[PyMOL] ANNOUNCE: apropos command to lookup commands matching a keyword.
Hi there,
I have written a little utility called apropos[1] (after a unix command of the
same name) to help in locating commands that might do something
you want done. It is like the grepset[2] command except this one looks
up commands instead of settings.
[1] http://www.pymolwiki.org/index.php/Apropos
[2] http://www.pymolwiki.org/index.php/Grepset
Comments are welcome.
Have fun,
Zac
#
# apropos.py
# Author: Ezequiel Panepucci
# Date: 2006-07-20
#
from pymol import cmd
import re
def apropos(regexp=''):
'''
DESCRIPTION
"apropos" searches through the documentation of all currently
defined commands and lists those commands for which the keyword
is either contained in the documentation or matches the command
name itself.
If an appropriate "DESCRIPTION" section is provided in the documentation
of the command, the first 80 characters are listed as a summary.
USAGE
apropos [keyword or regexp]
EXAMPLE
apropos fit
###EXACT MATCH FOR: fit ==> try 'help fit' at the prompt.
###The following commands are NOT documented.
vdw_fit
###The following commands are documented. 'help command'
fit : "fit" superimposes the model in the first selection on to the model
intra_fit : "intra_fit" fits all states of an object to an atom selection
rms : "rms" computes a RMS fit between two atom selections, but does not
pair_fit : "pair_fit" fits a set of atom pairs between two models. Each atom
intra_rms_cur : "intra_rms_cur" calculates rms values for all states of an object
commands : >>>>>>>> Ooopsie, no DESCRIPTION found for this command!!! <<<<<<
zoom : "zoom" scales and translates the window and the origin to cover the
intra_rms : "intra_rms" calculates rms fit values for all states of an object
align : "align" performs a sequence alignment followed by a structural
rms_cur : "rms_cur" computes the RMS difference between two atom
fitting : "fitting" allows the superpositioning of object1 onto object2 using
SEE ALSO
grepset(www.pymolwiki.org), Python re module
'''
cmd.set("text","1",quiet=1)
count=0
docre = re.compile(regexp, re.MULTILINE | re.IGNORECASE)
cmdre = re.compile(regexp, re.IGNORECASE)
matches_with_help = []
matches_without_help = []
maxcclen=0
for cc in cmd.keyword:
if cc == regexp:
print '\n###EXACT MATCH FOR: %s ==> try \'help %s\' at the prompt.' % (cc,cc)
doc = cmd.keyword[cc][0].__doc__
if doc == None:
if re.search(regexp, cc, re.IGNORECASE):
count += 1
matches_without_help.append(cc)
continue
if re.search(regexp, doc, re.MULTILINE | re.IGNORECASE):
count += 1
if len(cc) > maxcclen:
maxcclen = len(cc)
docmatches = re.match(r"""^\s+DESCRIPTION\s+(.{0,80})\S*""", doc, re.IGNORECASE)
if docmatches == None:
desc = '>>>>>>>> Ooopsie, no DESCRIPTION found for this command!!! <<<<<<'
else:
desc = docmatches.groups()[0]
matches_with_help.append( (cc, desc ) )
if len(matches_without_help) > 0:
fmt = '%' + str(maxcclen) + 's' # get the width of the lenghtiest command in a format
print '\n###The following commands are NOT documented.\n'
for cc in matches_without_help:
print fmt % (cc)
if len(matches_with_help) > 0:
fmt = '%' + str(maxcclen) + 's : %s' # get the width of the lenghtiest command in a format
print '\n###The following commands are documented. \'help command\' \n'
for (cc,desc) in matches_with_help:
print fmt % (cc,desc)
cmd.extend('apropos',apropos)
[PyMOL] ANNOUNCE: apropos command to lookup commands matching a keyword.
Hi there,
I have written a little utility called apropos[1] (after a unix command of the
same name) to help in locating commands that might do something
you want done. It is like the grepset[2] command except this one looks
up commands instead of settings.
[1] http://www.pymolwiki.org/index.php/Apropos
[2] http://www.pymolwiki.org/index.php/Grepset
Comments are welcome.
Have fun,
Zac
#
# apropos.py
# Author: Ezequiel Panepucci
# Date: 2006-07-20
#
from pymol import cmd
import re
def apropos(regexp=''):
'''
DESCRIPTION
"apropos" searches through the documentation of all currently
defined commands and lists those commands for which the keyword
is either contained in the documentation or matches the command
name itself.
If an appropriate "DESCRIPTION" section is provided in the documentation
of the command, the first 80 characters are listed as a summary.
USAGE
apropos [keyword or regexp]
EXAMPLE
apropos fit
###EXACT MATCH FOR: fit ==> try 'help fit' at the prompt.
###The following commands are NOT documented.
vdw_fit
###The following commands are documented. 'help command'
fit : "fit" superimposes the model in the first selection on to the model
intra_fit : "intra_fit" fits all states of an object to an atom selection
rms : "rms" computes a RMS fit between two atom selections, but does not
pair_fit : "pair_fit" fits a set of atom pairs between two models. Each atom
intra_rms_cur : "intra_rms_cur" calculates rms values for all states of an object
commands : >>>>>>>> Ooopsie, no DESCRIPTION found for this command!!! <<<<<<
zoom : "zoom" scales and translates the window and the origin to cover the
intra_rms : "intra_rms" calculates rms fit values for all states of an object
align : "align" performs a sequence alignment followed by a structural
rms_cur : "rms_cur" computes the RMS difference between two atom
fitting : "fitting" allows the superpositioning of object1 onto object2 using
SEE ALSO
grepset(www.pymolwiki.org), Python re module
'''
cmd.set("text","1",quiet=1)
count=0
docre = re.compile(regexp, re.MULTILINE | re.IGNORECASE)
cmdre = re.compile(regexp, re.IGNORECASE)
matches_with_help = []
matches_without_help = []
maxcclen=0
for cc in cmd.keyword:
if cc == regexp:
print '\n###EXACT MATCH FOR: %s ==> try \'help %s\' at the prompt.' % (cc,cc)
doc = cmd.keyword[cc][0].__doc__
if doc == None:
if re.search(regexp, cc, re.IGNORECASE):
count += 1
matches_without_help.append(cc)
continue
if re.search(regexp, doc, re.MULTILINE | re.IGNORECASE):
count += 1
if len(cc) > maxcclen:
maxcclen = len(cc)
docmatches = re.match(r"""^\s+DESCRIPTION\s+(.{0,80})\S*""", doc, re.IGNORECASE)
if docmatches == None:
desc = '>>>>>>>> Ooopsie, no DESCRIPTION found for this command!!! <<<<<<'
else:
desc = docmatches.groups()[0]
matches_with_help.append( (cc, desc ) )
if len(matches_without_help) > 0:
fmt = '%' + str(maxcclen) + 's' # get the width of the lenghtiest command in a format
print '\n###The following commands are NOT documented.\n'
for cc in matches_without_help:
print fmt % (cc)
if len(matches_with_help) > 0:
fmt = '%' + str(maxcclen) + 's : %s' # get the width of the lenghtiest command in a format
print '\n###The following commands are documented. \'help command\' \n'
for (cc,desc) in matches_with_help:
print fmt % (cc,desc)
cmd.extend('apropos',apropos)
Re: [PyMOL] pymol licensing questions
It is *not* the GPL. It is the Python license http://sourceforge.net/projects/pymol/ see also: http://www.python.org/doc/Copyright.html I hit the send too quickly, anyways there is a fundamental difference in that derivative works of pymol AFAIK can be made proprietary, not that this would be an advantadge since the current pymol development is so dynamic. Cheers, Zac
[PyMOL] NMR models
Hi There, How would I go about selecting a specific model from a PDB file which includes several NMR conformations? Thanks, Zac
RE: [PyMOL] pymol sys.argv, winnt, barks
Sounds good to me and besides the syntax is consistent with a few UNIX apps. On Thu, 8 Nov 2001, DeLano, Warren wrote: > > pymol -c myscript.py -- -pymol -will -ignore -these -arguments > pymol -c myscript.py -- -your -script -interpret -them -instead > > Any objections?
[PyMOL] molecule name from PK* selections
Hello, Is there a way to get the corresponding molecule (or model) name for a given PK1 selection? Thanks, Zac
[PyMOL] label wizard
Hello people,
This is a labeling wizard. It allows you to click
atoms and have a label show up near the atom position.
If the atom is a C-alpha the label is slighly
different. More info is shown in the "prompt" area.
To use it, put the attached file in
/pymol/modules/pymol/wizard/label.py
and from within pymol type "wizard label"
Comments?
Have fun,
Zac
file: label.py
####
#
# Author: Ezequiel Panepucci
# Last revision: 2001-11-14
#
from pymol.wizard import Wizard
from pymol import cmd
import pymol
class Label(Wizard):
atom=None
messages=1
labeling=1
obj_name=None
def get_prompt(self):
self.prompt = []
if (not self.messages):
return ['']
if (self.atom == None):
self.prompt = ['Click atoms...']
else:
if self.atom.chain == '':
self.prompt.append( '%s %s %s %s B = %.2f XYZ = %.3f %.3f %.3f' %
(self.obj_name,
self.atom.resn,
self.atom.resi,
self.atom.name,
self.atom.b,
self.atom.coord[0],
self.atom.coord[1],
self.atom.coord[2]) )
else:
self.prompt.append('%s %s %s%s %s B = %.2f XYZ = %.3f %.3f %.3f' %
(self.obj_name,
self.atom.resn,
self.atom.chain,
self.atom.resi,
self.atom.name,
self.atom.b,
self.atom.coord[0],
self.atom.coord[1],
self.atom.coord[2]) )
return self.prompt
def toggle_messages(self):
self.messages = not self.messages
def toggle_labeling(self):
self.labeling = not self.labeling
def get_panel(self):
return [
[ 1, 'Labeling',''],
[ 2, 'Toggle add/erase','cmd.get_wizard().toggle_labeling()'],
[ 2, 'Toggle messages','cmd.get_wizard().toggle_messages()'],
[ 2, 'Clear All','cmd.label()'],
[ 2, 'Done','cmd.set_wizard()'],
]
def do_pick(self,bondFlag):
self.obj_name = None
# if 'pk1' in cmd.get_names('selections'):
if cmd.count_atoms('pk1',1):
self.obj_name = cmd.identify('pk1',1)[0][0]
model = cmd.get_model("(pk1)")
self.atom = model.atom.pop()
if not self.labeling:
cmd.label("(pk1)", '""')
elif self.atom.name == 'CA':
cmd.label("(pk1)", '" %s %s" % (resn,resi)')
else:
cmd.label("(pk1)", '" %s %s" % (name,resi)')
cmd.unpick()
cmd.refresh_wizard()
Re: [PyMOL] RE: Resolution increase
A good tip when rendering unusual aspect ratio images is to set the viewport with the same aspect ratio as the final rendered image to better use the image area. It also helps to avoid unexpected crops due to the change in the aspect ratio. Cheers, Zac On Mon, 4 Feb 2002, DeLano, Warren wrote: > Jason, > >The resolution field in images is not uniformly supported or > understood, so the safest policy is to ignore it and stick with 72 dpi > for your images. As far as I can tell from the man page, PNG format > doesn't even support a DPI field. Just make sure that your image > contain enough pixels to look good when reduced. The page layout staff > at the journal are usually professionals and will take care of adjusting > the final image size and resolution provided that you give them enough > pixels to start with. > >For example, if you are submitting something which will end up being > 4x3 inches when published, then you want to give them a 4x300=1200 by > 3x300=900 pixel image. Thus, use the command "ray 1200,900" and then > save the file. For submission, you'll probably need to use Photoshop or > the ImageMagick "convert" command to convert this file into something > they can handle. > > To cite PyMOL, either use the URL: > >Warren L. DeLano "The PyMOL Molecular Graphics System." >DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org > > or cite the manual as a book > >Warren L. DeLano (2002) "The PyMOL User's Manual" >DeLano Scientific, San Carlos, CA, USA. > > Cheers, > Warren > > -- > mailto:war...@sunesis.com > Warren L. DeLano, Ph.D. > Informatics Manager > Sunesis Pharmaceuticals, Inc. > 341 Oyster Point Blvd. > S. San Francisco, CA 94080 > (650)-266-3606 FAX:(650)-266-3501 > > > > > -Original Message- > > From: Jason Yano [mailto:jky...@bragg.bio.uci.edu] > > Sent: Monday, February 04, 2002 10:33 AM > > To: DeLano, Warren > > Subject: Resolution increase > > > > > > Hey Warren, > > I want use one of the images that I made in PyMOL for > > publication, > > but I would like to increase the output resolution to 300 > > dpi, right now > > the program spits out images at 72 dpi. I have tried to do this > > artificially in photoshop, but the image doesn't look any > > better. Whats > > the easest way to increase the resolution? > > > > By the way how would you like me to reference the program in the > > publication? > > > > > > Thanks, > > > > > > Jason > > > > > > > > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Ezequiel Panepucci - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-926-5127 Cell: 650-714-9414
[PyMOL] lines same color as background
Hello There, I have this geforce4 ti 4400 with the latest nvidia drivers and xfree86 4.2 Problem: The lines are always colored the same color as the background. If I change the background to white the lines become white. all other representaions (sticks, spheres surface) work fine. So as a workaround I am using stick_radius really small but this is not the same, lines are way better for interactive work. Weird thing is, the same happens under Win2k (dual boot machine here so exactly the same hardware). More weirdness: also happens with Ono under both OSes. My feeling is that this has to do with the z-buffer/fog thingy. I did run a program drawing (GL_LINES) with GL_DEPTH_TEST enabled and that worked fine. any clues? Zac -- Ezequiel Panepucci - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-926-5127 Cell: 650-714-9414
RE: [PyMOL] lines same color as background
Results: on geforce4 ti 4400 from PNY WORKS: line_smooth=0 depth_cue=1 line_smooth=1 depth_cue=0 line_smooth=0 depth_cue=0 WORKS NOT line_smooth=1 depth_cue=1 On Thu, 30 May 2002, DeLano, Warren wrote: > Zac, > >Thanks for the report. > >The fact that it happens with Ono too indicates that it is a > driver/openGL-level bug. You can try some things like disabling > depth cuing (set depth_cue=0) or smoothing (set line_smooth=0), but > most likely you will need to wait for a driver upgrade. Please do > report the problem to nVidia tech support and clearly state that the > problem occurs across multiple OpenGL programs. > > Also, you might try using an older version of the driver. AFAICR, nVidia > uses a unified driver architecture which is both backwards and forwards > compatible. If you do find a robust solution, please pass it along! > > Cheers, > Warren > > -- > mailto:war...@sunesis.com > Warren L. DeLano, Ph.D. > > > > > -Original Message- > > From: Ezequiel Panepucci [mailto:z...@slac.stanford.edu] > > Sent: Thursday, May 30, 2002 1:39 PM > > To: PyMOL-users@lists.sourceforge.net > > Subject: [PyMOL] lines same color as background > > > > > > Hello There, > > > > I have this geforce4 ti 4400 with the latest nvidia > > drivers and xfree86 4.2 > > > > Problem: The lines are always colored the same color as the > > background. If I change the background to white the lines become > > white. > > > > all other representaions (sticks, spheres surface) work > > fine. So as a workaround I am using stick_radius really small > > but this is not the same, lines are way better for interactive work. > > > > Weird thing is, the same happens under Win2k (dual boot machine > > here so exactly the same hardware). > > > > More weirdness: also happens with Ono under both OSes. > > > > My feeling is that this has to do with the z-buffer/fog > > thingy. I did run a program drawing (GL_LINES) with GL_DEPTH_TEST > > enabled and that worked fine. > > > > any clues? > > Zac > > > > -- > > Ezequiel Panepucci - Laboratory of Prof. Axel Brunger > > HHMI - Stanford University > > Phone: 650-926-5127 > > Cell: 650-714-9414 > > > > > > ___ > > > > Don't miss the 2002 Sprint PCS Application Developer's Conference > > August 25-28 in Las Vegas -- http://devcon.sprintpcs.com/adp/index.cfm > > > > ___ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > -- Ezequiel Panepucci - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-926-5127 Cell: 650-714-9414
Re: [PyMOL] Loss of resolution when printing or converting to PDF
Fred, Make sure you create images which are "big" enough for the size of the print you want to make, e.g. images 3000x3000 print really well on an area of about 5in x 5in (600 dpi printing resolution). Also, you should use some application in which you can properly resize the image to print the apropriate size on paper. I've used adobe photoshop and it does a terrific job. Cheers, Zac On Fri, 7 Mar 2003, Fred Berkovitch wrote: > Hello all, > > I have made some really nice .png images with pymol, but when I print them > out they lose quite a bit of resolution. Likewise, when I convert them to > PDF with Acrobat, the resulting .pdf file looks much worse (on my LCD > screen) than the original .png. Is there a way around this problem? Could > it be the colors that I'm using in Pymol that's causing this trouble? > > -Fred
Re: [PyMOL] Loss of resolution when printing or converting to PDF
when I said "big" I meant using the pymol command "ray" with arguments specifying the width and heigth: ray 3000,3000 this works on all platforms/OSes zac > Are we talking Windows here? What would be a good way to enhance this > resolution within linux? How does one make a "big" png? Is it a > command-line option, or you just make the window the size of the screen? > > > Make sure you create images which are "big" enough for the size of the > print you want to make, e.g. images 3000x3000 print really well on an > area of about 5in x 5in (600 dpi printing resolution). > > Also, you should use some application in which you can properly resize > the image to print the apropriate size on paper. I've used adobe > photoshop and it does a terrific job. >
Re: [PyMOL] knobs on spheres
Hi Reiko, I think you are also ray traycing the "nonbonded" representation of the atoms as well as the "nb_spheres". Try hide nonbonded, (selection that contains your "knobed" atoms) and then ray traycing again. Cheers, Zac On Thu, 10 Apr 2003, Reiko Kagawa wrote: > Hi everybody, > > When I ray-trace my ball-and-stick models, some knobs suddenly appear > on a sphere that is sitting alone, not bonded to anything in the > figure, hence turning into a shape that can no longer be called a > perfect sphere! This was seen in all ball-and-stick models I produced > and ray-traced, but normally happens to only one of the spheres in each > figure even if there are more than one spheres that are sitting alone. > > Has anybody experienced this? It would be great if somebody could tell > me how to get my perfect spheres back! > > Cheers, > > Reiko Kagawa > PhD Student > ATPase Group > MRC Dunn Human Nutrition Unit > Hills Road > Cambridge CB2 2XY > U.K. > > > > --- > This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger > for complex code. Debugging C/C++ programs can leave you feeling lost and > disoriented. TotalView can help you find your way. Available on major UNIX > and Linux platforms. Try it free. www.etnus.com > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-736-1714 Cell: 650-714-9414
Re: [PyMOL] redhat 9.0/pymol - missing something
JP, You must install the rpm package "tix" as well. Zac On Tue, 12 Aug 2003, JP Cartailler wrote: > greetings, > > I just finished building a new redhat 9.0 box and i am having some > troubles getting the pymol rpm to run correctly. The RPM installs without > issues, but when I run pymol, I get: > > OpenGL based graphics front end: > GL_VENDOR: NVIDIA Corporation > GL_RENDERER: Quadro4 750 XGL/AGP/SSE/3DNOW! > GL_VERSION: 1.4.0 NVIDIA 44.96 > Traceback (most recent call last): > File "modules/pymol/__init__.py", line 177, in exec_str > exec s in globals(),globals() > File "", line 1, in ? > File "modules/pymol/__init__.py", line 292, in launch_gui > __import__(invocation.options.gui) > File "modules/pmg_tk/__init__.py", line 22, in ? > # as /usr/lib/python2.1/site-packages > File "modules/pmg_tk/PMGApp.py", line 15, in ? > ImportError: No module named Tkinter > Adapting to Quadro hardware... > Detected 2 CPUs. Enabled multithreaded rendering. > > > the display window does come up, but not the floating menu bar. > > so I hit Google and found something about needing tkinter. I found a > redhat 9.0 rpm (tkinter-2.2.2-26.i386.rpm) for that, but trying doing a > test install of it yielded: > > rpm -ivh --test tkinter-2.2.1-17.i386.rpm > error: Failed dependencies: > libtix8.1.8.3.so is needed by tkinter-2.2.2-26 > > What is libtix? and where can I nab it for readhat 9.0 or just the source? > > Cheers, > > JP Cartailler > > 3205 McGaugh Hall > Dept. of Molecular Biology & Biochemistry > Irvine Research Unit in Macromolecular Structure > UC Irvine > Irvine, CA 92697-3900 > USA > > (949) 824 4322 (T) > j...@bragg.bio.uci.edu (email) > www.cartailler.com (www) > > > > > --- > This SF.Net email sponsored by: Free pre-built ASP.NET sites including > Data Reports, E-commerce, Portals, and Forums are available now. > Download today and enter to win an XBOX or Visual Studio .NET. > http://aspnet.click-url.com/go/psa0013ave/direct;at.aspnet_072303_01/01 > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-736-1714 Cell: 650-714-9414
Re: [PyMOL] Get rid of border around my images !!
antialiasing does different things to the rendering than doubling the image size can fix/make better. I would keep antialiasing and go through the added work of cropping the image. > This is a known bug when using antialiasing. You can either remove the > border in Photoshop or equivalent editing program or render your image > 2X larger and turn off antialiasing.
Re: [PyMOL] force cartoons through ca
Hi Wataru, use the cartoon_smooth_loops setting: set cartoon_smooth_loops, 0 # through C-alpha set cartoon_smooth_loops, 1 # NOT through C-alpha cheers, Zac On Tue, 23 Sep 2003 wkag...@jota.gsc.riken.go.jp wrote: > How can we force cartoons through the alpha-carbon? I apologize if > this question was posted earlier. > > > Wataru Kagawa, Ph. D. > Special Postdoctoral Researcher > Protein Research Group > RIKEN (Physical and Chemical Research Institute) > > W221, West Research Bldg. > 1-7-22 Suehiro-cho, Tsurumi-ku > Yokohama, Japan 230-0045 > > tel. 045-503-9206 > fax. 045-503-9201 > > > > --- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-736-1714 Cell: 650-714-9414
Re: [PyMOL] Need advice on graphic card
> What does "merged mode" mean? i'm curious about this mode too. > As far as I know, nVidia claims, that their driver can do that though > (but I haven't tested it, due to lack of a second screen and a dual-head > graphics-card. it is true. I've tried it on a Quadro 700XGL under RH9 and it is really nice, and you can have a vmware windows session running on one of the displays (in quick switch) and Linux on the other with all of the 3D accel available. Cheers, Zac
[PyMOL] powermate in linux
Hello There,
I've written a very little piece of python code that uses
William R Sowerbutts's rudimentary (his own words) python
interface to the powermate device.
BE WARNED!! This hack will crash your pymol session when you type
"quit" to terminate your pymol session. this wouldn't be a problem if
it didn't leave python threads floating around...Anyone knows a workaround?
The safest way to quit is to "CTRL-C" the prompt that started pymol.
This a first announcement. /dev/input/event* is indeed the future...
Cheers,
Zac
HOWTO:
1) put the python interface (powermate.py) in ${PYMOL_PATH}/modules
http://www.sowerbutts.com/powermate/powermate.py
2) put the code below in your $HOME/.pymolrc.py
3) tweak the line that says CONFIGURE to match your setup
#
# code below starts here
#
def powermate_reader(): # thread for reading powermate dial
import sys
from pymol import cmd
from powermate import PowerMate
dial_down = 0
pm1 = PowerMate('/dev/input/event1') #CONFIGURE
while 1:
event = pm1.WaitForEvent(1)
if event == None:
continue
sec,usec,type,code,value = event
if code == 256:
dial_down = not dial_down
continue
if dial_down:
cmd.turn('x',value)
else:
cmd.turn('y',value)
pm = threading.Thread(target=powermate_reader)
print 'PowerMate'
pm.setDaemon(1)
pm.start()
[PyMOL] detecting focus on the graphics window
Hello There, Anyone knows of a way of detecting if the graphics window has input focus? Thanks much, Zac -- Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-736-1714 Cell: 650-714-9414
[PyMOL] grep settings
Hi There,
Below is a little function (also attached) that gives
you the command 'grepset' so you can grep settings
using a regexp.
Use it like this:
### example ###
PyMOL>grepset dot|line
auto_show_lineson
cgo_dot_radius -1.0
cgo_dot_width 2.0
cgo_line_radius-0.05000
cgo_line_width 1.0
dot_color default
dot_density2
dot_hydrogens on
dot_mode 0
dot_radius 0.0
dot_solvent0
dot_width 2.0
line_radius0.0
line_smoothon
line_width 2.0
roving_lines 10.0
sculpt_line_weight 1.0
trim_dots on
18 settings matched
end example ###
To install:
Just put the code below in a file and 'run '
from within pymol to get the command activated.
Cheers,
Zac
code below
from pymol import cmd
import pymol.setting
def grepset(regexp=''):
'''
DESCRIPTION
"grepset" greps through the list of settings using a python
regular expression as defined in the 're' module.
It returns a list of settings/values matching the regexp.
No regexp returns every setting.
USAGE
grepset [regexp]
EXAMPLE
grepset line
grepset ray
SEE ALSO
Python re module
'''
from re import compile
count=0
regexp=compile(regexp)
for a in pymol.setting.get_index_list():
setting=pymol.setting._get_name(a)
if regexp.search(setting):
count = count + 1
print '%-30s %s' % (setting, cmd.get_setting_text(a,'',-1))
print '%d settings matched' % count
cmd.extend('grepset',grepset)
from pymol import cmd
import pymol.setting
def grepset(regexp=''):
'''
DESCRIPTION
"grepset" greps through the list of settings using a python
regular expression as defined in the 're' module.
It returns a list of settings/values matching the regexp.
No regexp returns every setting.
USAGE
grepset [regexp]
EXAMPLE
grepset line
grepset ray
SEE ALSO
Python re module
'''
from re import compile
count=0
regexp=compile(regexp)
for a in pymol.setting.get_index_list():
setting=pymol.setting._get_name(a)
if regexp.search(setting):
count = count + 1
print '%-30s %s' % (setting, cmd.get_setting_text(a,'',-1))
print '%d settings matched' % count
cmd.extend('grepset',grepset)
Re: [PyMOL] adding residues
Oi Sergio, You should pick (PkAt) either the atom N or C depending towards which end you want to extend the chain: N ==> to extend the N-terminus C ==> to extend the C-terminus and then select the residue you want to add from the Build->Residue menu. Um abraco, Zac On Fri, 26 Mar 2004, Sergio Modesto Vechi wrote: | Hi all, | | | I load my protein pdb file and I'm trying to add the missing residues to | this molecule. Anyone knows how to do it? | | Thanks in advance, | | | Sergio. | | | | --- | This SF.Net email is sponsored by: IBM Linux Tutorials | Free Linux tutorial presented by Daniel Robbins, President and CEO of | GenToo technologies. Learn everything from fundamentals to system | administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click | ___ | PyMOL-users mailing list | PyMOL-users@lists.sourceforge.net | https://lists.sourceforge.net/lists/listinfo/pymol-users | Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-736-1714 Cell: 650-714-9414
Re: [PyMOL] graphics boards
Mark, You can get an Nvidia Quadro4 380 XGL which has a stereo connector. Nvidia keeps their drivers on almost the same (if not the same) release schedule as their MS Windows drivers, they are very stable and easy to install and maintain. Zac | I know this has been discussed before on this list. I need a graphics | board for a Linux RH 9.0 running on Dell Optiplex GX270. The | applications will be O and Pymol and similar programs. Stereo-capable | would be preferred. I've been told that NVidia is more compatible with | Linux. Of the myriad of models available, could anyone help narrow the | choices for me? Price range <$150.
[PyMOL] nvidia quadro 700xgl opengl error
Hello There, I think this message is mostly for Warren and an FYI for nvidia users. There is a question at the end though. Scenario: Graphics card = Nvidia Quadro 700 XGL NVIDIA Driver = Either 53.36 or the previous one. PyMOL = 0.95 Error message: OpenGL-Error: Where? During Rendering: invalid operation All other nvidia cards work well without errors which makes me believe there is something funny with this specific card model (we have 2 of these cards giving the error). I noticed that up to 0.93 you didn't have the glGetError on the C code so maybe it could be something happening prior to 0.95. PyMOL seems to run fine but it keeps spitting the error messages constantly. I tried disabling feedback of opengl errors with feedback disable,opengl,everything but it didn't work feedback disable,all,everything works but some feed back is always nice. Is there a good combination of the feedback args that will only disable the opengl messages? Many thanks, Zac -- Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-736-1714 Cell: 650-714-9414
Re: [PyMOL] Powermate dial with Pymol on OS X
Nat, The short answer to your question is yes. I have developed a small python driver and an extension to pymol that allows you to use any USB input device as a 3D controller. It works with any USB device that generates events on /dev/input/event* I have also a torsion function that you can use to change dihedrals interactively on any amino acid using your altrnate 3D input device. In my opinion the best input device for this is a trackball with many buttons (Kensington Expert Mouse Pro Trackball). This model has a scroll wheel that you can configure to change rotamers of the currently Pk1 selection if you scroll it while keeping the scroll wheel pressed. Check my webpage for details: http://atb.slac.stanford.edu/~zac/pymol/ Cheers, Zac On Thu, 6 May 2004, Nat Echols wrote: | | I'm very curious about this dial all of a sudden - I just started doing | refinements, and I'd love to use my laptop as much as possible instead of | our slow old SGIs. Has anyone used it on Linux? How's it work with O? | Could it theoretically be programmed to, say, flip through rotamer | libraries or tweak torsion angles in PyMOL, with some additions to the | Python layer? $40 isn't a lot of it's a decent partial replacement for | SGI dial boxes. | | thanks, | Nat | | | | --- | This SF.Net email is sponsored by Sleepycat Software | Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to deliver | higher performing products faster, at low TCO. | http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3 | ___ | PyMOL-users mailing list | PyMOL-users@lists.sourceforge.net | https://lists.sourceforge.net/lists/listinfo/pymol-users | Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-736-1714 Cell: 650-714-9414
[PyMOL] giving back to the list: summaries on questions posted
Hi All, Because some people prefer to answer mailing list questions directly to the poster of the question it would be great if the poster would take a few minutes to compile a summary quoting all the unique answers he or she received. I have used other lists where this was done and all summaries were sent back to the list with the word "SUMMARY" on the subject line making it very easy to find answers. Of course this is not enforceable but I think suggesting it to posters would help getting it done. Cheers, Zac -- Ezequiel Panepucci, Ph.D. - Laboratory of Prof. Axel Brunger HHMI - Stanford University Phone: 650-736-1714 Cell: 650-714-9414
Re: [PyMOL] loading electrostatic maps generated with apbs
Michael, | If really do have an up-to-date version of my code, we should probably | figure out what's wrong off-list. I have merged your extensions into PyMOL 0.95. Terrific work. I would like to suggest, although it may be added work for you, that you keep a set of files for the current stable version of PyMOL in your web-page. This would make it easier for those who can't/won't use CVS versions of the program and also it makes it guaranteed that people will be able to download the actual source code against which to patch with your extensions. Thanks again for the great work. Zac
[PyMOL] Question: general purpose "get_prompt" function
Hello People, Anyone would know how to go about generating text messages on the viewer window like the ones you get when using the Wizard's get_prompt method, without having to resort to a wizard? reason: I have a little script to deal with a trackball and I use the buttons and scrollwheel to change the device's actions. I would like to put a brief message letting me know things I think I should know when I press buttons or scroll the wheel. Thanks much, Zac
