the program is run.
2) What exactly is supposed to go into ObjectMapState->Field->Points?
I think it's just the x,y,z coordinates of the points starting at
minCorner and working up through maxCorner by incrementing z then y then x
([x1,y1,z1,x1,y1,z2,...]. But, when I first tried to set points myself, I
got a few things wrong .. it looks like n_dim is supposed to be 4. I had
guessed 3. It also looks like Dim should be four ints, the grid
dimensions followed by the number 3. Finally, it looks like stride should
be the normal stride followed by the base_size. What am I missing here?
Why is points a four-dimensional thing while data is a three-dimensional
thing?
thanks,
-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 Thu, 11 Dec 2003, Warren L. DeLano wrote:
> Michael,
>
> Impressive! I think you're one of the few people to delve into
> PyMOL's source like this.
>
> Obviously I'd be the best person to look at your code, but I'm
> crunched right now getting ready for this upcoming trip. Also, if the
> code is GPL-contaminated, then it can't be useful in the main version,
> but perhaps we can rewrite this cleanly later on. I can probably help
> you in January. What you've written sounds right...
>
> One thing I'd suggest for debugging in the meantime is that you
> use the isomesh or isosurface routines to explore what data is ending up
> in the Map, before trying to use the color ramps. There may also be
> some code in the chempy brick stuff which could serve as an example for
> populating the list.
>
> Cheers,
> Warren
>
> --
> mailto:war...@delanoscientific.com
> Warren L. DeLano, Ph.D.
> Principal Scientist
> DeLano Scientific LLC
> Voice (650)-346-1154
> Fax (650)-593-4020
>
>
>
Re: [PyMOL] assign secondary structure?
* Michael Bovee [2003-12-16 14:27] wrote: > Hmm. When I try this I get a syntax error: > __ > PyMOL>load EcHRSade.pdb > Executive: object "EcHRSade" created. > PyMOL>hide > PyMOL>show cartoon > PyMOL>dss EcHRSade > Traceback (most recent call last): > File "/sw/lib/pymol/modules/pymol/parser.py", line 251, in parse > exec(com2[nest]+"\n",pymol_names,pymol_names) > File "", line 1 > dss EcHRSade > ^ > SyntaxError: invalid syntax > _ > > I also get the error if I type on the command line "dss EcHRSade.pdb" > > Apparently pymol's dss works for others? Maybe a problem in the fink > package, or on my particular system? > I'm running the current fink package, 0.90-2, compiled from source on > my PBG3(Lombard/Bronze). I think this is the problem. The dss command was introduced in version 0.91. I think you need to upgrade. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
Re: [PyMOL] adjust surface?
On Wed, 2003-12-17 at 17:39, Scott Classen wrote: > Hi Ann, > you can set the radius of the "water" probe used to construct the > surface by setting solvent_radius to something smaller than 1.4. You > can either look in the pulldown menus for the settings panel to adjust > the value in a GUI or type: > Scott, I think that Ann wants a sphere radius larger than 1.4, since she is looking for a less detailed surface... reducing the probe radius will increase the amount of detail, or roughness (tending towards the vdw surface, for radius=0.0) Cheers, Paulo > set solvent_radius, 1.2in the text window. > > Good Luck > Scott > > On Dec 16, 2003, at 3:05 PM, Ann Mullin wrote: > > > Hello, > > > > I have been using PyMol for a few months now, and I am wondering if I > > can adjust the radius about which the surface is calculated. I have > > a very large protein (28,000 atoms) to model, and I would like to be > > able to create a more evenly rounded surface. Not "realistic" > > perhaps, but easier for students to see the larger view than marveling > > at all the nooks and crannies. All suggestions greatly appreciated. > > > > Ann > > > > > > Ann Mullin > > Cell and Molecular Biology Dept. > > Tulane University > > New Orleans, LA 70118-5698 > > 504-865-6742 (Ph) > > 504-865-6785 (FAX) > > amul...@tulane.edu > >Scott Classen, Ph.D. >ACS Postdoctoral Fellow >Department of Molecular & Cell Biology >University of California, Berkeley >237 Hildebrand Hall #3206 >Berkeley, CA 94720-3206 >LAB 510.643.9491 >FAX 510.643.9290 > -- Paulo Martel Dept. de Química e Bioquímica Faculdade de Ciências e Tecnologia Universidade do Algarve Campus de Gambelas, 8000-117 FARO Tel: 289800900 Ext.7402
Re: [PyMOL] adjust surface?
Hi Ann, you can set the radius of the "water" probe used to construct the surface by setting solvent_radius to something smaller than 1.4. You can either look in the pulldown menus for the settings panel to adjust the value in a GUI or type: set solvent_radius, 1.2in the text window. Good Luck Scott On Dec 16, 2003, at 3:05 PM, Ann Mullin wrote: Hello, I have been using PyMol for a few months now, and I am wondering if I can adjust the radius about which the surface is calculated. I have a very large protein (28,000 atoms) to model, and I would like to be able to create a more evenly rounded surface. Not "realistic" perhaps, but easier for students to see the larger view than marveling at all the nooks and crannies. All suggestions greatly appreciated. Ann Ann Mullin Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) amul...@tulane.edu Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular & Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290
