pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] state variables

[Ricardo A. <apa...@if...>]

Dear PyMOL users:

	I am a new user and I need to make a mask around a pdb model, I tried
mesh and surface options.
	Problem is that I would like a surface without high definition, without
smaller details, I mean, I want to make a very low resolution mask (in
NCSMASK - ccp4, this can be done by increasing parameters "radius"
and/or "smooth").
	I found some PyMOL "state variables" which could help me, like
surface_proximity, etc.
	I didn't find the default values for those variables nor their
function!
	
	Please, you help is very welcomed. 
	In short:

1) how to make a rough, not detailed mask around my pdb? Is "surface"
option the right way?

2) what parameters do have influence in making a "rough" surface, what
are their functions and default values?


Thanks in advance,



Ricardo Aparicio
PhD student
USP - Sao Carlos - Sao Paulo
Brazil

Re: [PyMOL] (no subject)

[Warren L. D. <wa...@su...>]

On Thu, 22 Nov 2001, Sona Vasudevan wrote:
 
> Hi!
> 
> Just wondering if there is a way to save a pymol session like in Insight
> and setor if I want to get back to it.

PyMOL isn't quite as sophisticated as Insight II in this respect, however
the logging features can achieve session-like behavior.  It works sort-of
like Grasp but with log files that are much more straight-forward to edit
and modify, since they are written in the PyMOL command language (.pml
files) or using PyMOL's Python API (.pym files).  Example:

Select "Log..." from the file menu immediately after you start PyMOL to
start writing a ".pml" or ".pym" log file.  Go about your business.

When done, press the "Get View" button and quit the program.

To resume your "session", launch PyMOL and select "Resume..." from the
file menu.  Open your log file and *PRESTO* PyMOL should be in
the same state as when you left. Any additional actions you then take will
be appended on to the log.  

Note that any "ray", "png", or "save" operations will be repeated when you
resume the log file.  Thus, you may want to edit the log file and
remove these commands with a text editor (Notepad on Windows) before
resuming.  Perhaps it would be nice to have a setting which ignores this
kinds of commands when resuming.  Hmm...

- Warren

PS. There is only bug I know of in the logging feature of 0.68 which
affects conformational editing when logging to .pml files.  It will be
fixed in the next release, but for now just log to .pym files if you
are going to edit conformations.



 

Re: [PyMOL] MacOSX.1 port of 0.68, anyone?

[Warren L. D. <wa...@su...>]

Morgan Ryan wrote.

> Has anyone successfully ported PyMol 0.68 to OSX yet? The excellent 
> Gnu-Darwin project hasn't gone past 0.64. An OSX port or an edited 
> Makefile would be nifty. Morgan 

Unfortunately, building natively under OSX isn't as simple as using an
updated Makefile.  Apple's GLUT implementation isn't 100% complete, so
tricky source-code workarounds in PyMOL are required.  I don't currently 
have a suitable Mac for OSX development, so unless I can pool together
donations to purchase one, stable and updated Aqua ports from me will
be delayed indefinitely.  Given that only about 15-20% of the PyMOL 
user base is OSX, I wouldn't feel right about devoting more than 15-20%
of the general PyMOL budget to the platform.  If people would like to
make specific donations for Mac hardware, then that's different.
   
An outside possibility for the Mac is that the XFree86/DRI project
might eventually enable accelerated OpenGL on the Mac platform outside the
Aqua environment.  However, I think this is held up right now because
nVidia hasn't made XFree86 drivers available for the Mac in the way they
have for PC Linux.  Consider emailing nVidia with this specific request.

Without hardware acceleration, PyMOL on an OSX Mac gives only about 1/20th
the OpenGL performance of an equivalent Linux PC.  Thus, today you are
better off spending $500-600 for a hardware-accelerated Linux box than 
trying to use PyMOL exclusively on a Mac, unless ray-tracing is all you 
do.  Given that Apple has so far been unwilling to assist PyMOL 
development on the Mac, they apparently agree with me. 8-(

I'm sorry Mac users of PyMOL are at a huge disadvantage, but there's
little I can do all by myself.  Here's what your options are:

(1) donate $$ to help me buy a Mac and support the platform.
(2) tell Apple why they should loan me a Mac for PyMOL development
    (direct comments to John Martellaro).
(3) tell nVidia why they should provide XFree86 drivers for GNU/Darwin.
(4) switch to a Windows or Linux machine for your OpenGL graphics work.
(5) continue using the very slow version of PyMOL from GNU/Darwin.
(6) use some package other than PyMOL.

If you are a serious developer, you can also

(7) port and suppport PyMOL under Aqua yourself.  This would be difficult
    given that PyMOL's C core isn't particularly clean or transparent.

Cheers,
- Warren

[PyMOL] (no subject)

[Sona V. <vas...@nc...>]

Hi!

Just wondering if there is a way to save a pymol session like in Insight
and setor if I want to get back to it.

Thanks.

sona



----------------------------------------------------------------
Sona Vasudevan
National Center for Biotechnology Information
National Library of Medicine
National Institutes of Health,Bldg. 38A, Rm. B2N21I,
8600 Rockville pike, Bethesda, MD 20894, USA 
Voice: (301)594-3154; Home: (703)-893-8424
Email: vas...@nc... or son...@ni...
-----------------------------------------------------------------

[PyMOL] MacOSX.1 port of 0.68, anyone?

[Morgan R. <mr...@nc...>]

Has anyone successfully ported PyMol 0.68 to OSX yet? The excellent 
Gnu-Darwin project hasn't gone past 0.64. An OSX port or an edited 
Makefile would be nifty. Morgan  

[PyMOL] label wizard

[Ezequiel P. <za...@SL...>]

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] molecule name from PK* selections

[DeLano, W. <wa...@su...>]

There are a number of different ways to do this, but the easiest is:

obj_name =3D cmd.identify('pk1',1)[0][0]

To be safe, your code should probably make sure that the selection pk1
exists and contains at least one atom:

obj_name =3D None

if 'pk1' in cmd.get_names('selections'):
   if cmd.count_atoms('pk1',1):
	obj_name =3D cmd.identify('pk1',1)[0][0]

if obj_name:
   # do something here...

Cheers,
Warren


--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Scientist
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501



> -----Original Message-----
> From: Ezequiel Panepucci [mailto:za...@SL...]
> Sent: Wednesday, November 14, 2001 4:30 PM
> To: PyM...@li...
> Subject: [PyMOL] molecule name from PK* selections
>=20
>=20
> Hello,
> Is there a way to get the corresponding molecule (or model)
> name for a given PK1 selection?
> Thanks,
> 	Zac
>=20
>=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] molecule name from PK* selections

[Ezequiel P. <za...@SL...>]

Hello,
Is there a way to get the corresponding molecule (or model)
name for a given PK1 selection?
Thanks,
	Zac

[PyMOL] Re: pymol sys.argv, winnt, barks

[Andrey K. <ak...@kd...>]

Warren,

"DW" == DeLano, Warren wrote:

 DW> import sys
 DW> sys.argv = copy.deepcopy(argv)

 DW> Directly under "def parse_args(argv):" (line 79) in
 DW> PyMOL/modules/pymol/invocation.py.  

Will try.

[...]

 DW> pymol -c myscript.py -- -pymol -will -ignore -these -arguments
 DW> pymol -c myscript.py -- -your -script -interpret -them -instead

Looks good to me.

-- 
Andrey V Khavryuchenko          http://www.kds.com.ua/
Offshore Software Development

RE: [PyMOL] pymol sys.argv, winnt, barks

[Ezequiel P. <za...@SL...>]

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?

RE: [PyMOL] pymol sys.argv, winnt, barks

[DeLano, W. <wa...@su...>]

It looks like Andrey wants his script to be able to interpret command
line arguments.  Unfortunately, PyMOL doesn't enable this in a
consistent way, since Launching under Windows (embedded Python) is quite
different than unix (non-embedded Python).

With embedded Python, arguments aren't making it to sys.argv.  Instead,
they are being passed straight from C into PyMOL's invocation routine.
I will fix this in the next version by reassigning them to sys.argv, but
you can do this immediate by inserting

   import sys
   sys.argv =3D copy.deepcopy(argv)

Directly under "def parse_args(argv):" (line 79) in
PyMOL/modules/pymol/invocation.py. =20

I'd also like to provide a means by which certain can be ignored by
PyMOL and be available directly to Python scripts in PyMOL.

Here is my proposal: =20

Ignore any arguments after a double-hyphen ("--") sentinel.  For
example:

pymol -c myscript.py -- -pymol -will -ignore -these -arguments
pymol -c myscript.py -- -your -script -interpret -them -instead

Any objections?=20

- Warren


--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Scientist
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501

> From: Frank Vondelft=20
>=20
> Andrey,
>=20
> I deduce you're referring to windows?  I think this is what=20
> you get when python gets installed in C:\Program Files\python=20
> or some other location that is not on the (hardcoded?) search=20
> path of pymol, which means it can't find the tcltk libraries.=20
>  The solution is to install python on C:\python, and=20
> everything is hunky-dory -- I think you don't even have to=20
> reinstall pymol, but you can check that, it doesn't take long.=20
>=20
> Good luck
> phx.
>=20

> From:	Andrey Khavryuchenko
>=20
> Hi!
>=20
> Is it only me who gets the following:
>=20
> for i in argv:
>     print i
>=20
> [...]
>=20
> $ pymol -c mov.py
> [...]
>  Hit ESC anytime to toggle between text and graphics.
>=20
>  Command mode. No graphics front end.
> Traceback (most recent call last):
>   File "C:\Program Files\DeLano=20
> Scientific\PyMOL/modules\pymol\parser.py", lin
> e 174, in parse
>     execfile(args[nest][0],pymol_names,pymol_names)
>   File "mov.py", line 90, in ?
>     for i in sys.argv:
> AttributeError: 'sys' module has no attribute 'argv'
>  Memory: 0 blocks expected, 0 found, 42 maximum allocated.
>=20
> Linux version and plain python under winnt are ok.  It's only=20
> pymol that
> gives that strange behaviour.
>=20
> --=20
> Andrey V Khavryuchenko          http://www.kds.com.ua/
> Offshore Software Development
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20

[PyMOL] Re: pymol sys.argv, winnt, barks

[Andrey K. <ak...@kd...>]

Frank,

"FV" == Frank Vondelft wrote:

 FV> I deduce you're referring to windows?  

Yes.

 FV> I think this is what you get when python gets installed in C:\Program
 FV> Files\python or some other location that is not on the (hardcoded?)
 FV> search path of pymol, which means it can't find the tcltk libraries.
 FV> The solution is to install python on C:\python, and everything is
 FV> hunky-dory -- I think you don't even have to reinstall pymol, but you
 FV> can check that, it doesn't take long.

I've got python installed in c:\python21.  I had to copy tcl and tk
libraries manually, so Pymol would find them.  After that Pymol started and
work w/o any problem expect it could not find sys.argv

Checking if you suggestion works...

No.  It looks like a problem with python, embedded in pymol.exe

-- 
Andrey V Khavryuchenko          http://www.kds.com.ua/
Offshore Software Development

RE: [PyMOL] pymol sys.argv, winnt, barks

[Frank V. <Fra...@sy...>]

Andrey,

I deduce you're referring to windows?  I think this is what you get when
python gets installed in C:\Program Files\python or some other location
that is not on the (hardcoded?) search path of pymol, which means it
can't find the tcltk libraries.  The solution is to install python on
C:\python, and everything is hunky-dory -- I think you don't even have
to reinstall pymol, but you can check that, it doesn't take long.=20

Good luck
phx.



-----Original Message-----
From:	Andrey Khavryuchenko
Sent:	Thu 11/8/2001 9:06 AM
To:	pym...@li...
Cc:=09
Subject:	[PyMOL] pymol sys.argv, winnt, barks

Hi!

Is it only me who gets the following:

for i in argv:
    print i

[...]

$ pymol -c mov.py
[...]
 Hit ESC anytime to toggle between text and graphics.

 Command mode. No graphics front end.
Traceback (most recent call last):
  File "C:\Program Files\DeLano
Scientific\PyMOL/modules\pymol\parser.py", lin
e 174, in parse
    execfile(args[nest][0],pymol_names,pymol_names)
  File "mov.py", line 90, in ?
    for i in sys.argv:
AttributeError: 'sys' module has no attribute 'argv'
 Memory: 0 blocks expected, 0 found, 42 maximum allocated.

Linux version and plain python under winnt are ok.  It's only pymol that
gives that strange behaviour.

--=20
Andrey V Khavryuchenko          http://www.kds.com.ua/
Offshore Software Development

_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users

[PyMOL] pymol sys.argv, winnt, barks

[Andrey K. <ak...@kd...>]

Hi!

Is it only me who gets the following:

for i in argv:
    print i

[...]

$ pymol -c mov.py
[...]
 Hit ESC anytime to toggle between text and graphics.

 Command mode. No graphics front end.
Traceback (most recent call last):
  File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py", lin
e 174, in parse
    execfile(args[nest][0],pymol_names,pymol_names)
  File "mov.py", line 90, in ?
    for i in sys.argv:
AttributeError: 'sys' module has no attribute 'argv'
 Memory: 0 blocks expected, 0 found, 42 maximum allocated.

Linux version and plain python under winnt are ok.  It's only pymol that
gives that strange behaviour.

-- 
Andrey V Khavryuchenko          http://www.kds.com.ua/
Offshore Software Development

[PyMOL] Re: pymol segfaults

[Andrey K. <ak...@kd...>]

Warren,

"WLD" == Warren L DeLano wrote:

 WLD> Running "pymol -c script.py" is almost equivalent to "python  
 WLD> script.py" for command-line only mode.

Ok, that does exactly what I wanted -- run pymol in batch mode.

Thanks!

-- 
Andrey V Khavryuchenko          http://www.kds.com.ua/
Offshore Software Development

Re: [PyMOL] pymol segfaults

[Warren L. D. <wa...@su...>]

Launching PyMOL isn't as simple as simply including the "pymol" module
(although that could change).  However, under unix at least, you can
launch it from within a python interpreter.  Just take a look at the
"pymol.com" file, which does exactly that.

PyMOL needs a little bit more information to start (PYMOL_PATH and
LD_LIBRARY_PATH for instance), and PyMOL will steal the main thread for
the GLUT/OpenGL event loop (so you should fork off a new thread first if
you want to run something in parallel).  PyMOL will also
attempt to interpret command arguments, but you can alter sys.argv
accordingly to prevent this.

With PYMOL_PATH and LD_LIBRARY_PATH set (after sourceing pymol.csh), you
could issue:

   python $PYMOL_PATH/modules/launch_pymol.py script.py

but that is basically what pymol.com does for you anyway, so you might as
well use it instead.  "pymol script.py" is the recommended (and
robust) way to launch pymol.

Running "pymol -c script.py" is almost equivalent to "python  
script.py" for command-line only mode.

The seg-fault you're getting arises from calling an uninitialized instance
of PyMOL where none of the data structures yet exist.

Cheers,
Warren

On 3 Nov 2001, Andrey Khavryuchenko wrote:

> Hi!
> 
> I've got the following problem (it may be tied to python v2 that I'm
> using):
> 
> [akhavr@netmaster molmov]$ PYMOL_PATH=~/src/pymol/modules/ PYTHONPATH=/homvr/src/pymol/modules/ gdb python2
> GNU gdb 5.0
> Copyright 2000 Free Software Foundation, Inc.
> GDB is free software, covered by the GNU General Public License, and you are
> welcome to change it and/or distribute copies of it under certain conditions.
> Type "show copying" to see the conditions.
> There is absolutely no warranty for GDB.  Type "show warranty" for details.
> This GDB was configured as "i386-redhat-linux"...
> (no debugging symbols found)...
> (gdb) run
> Starting program: /usr/bin/python2 
> [New Thread 1024 (LWP 3246)]
> Python 2.1.1 (#1, Aug 13 2001, 19:37:40) 
> [GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-96)] on linux2
> Type "copyright", "credits" or "license" for more information.
> >>> from glob import glob
> >>> import thread 
> >>> import threading 
> >>> import os
> >>> import sys
> >>> import time
> >>> from pymol import cmd
> >>> cmd.hide("lines")
> 
> Program received signal SIGSEGV, Segmentation fault.
> [Switching to Thread 1024 (LWP 3246)]
> 0x402fc2be in APIEntry () at Cmd.c:106
> 106	  PRINTFD(FB_API)
> (gdb) bt
> #0  0x402fc2be in APIEntry () at Cmd.c:106
> #1  0x40301b98 in CmdShowHide (self=0x0, args=0x8113d64) at Cmd.c:2517
> #2  0x80593ed in PyEval_CallObjectWithKeywords () at eval.c:41
> #3  0x8057c75 in PyEval_EvalCode () at eval.c:41
> #4  0x80597dd in PyEval_CallObjectWithKeywords () at eval.c:41
> #5  0x8057d44 in PyEval_EvalCode () at eval.c:41
> #6  0x80550d5 in PyEval_EvalCode () at eval.c:41
> #7  0x806e031 in PyRun_FileExFlags () at eval.c:41
> #8  0x806d0fc in PyRun_InteractiveOneFlags () at eval.c:41
> #9  0x806cf5e in PyRun_InteractiveLoopFlags () at eval.c:41
> #10 0x806ce2d in PyRun_AnyFileExFlags () at eval.c:41
> #11 0x8051f30 in Py_Main () at eval.c:41
> #12 0x40084777 in __libc_start_main (main=0x80519d0 <main>, argc=1, 
>     ubp_av=0xbffff704, init=0x8050e38 <_init>, fini=0x80a48f0 <_fini>, 
>     rtld_fini=0x4000dd44 <_dl_fini>, stack_end=0xbffff6fc)
>     at ../sysdeps/generic/libc-start.c:129
> (gdb) 
> 
> Red Hat Linux 7.2
> Pmw-0.8.5-1
> Numeric-20.2.1-1
> pymol both 0.68 and CVS versions
> 
> This happens only if I try to run python script utilizing pymol directly
> from python.  Launching via 'pymol script.py' goes ok.
> 
> What I'm doing wrong?
> 
> 

[PyMOL] pymol segfaults

[Andrey K. <ak...@kd...>]

Hi!

I've got the following problem (it may be tied to python v2 that I'm
using):

[akhavr@netmaster molmov]$ PYMOL_PATH=~/src/pymol/modules/ PYTHONPATH=/homvr/src/pymol/modules/ gdb python2
GNU gdb 5.0
Copyright 2000 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for details.
This GDB was configured as "i386-redhat-linux"...
(no debugging symbols found)...
(gdb) run
Starting program: /usr/bin/python2 
[New Thread 1024 (LWP 3246)]
Python 2.1.1 (#1, Aug 13 2001, 19:37:40) 
[GCC 2.96 20000731 (Red Hat Linux 7.1 2.96-96)] on linux2
Type "copyright", "credits" or "license" for more information.
>>> from glob import glob
>>> import thread 
>>> import threading 
>>> import os
>>> import sys
>>> import time
>>> from pymol import cmd
>>> cmd.hide("lines")

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 1024 (LWP 3246)]
0x402fc2be in APIEntry () at Cmd.c:106
106	  PRINTFD(FB_API)
(gdb) bt
#0  0x402fc2be in APIEntry () at Cmd.c:106
#1  0x40301b98 in CmdShowHide (self=0x0, args=0x8113d64) at Cmd.c:2517
#2  0x80593ed in PyEval_CallObjectWithKeywords () at eval.c:41
#3  0x8057c75 in PyEval_EvalCode () at eval.c:41
#4  0x80597dd in PyEval_CallObjectWithKeywords () at eval.c:41
#5  0x8057d44 in PyEval_EvalCode () at eval.c:41
#6  0x80550d5 in PyEval_EvalCode () at eval.c:41
#7  0x806e031 in PyRun_FileExFlags () at eval.c:41
#8  0x806d0fc in PyRun_InteractiveOneFlags () at eval.c:41
#9  0x806cf5e in PyRun_InteractiveLoopFlags () at eval.c:41
#10 0x806ce2d in PyRun_AnyFileExFlags () at eval.c:41
#11 0x8051f30 in Py_Main () at eval.c:41
#12 0x40084777 in __libc_start_main (main=0x80519d0 <main>, argc=1, 
    ubp_av=0xbffff704, init=0x8050e38 <_init>, fini=0x80a48f0 <_fini>, 
    rtld_fini=0x4000dd44 <_dl_fini>, stack_end=0xbffff6fc)
    at ../sysdeps/generic/libc-start.c:129
(gdb) 

Red Hat Linux 7.2
Pmw-0.8.5-1
Numeric-20.2.1-1
pymol both 0.68 and CVS versions

This happens only if I try to run python script utilizing pymol directly
from python.  Launching via 'pymol script.py' goes ok.

What I'm doing wrong?

-- 
Andrey V Khavryuchenko          http://www.kds.com.ua/
Offshore Software Development

[PyMOL] pymol rpms are available

[Andrey K. <ak...@kd...>]

Hi!

Pymol 0.68 RPMs (both source and i386) are available at 

        http://office.kds.com.ua/~akhavr/pymol/

The packages are build for python 2.1, since latest Numeric is supported
only for python 2.

Bug reports are welcome.

-- 
Andrey V Khavryuchenko          http://www.kds.com.ua/
Offshore Software Development

[PyMOL] pymol as rpm anyone?

[Andrey K. <ak...@kd...>]

Hello!

Had anyone created an RPM for pymol?  Even .spec would be good.

Thanks in advance!

-- 
Andrey V Khavryuchenko          http://www.kds.com.ua/
Offshore Software Development

RE: [PyMOL] CCP4 density maps and PyMol

[Warren L. D. <wa...@su...>]

> > Does anyone know how to disable automatic normalization of an
> > input map?

The "normalize_ccp4_maps" setting is now functional in the CVS source
version, and will work in 0.69+.  Note that this setting must be
changed before loading the map.  On-the-fly map transformations (ala
CNS/X-PLOR) would be a cool and very easy feature to implement in
future versions...

> > Also does anyone has a script which draws a "carved" density? 
> > I've tried to
> > do this but without success.

load tst.ccp4
load ref.pdb
isomesh m1, tst, 1.0, (resi 100-105), carve=2.0

- Warren

RE: [PyMOL] CCP4 density maps and PyMol

[DeLano, W. <wa...@su...>]

Whoops, it looks like I created this setting without actually utilizing
it in the code.  I'll fix this in the CVS repository late tonight. =20

Although I've sworn off adding any major new functionality to PyMOL for
a while, minor monthly updates are planned which will incorporate
bugfixes and outside user contributions (next one around Dec. 1st).

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Scientist
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501



> -----Original Message-----
> From: Fischmann, Thierry [mailto:thi...@sp...]
> Sent: Thursday, November 01, 2001 2:17 PM
> To: 'pym...@li...'
> Subject: [PyMOL] CCP4 density maps and PyMol
>=20
>=20
>=20
> Unless I'm mistaken (which is very possible), it appears that=20
> by default
> PyMol normalizes an input map upon loading.
>=20
> I'd like to disable this feature. Looking in the menu at=20
> Settings .../Edit
> All ... I've found the variable normalize_ccp4_maps and=20
> changed its default
> value from 1 to 0 (or in a script I've added "set=20
> normalize_ccp4_maps, 0").
> This does not appear to have any effect at all.
>=20
> Does anyone know how to disable automatic normalization of an=20
> input map?
>=20
> Also does anyone has a script which draws a "carved" density?=20
> I've tried to
> do this but without success.
>=20
> Thanks in advance for any tip,
>=20
> Thierry
>=20
> thi...@sp...
>=20
> ***************************************************************
>  This message and any attachments is solely for the intended=20
> recipient. If
> you are not the intended recipient, disclosure, copying, use, or
> distribution of the information included in this message is=20
> prohibited --
> please immediately and permanently delete this message.
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] CCP4 density maps and PyMol

[Fischmann, T. <thi...@sp...>]

Unless I'm mistaken (which is very possible), it appears that by default
PyMol normalizes an input map upon loading.

I'd like to disable this feature. Looking in the menu at Settings .../Edit
All ... I've found the variable normalize_ccp4_maps and changed its default
value from 1 to 0 (or in a script I've added "set normalize_ccp4_maps, 0").
This does not appear to have any effect at all.

Does anyone know how to disable automatic normalization of an input map?

Also does anyone has a script which draws a "carved" density? I've tried to
do this but without success.

Thanks in advance for any tip,

Thierry

thi...@sp...

***************************************************************
 This message and any attachments is solely for the intended recipient. If
you are not the intended recipient, disclosure, copying, use, or
distribution of the information included in this message is prohibited --
please immediately and permanently delete this message.

Re: [PyMOL] ca-trace

[Ben C. <ac...@em...>]

But that's what you should get, since alpha carbons aren't bonded
directly to other alpha carbons, right?  Perhaps what you really want
to do is draw the protein "backbone only"?  Try this:

hide all
show (name ca,c,n,o)

Cheers,

Ben

"Frank Vondelft" <Fra...@sy...> writes:

> Hidy Pymollers....
> 
> I *think* I've RTFMed everywhere I can, but I haven't been able to
> figure out how to draw a molecule C-alpha only.  When I selected all CA
> atoms, I got a cloud of dots that were not connected.  I suspect I've
> missed something fundamental...
> 
> Thanks for any tips
> Phraenquex
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

RE: [PyMOL] ca-trace

[DeLano, W. <wa...@su...>]

A UCSF MidasPlus style CA trace can be obtained with:

set ribbon_sampling=3D1
show ribbon

A space filling version can be had with:

set cartoon_smooth_loops=3D0
set cartoon_sampling=3D1
cartoon loop
show cartoon

All of the above can be restricted so as to apply to only a single
object as described in the manual/online help.

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Scientist
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501



> -----Original Message-----
> From: Frank Vondelft [mailto:Fra...@sy...]
> Sent: Tuesday, October 30, 2001 3:03 PM
> To: pym...@li...
> Subject: [PyMOL] ca-trace
>=20
>=20
> Hidy Pymollers....
>=20
> I *think* I've RTFMed everywhere I can, but I haven't been able to
> figure out how to draw a molecule C-alpha only.  When I=20
> selected all CA
> atoms, I got a cloud of dots that were not connected.  I suspect I've
> missed something fundamental...
>=20
> Thanks for any tips
> Phraenquex
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

[PyMOL] ca-trace

[Frank V. <Fra...@sy...>]

Hidy Pymollers....

I *think* I've RTFMed everywhere I can, but I haven't been able to
figure out how to draw a molecule C-alpha only.  When I selected all CA
atoms, I got a cloud of dots that were not connected.  I suspect I've
missed something fundamental...

Thanks for any tips
Phraenquex