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From: Michael G. L. <ml...@um...> - 2005-01-31 21:52:08
|
select thingy, id 688+689+690+1247+1259+1961+1862
- for some reason, 688-690... doesn't seem to work for me
- i've had problems with id in the past .. PyMOL used to re-number
things, but i don't think it re-numbers them these days (i could easily
be wrong about this)
- be careful in scripts: 'id' is a builtin python function. if you're
using it as a variable name, use something like ID instead.
you could also use
select thingy, 87/CG+OD1+OD2 or 157/OG or 159/OG1 or 234/CZ3+CH2
actually, the second way seems more meaningful to me anyway.
-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
| / \ | mlerner@umich
On Mon, 31 Jan 2005, Jon Binkley wrote:
>
> Greetings,
>
> I want to define and display a patch of functionally related atoms on a
> protein-- but only the individual atoms of interest, not the entire
> residues to which they might belong. Is there a way to select atoms by
> their serial number in the PDB file, rather than name or residue
> membership? Failing a direct selection, is there another way I can group
> multiple, disparate atoms into a single selection?
>
> This is the best I've come up with so far, using residue and name:
>
> To group the following atoms:
>
> ATOM 688 CG ASP A 87
> ATOM 689 OD1 ASP A 87
> ATOM 690 OD2 ASP A 87
> ATOM 1247 OG SER A 157
> ATOM 1259 OG1 THR A 159
> ATOM 1861 CZ3 TRP A 234
> ATOM 1862 CH2 TRP A 234
>
> I give the following four selection commands:
>
> select a87, (resi 87 and name CG,OD1,OD2)
> select a157, (resi 157 and name OG)
> select a159, (resi 159 and name OG1)
> select a234, (resi 234 and name CZ3,CH2)
>
> Which leaves me with with 4 separate selections. What's the most
> efficient way to get a single selection or object out of this?
>
> Many thanks in advance,
>
> -Jon Binkley
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
> Tool for open source databases. Create drag-&-drop reports. Save time
> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
> Download a FREE copy at http://www.intelliview.com/go/osdn_nl
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>
|
|
From: Jon B. <bi...@ge...> - 2005-01-31 21:10:29
|
Greetings,
I want to define and display a patch of functionally related atoms on a
protein-- but only the individual atoms of interest, not the entire
residues to which they might belong. Is there a way to select atoms by
their serial number in the PDB file, rather than name or residue
membership? Failing a direct selection, is there another way I can group
multiple, disparate atoms into a single selection?
This is the best I've come up with so far, using residue and name:
To group the following atoms:
ATOM 688 CG ASP A 87
ATOM 689 OD1 ASP A 87
ATOM 690 OD2 ASP A 87
ATOM 1247 OG SER A 157
ATOM 1259 OG1 THR A 159
ATOM 1861 CZ3 TRP A 234
ATOM 1862 CH2 TRP A 234
I give the following four selection commands:
select a87, (resi 87 and name CG,OD1,OD2)
select a157, (resi 157 and name OG)
select a159, (resi 159 and name OG1)
select a234, (resi 234 and name CZ3,CH2)
Which leaves me with with 4 separate selections. What's the most
efficient way to get a single selection or object out of this?
Many thanks in advance,
-Jon Binkley
|
|
From: Lan Xu <xu...@sc...> - 2005-01-31 20:50:54
|
Hello, I would like to display crystal packing of my molecule with unit cell labeled and colored in black. I was able to show the unit cell by using the command, (show cell, hex). But I could not figure out how to change the color of the unit cell, the default color is orange. I also want to label the x, y, z axes and the origin. Many thanks, Lan Xu |
|
From: <Sus...@as...> - 2005-01-31 17:28:39
|
Hi,
I am trying to open a *.pse file and I keep getting the following error:
Error: 1
EOFError Exception in Tk callback
Function: <bound method PMGApp.file_open of <pmg_tk.PMGApp.PMGApp instance
at 0x08EDA3A0>> (type: <type 'instancemethod'>)
Args: ()
Traceback (innermost last):
File "C:\Program Files\DeLano
Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in __call__
return apply(self.func, args)
File "C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\PMGApp.py",
line 411, in file_open
cmd.load(ofile)
File "C:\Program Files\DeLano
Scientific\PyMOL/modules\pymol\importing.py", line 528, in load
cmd.set_session(io.pkl.fromFile(fname))
File "C:\Program Files\DeLano Scientific\PyMOL/modules\chempy\pkl.py",
line 24, in fromFile
result = cPickle.load(fp)
EOFError:
Please help!!!
Thanks in advance,
-Sushmita
-----Original Message-----
From: pym...@li...
[mailto:pym...@li...]
Sent: Monday, January 31, 2005 1:59 AM
To: pym...@li...
Subject: PyMOL-users digest, Vol 1 #802 - 2 msgs
Send PyMOL-users mailing list submissions to
pym...@li...
To subscribe or unsubscribe via the World Wide Web, visit
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When replying, please edit your Subject line so it is more specific
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Today's Topics:
1. RE: electron density map manipulation (dieter blaas)
2. RE: electron density map manipulation (Warren DeLano)
--__--__--
Message: 1
From: "dieter blaas" <die...@un...>
To: pym...@li...
Date: Fri, 28 Jan 2005 10:18:41 +0100
Subject: RE: [PyMOL] electron density map manipulation
Reply-to: die...@un...
CC: "Warren DeLano" <wa...@de...>
--Alt-Boundary-8494.13938296
Content-type: text/plain; charset=US-ASCII
Content-transfer-encoding: 7BIT
Content-description: Mail message body
Thanx Warren, perfect! But when entering:
"> load map1.dsn6
> slice_new slice1,map1
I get the message:
Syntax Error: invalid syntax with a ^ pointing to the "1" in slice1
I have tried several permutations of the syntax, but always receive an
error message!
On 27 Jan 2005 at 22:51, Warren DeLano wrote:
> > 1/ can I make a solid surface?
>
> Solid (opaque) surface with isosurface command (just like isomesh)
>
> > 2/ can I make volume slices?
>
> Slices are possible:
>
> load map1.dsn6
> slice_new slice1,map1
> ramp_new ramp1,map1
> color ramp1, slice1
>
> Then ctrl-middle-click and drag to change slice contour coloring
>
> > 3/ can I load the map in the same way I load pdb files
> > without command line input and manipulate the parameters with
> > the mouse?
>
> Not yet.
>
> > is it O.K. to answer in this way or should I send the mail to
> > the mailing list?
>
> The mailing list is preferable.
>
> Cheers,
> Warren
>
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080
> . Biz:(650)-872-0942 Tech:(650)-872-0834
> . Fax:(650)-872-0273 Cell:(650)-346-1154
> . mailto:wa...@de...
>
>
> > -----Original Message-----
> > From: dieter blaas [mailto:die...@un...]
> > Sent: Thursday, January 27, 2005 9:20 PM
> > To: Warren DeLano
> > Subject: RE: [PyMOL] electron density map manipulation
> >
> > Thanx a lot, this works! I have three additional questions:
> > 1/ can I make a solid surface?
> > 2/ can I make volume slices?
> > 3/ can I load the map in the same way I load pdb files
> > without command line input and manipulate the parameters with
> > the mouse?
> >
> > is it O.K. to answer in this way or should I send the mail to
> > the mailing list?
> > Dieter
> >
> >
> > On 27 Jan 2005 at 16:49, Warren DeLano wrote:
> >
> > > Dieter,
> > >
> > > Have you tried the isomesh and isosurf commands?
> > >
> > > load map1.dsn6, map1
> > > isomesh mesh1, map1, 1.0
> > >
> > > Cheers,
> > > Warren
> > >
> > > --
> > > Warren L. DeLano, Ph.D.
> > > Principal Scientist
> > >
> > > . DeLano Scientific LLC
> > > . 400 Oyster Point Blvd., Suite 213
> > > . South San Francisco, CA 94080
> > > . Biz:(650)-872-0942 Tech:(650)-872-0834
> > > . Fax:(650)-872-0273 Cell:(650)-346-1154
> > > . mailto:wa...@de...
> > >
> > >
> > > > -----Original Message-----
> > > > From: pym...@li...
> > > > [mailto:pym...@li...] On Behalf Of
> > > > Dieter Blaas
> > > > Sent: Monday, January 24, 2005 6:54 AM
> > > > To: pym...@li...
> > > > Subject: [PyMOL] electron density map manipulation
> > > >
> > > > Hi, I have been trying to visualize a DN6 electron density
> > > > map. Although it is read in apparently correctly nothing
> > > > shows on the screen. Are there any particular parameters to
> > > > be set? I can visualize it in SwisspdbViewer but I was unable
> > > > to produce surface rendering. Can Pymol produce a surface at
> > > > a particular cut-off value as can Amira?
> > > > Thanx for hints, Dieter
> > > >
> > > >
> > > > -------------------------------------------------------
> > > > This SF.Net email is sponsored by: IntelliVIEW -- Interactive
> > > > Reporting Tool for open source databases. Create drag-&-drop
> > > > reports. Save time by over 75%! Publish reports on the web.
> > > > Export to DOC, XLS, RTF, etc.
> > > > Download a FREE copy at http://www.intelliview.com/go/osdn_nl
> > > > _______________________________________________
> > > > PyMOL-users mailing list
> > > > PyM...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > > >
> > >
> > >
> >
> >
> >
>
>
--Alt-Boundary-8494.13938296
Content-type: text/html; charset=US-ASCII
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Content-description: Mail message body
<?xml version="1.0" ?><html>
<head>
<title></title>
</head>
<body>
<div align="left"><font face="Arial"><span style="font-size:10pt">Thanx
Warren, perfect! But when entering:</span></font></div>
<div align="left"><br/></div>
<div align="left"><font face="Arial"><span
style="font-size:10pt">"</span></font><font face="Arial"
color="#7f0000"><span style="font-size:10pt">> load
map1.dsn6</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> slice_new slice1,map1</span></font></div>
<div align="left"><br/>
</div>
<div align="left"><font face="Arial"><span style="font-size:10pt">I get the
message:</span></font></div>
<div align="left"><font face="Arial"><span style="font-size:10pt">Syntax
Error: invalid syntax with a ^ pointing to the "1" in
slice1</span></font></div>
<div align="left"><font face="Arial"><span style="font-size:10pt">I have
tried several permutations of the syntax, but always receive an
error message!</span></font></div>
<div align="left"><font face="Arial"><span style="font-size:10pt">
</span></font></div>
<div align="left"><font face="Arial"><span style="font-size:10pt">On 27 Jan
2005 at 22:51, Warren DeLano wrote:</span></font></div>
<div align="left"><br/>
</div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > 1/ can I make a solid
surface?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> Solid (opaque) surface with isosurface command
(just like isomesh)</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > 2/ can I make volume
slices?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> Slices are possible:</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> load map1.dsn6</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> slice_new slice1,map1</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> ramp_new ramp1,map1</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> color ramp1, slice1</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> Then ctrl-middle-click and drag to change slice
contour coloring</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > 3/ can I load the map in the same way I
load pdb files </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > without command line input and manipulate
the parameters with </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > the mouse?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> Not yet.</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > is it O.K. to answer in this way or should
I send the mail to </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > the mailing list?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> The mailing list is
preferable.</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> Cheers,</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> Warren</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> --</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> Warren L. DeLano,
Ph.D.            
;         </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> Principal Scientist</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> . DeLano Scientific LLC 
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> . 400 Oyster Point Blvd., Suite
213          
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> . South San Francisco, CA
94080    </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> . Biz:(650)-872-0942 
Tech:(650)-872-0834     </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> . Fax:(650)-872-0273 
Cell:(650)-346-1154</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> .
mailto:wa...@de...      </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">>  </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > -----Original
Message-----</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > From: dieter blaas
[mailto:die...@un...] </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > Sent: Thursday, January 27, 2005 9:20
PM</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > To: Warren DeLano</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > Subject: RE: [PyMOL] electron density map
manipulation</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > Thanx a lot, this works! I have three
additional questions:</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > 1/ can I make a solid
surface?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > 2/ can I make volume
slices?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > 3/ can I load the map in the same way I
load pdb files </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > without command line input and manipulate
the parameters with </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > the mouse?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > is it O.K. to answer in this way or should
I send the mail to </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > the mailing list?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > Dieter</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > On 27 Jan 2005 at 16:49, Warren DeLano
wrote:</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > Dieter,</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > Have you tried the isomesh and isosurf
commands?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > load map1.dsn6,
map1</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > isomesh mesh1, map1,
1.0</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > Cheers,</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > Warren</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > --</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > Warren L. DeLano,
Ph.D.            
;         </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > Principal
Scientist</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > . DeLano Scientific LLC 
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > . 400 Oyster Point Blvd., Suite
213          
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > . South San Francisco, CA
94080    </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > . Biz:(650)-872-0942 
Tech:(650)-872-0834     </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > . Fax:(650)-872-0273 
Cell:(650)-346-1154</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > .
mailto:wa...@de...      </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > >  </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > -----Original
Message-----</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > From:
pym...@li... </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > >
[mailto:pym...@li...] On Behalf Of
</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > Dieter Blaas</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > Sent: Monday, January 24, 2005
6:54 AM</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > To:
pym...@li...</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > Subject: [PyMOL] electron density
map manipulation</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > Hi, I have been trying to
visualize a DN6 electron density </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > map. Although it is read in
apparently correctly nothing </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > shows on the screen. Are there
any particular parameters to </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > be set? I can visualize it in
SwisspdbViewer but I was unable </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > to produce surface rendering. Can
Pymol produce a surface at </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > a particular cut-off value as can
Amira?</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > Thanx for hints,
Dieter</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > >
-------------------------------------------------------</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > This SF.Net email is sponsored
by: IntelliVIEW -- Interactive </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > Reporting Tool for open source
databases. Create drag-&-drop </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > reports. Save time by over 75%!
Publish reports on the web. </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > Export to DOC, XLS, RTF,
etc.</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > Download a FREE copy at
" rel="nofollow">http://www.intelliview.com/go/osdn_nl</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > >
_______________________________________________</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > PyMOL-users mailing
list</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > >
PyM...@li...</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > >
" rel="nofollow">https://lists.sourceforge.net/lists/listinfo/pymol-users</span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> > </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><font face="Arial" color="#7f0000"><span
style="font-size:10pt">> </span></font></div>
<div align="left"><br/>
</div>
<div align="left"></div>
</body>
</html>
--Alt-Boundary-8494.13938296--
--__--__--
Message: 2
From: "Warren DeLano" <wa...@de...>
To: <die...@un...>,
<pym...@li...>
Subject: RE: [PyMOL] electron density map manipulation
Date: Sun, 30 Jan 2005 10:19:30 -0800
Dieter,
Slices are a relatively new feature only found in the beta versions:
http://delsci.com/beta
http://delsci.com/macbeta
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:wa...@de...
> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...] On Behalf Of
> dieter blaas
> Sent: Friday, January 28, 2005 1:19 AM
> To: pym...@li...
> Cc: Warren DeLano
> Subject: RE: [PyMOL] electron density map manipulation
>
> Thanx Warren, perfect! But when entering:
>
> "> load map1.dsn6
> > slice_new slice1,map1
>
> I get the message:
> Syntax Error: invalid syntax with a ^ pointing to the "1" in
> slice1 I have tried several permutations of the syntax, but
> always receive an error message!
> On 27 Jan 2005 at 22:51, Warren DeLano wrote:
>
> > > 1/ can I make a solid surface?
> >
> > Solid (opaque) surface with isosurface command (just like isomesh)
> >
> > > 2/ can I make volume slices?
> >
> > Slices are possible:
> >
> > load map1.dsn6
> > slice_new slice1,map1
> > ramp_new ramp1,map1
> > color ramp1, slice1
> >
> > Then ctrl-middle-click and drag to change slice contour coloring
> >
> > > 3/ can I load the map in the same way I load pdb files without
> > > command line input and manipulate the parameters with the mouse?
> >
> > Not yet.
> >
> > > is it O.K. to answer in this way or should I send the mail to the
> > > mailing list?
> >
> > The mailing list is preferable.
> >
> > Cheers,
> > Warren
> >
> >
> > --
> > Warren L. DeLano, Ph.D.
> > Principal Scientist
> >
> > . DeLano Scientific LLC
> > . 400 Oyster Point Blvd., Suite 213
> > . South San Francisco, CA 94080
> > . Biz:(650)-872-0942 Tech:(650)-872-0834
> > . Fax:(650)-872-0273 Cell:(650)-346-1154
> > . mailto:wa...@de...
> >
> >
> > > -----Original Message-----
> > > From: dieter blaas [mailto:die...@un...]
> > > Sent: Thursday, January 27, 2005 9:20 PM
> > > To: Warren DeLano
> > > Subject: RE: [PyMOL] electron density map manipulation
> > >
> > > Thanx a lot, this works! I have three additional questions:
> > > 1/ can I make a solid surface?
> > > 2/ can I make volume slices?
> > > 3/ can I load the map in the same way I load pdb files without
> > > command line input and manipulate the parameters with the mouse?
> > >
> > > is it O.K. to answer in this way or should I send the mail to the
> > > mailing list?
> > > Dieter
> > >
> > >
> > > On 27 Jan 2005 at 16:49, Warren DeLano wrote:
> > >
> > > > Dieter,
> > > >
> > > > Have you tried the isomesh and isosurf commands?
> > > >
> > > > load map1.dsn6, map1
> > > > isomesh mesh1, map1, 1.0
> > > >
> > > > Cheers,
> > > > Warren
> > > >
> > > > --
> > > > Warren L. DeLano, Ph.D.
> > > > Principal Scientist
> > > >
> > > > . DeLano Scientific LLC
> > > > . 400 Oyster Point Blvd., Suite 213
> > > > . South San Francisco, CA 94080
> > > > . Biz:(650)-872-0942 Tech:(650)-872-0834
> > > > . Fax:(650)-872-0273 Cell:(650)-346-1154
> > > > . mailto:wa...@de...
> > > >
> > > >
> > > > > -----Original Message-----
> > > > > From: pym...@li...
> > > > > [mailto:pym...@li...] On Behalf Of
> > > > > Dieter Blaas
> > > > > Sent: Monday, January 24, 2005 6:54 AM
> > > > > To: pym...@li...
> > > > > Subject: [PyMOL] electron density map manipulation
> > > > >
> > > > > Hi, I have been trying to visualize a DN6 electron
> density map.
> > > > > Although it is read in apparently correctly nothing
> shows on the
> > > > > screen. Are there any particular parameters to be set? I can
> > > > > visualize it in SwisspdbViewer but I was unable to produce
> > > > > surface rendering. Can Pymol produce a surface at a
> particular
> > > > > cut-off value as can Amira?
> > > > > Thanx for hints, Dieter
> > > > >
> > > > >
> > > > > -------------------------------------------------------
> > > > > This SF.Net email is sponsored by: IntelliVIEW -- Interactive
> > > > > Reporting Tool for open source databases. Create drag-&-drop
> > > > > reports. Save time by over 75%! Publish reports on the web.
> > > > > Export to DOC, XLS, RTF, etc.
> > > > > Download a FREE copy at http://www.intelliview.com/go/osdn_nl
> > > > > _______________________________________________
> > > > > PyMOL-users mailing list
> > > > > PyM...@li...
> > > > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > > > >
> > > >
> > > >
> > >
> > >
> > >
> >
> >
>
>
--__--__--
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users
End of PyMOL-users Digest
|
|
From: Geoui T. <ge...@em...> - 2005-01-31 16:56:09
|
Hi everybody, is anyone know how i can split the screen into different windows and load different protein in each window. To be more precise, i have 5 different proteins and i would like to have them all at the same time on the screen, but I would like them to have their own repair, just like if I had 5 pymol windows opened at the same time, but, in my exemple all would be in the same window but the protein would have their own origin and not centered on one point ... I don't know if I am clear enough ...? but if anyone understand my problem and has a solution it would be very kind to help me. Many thanks, Thibault |
|
From: Peter H. <pet...@st...> - 2005-01-31 15:16:04
|
not sure, but ... the chain ids are identical for both models. this might cause problems, whe= n=20 you merge both models into the same pdb file. try renaming the chain id of= =20 your second molecule... cheers, peter On Friday 28 January 2005 23:00, Michael George Lerner wrote: > hi, > > i want to combine the models in a biounit file. for example, > ftp://ftp.rcsb.org/pub/pdb/data/biounit/coordinates/divided/ky/1kyw.pdb2.= gz > has two models. so, i > > - load it > - split_states on it > - save everything into a pdb file > > but .. the pdb file ends up empty (it's just an END line). am i doing > something wrong? is there a workaround? > > 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 > > | / \ | mlerner@umich > > ------------------------------------------------------- > This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting > Tool for open source databases. Create drag-&-drop reports. Save time > by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users =2D-=20 ___________________________________________ Dr. Peter Haebel Philipps-Universit=E4t Marburg Institut f=FCr Pharmazeutische Chemie Marbacher Weg 6 D-35032 Marburg phone: +49-6421-28-25072 fax: +49-6421-28-28994 email: pet...@st... http://www.agklebe.de NAD3-Workshop 2005 - Divide&Conquer http://www.agklebe.de/workshop2005 |
|
From: Andreas H. <ah...@bi...> - 2005-01-31 11:24:17
|
Hi all,
I want to color code scop domains in PDB entries by querrying a database
server.
It works fine if I just call the function from the python script,
however if I define the function to be a Pymol fct, the call from pymol
causes an undefined MySQL Error in subchainString:
Traceback (most recent call last):
File "/usr/lib/python2.3/site-packages/pymol/parser.py", line 255, in
parse
exec(com2[nest]+"\n",pymol_names,pymol_names)
File "<string>", line 1, in ?
File "scop1.py", line 19, in domainDef
cmd.select("domain", "/%s//%s/"%(pdb, subchainString(px)))
File "scop1.py", line 11, in subchainString
cursor.execute("SELECT chain_id, begin, end FROM subchain WHERE
subchain.px='%s' LIMIT 1"% px )
File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 95,
in execute
return self._execute(query, args)
File "/usr/lib/python2.3/site-packages/MySQLdb/cursors.py", line 114,
in _execute
self.errorhandler(self, exc, value)
File "/usr/lib/python2.3/site-packages/MySQLdb/connections.py", line
33, in defaulterrorhandler
raise errorclass, errorvalue
InterfaceError: (0, '')
I have a suspecion it's to do with the quoting?
Also, is there a command similar to Rasmol's "pause"? Or do I have to use raw_input in the terminal I called pymol from?
Here is the simplified code:
##################################################################################
pdbLinkDir="/group/bioinf/Data/PDBLinks/"
from pymol import cmd
from pymol.cgo import *
import MySQLdb
from MySQLdb.cursors import DictCursor
def subchainString(px):
cursor.execute("SELECT chain_id, begin, end FROM subchain WHERE subchain.px='%s' LIMIT 1"% px )
data=cursor.fetchone()
if data["begin"]: return "%s/%s-%s"%(data["chain_id"], data["begin"], data["end"])
else: return "%s"%(data["chain_id"])
def domainDef(px, pdb):
cmd.load(pdbLinkDir+"%s.pdb"%pdb)
cmd.hide("everything","all")
cmd.select("domain", "/%s//%s/"%(pdb, subchainString(px)))
cmd.color("blue","domain")
cmd.show("cartoon", "all")
conn = MySQLdb.connect(db="pqs_psimap", host="dbserver", user="...", passwd="...")
cursor = conn.cursor(DictCursor)
#domainDef("25880E", "1tab") ## This works fine!!!
cmd.extend("domainDef", domainDef) ## breaks when called from pymol with
## domainDef("25880E", "1tab")
conn.close()
##################################################################################
Many thanks
--
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany
Phone: +49 351 463 40063
EMail: ah...@bi...
|
|
From: Warren D. <wa...@de...> - 2005-01-30 18:20:14
|
Dieter, Slices are a relatively new feature only found in the beta versions: http://delsci.com/beta http://delsci.com/macbeta Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of > dieter blaas > Sent: Friday, January 28, 2005 1:19 AM > To: pym...@li... > Cc: Warren DeLano > Subject: RE: [PyMOL] electron density map manipulation > > Thanx Warren, perfect! But when entering: > > "> load map1.dsn6 > > slice_new slice1,map1 > > I get the message: > Syntax Error: invalid syntax with a ^ pointing to the "1" in > slice1 I have tried several permutations of the syntax, but > always receive an error message! > On 27 Jan 2005 at 22:51, Warren DeLano wrote: > > > > 1/ can I make a solid surface? > > > > Solid (opaque) surface with isosurface command (just like isomesh) > > > > > 2/ can I make volume slices? > > > > Slices are possible: > > > > load map1.dsn6 > > slice_new slice1,map1 > > ramp_new ramp1,map1 > > color ramp1, slice1 > > > > Then ctrl-middle-click and drag to change slice contour coloring > > > > > 3/ can I load the map in the same way I load pdb files without > > > command line input and manipulate the parameters with the mouse? > > > > Not yet. > > > > > is it O.K. to answer in this way or should I send the mail to the > > > mailing list? > > > > The mailing list is preferable. > > > > Cheers, > > Warren > > > > > > -- > > Warren L. DeLano, Ph.D. > > Principal Scientist > > > > . DeLano Scientific LLC > > . 400 Oyster Point Blvd., Suite 213 > > . South San Francisco, CA 94080 > > . Biz:(650)-872-0942 Tech:(650)-872-0834 > > . Fax:(650)-872-0273 Cell:(650)-346-1154 > > . mailto:wa...@de... > > > > > > > -----Original Message----- > > > From: dieter blaas [mailto:die...@un...] > > > Sent: Thursday, January 27, 2005 9:20 PM > > > To: Warren DeLano > > > Subject: RE: [PyMOL] electron density map manipulation > > > > > > Thanx a lot, this works! I have three additional questions: > > > 1/ can I make a solid surface? > > > 2/ can I make volume slices? > > > 3/ can I load the map in the same way I load pdb files without > > > command line input and manipulate the parameters with the mouse? > > > > > > is it O.K. to answer in this way or should I send the mail to the > > > mailing list? > > > Dieter > > > > > > > > > On 27 Jan 2005 at 16:49, Warren DeLano wrote: > > > > > > > Dieter, > > > > > > > > Have you tried the isomesh and isosurf commands? > > > > > > > > load map1.dsn6, map1 > > > > isomesh mesh1, map1, 1.0 > > > > > > > > Cheers, > > > > Warren > > > > > > > > -- > > > > Warren L. DeLano, Ph.D. > > > > Principal Scientist > > > > > > > > . DeLano Scientific LLC > > > > . 400 Oyster Point Blvd., Suite 213 > > > > . South San Francisco, CA 94080 > > > > . Biz:(650)-872-0942 Tech:(650)-872-0834 > > > > . Fax:(650)-872-0273 Cell:(650)-346-1154 > > > > . mailto:wa...@de... > > > > > > > > > > > > > -----Original Message----- > > > > > From: pym...@li... > > > > > [mailto:pym...@li...] On Behalf Of > > > > > Dieter Blaas > > > > > Sent: Monday, January 24, 2005 6:54 AM > > > > > To: pym...@li... > > > > > Subject: [PyMOL] electron density map manipulation > > > > > > > > > > Hi, I have been trying to visualize a DN6 electron > density map. > > > > > Although it is read in apparently correctly nothing > shows on the > > > > > screen. Are there any particular parameters to be set? I can > > > > > visualize it in SwisspdbViewer but I was unable to produce > > > > > surface rendering. Can Pymol produce a surface at a > particular > > > > > cut-off value as can Amira? > > > > > Thanx for hints, Dieter > > > > > > > > > > > > > > > ------------------------------------------------------- > > > > > This SF.Net email is sponsored by: IntelliVIEW -- Interactive > > > > > Reporting Tool for open source databases. Create drag-&-drop > > > > > reports. Save time by over 75%! Publish reports on the web. > > > > > Export to DOC, XLS, RTF, etc. > > > > > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > > > > > _______________________________________________ > > > > > PyMOL-users mailing list > > > > > PyM...@li... > > > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > > > > > > > > > > > > > > > > > > > > |
|
From: Michael G. L. <ml...@um...> - 2005-01-28 22:01:04
|
hi, i want to combine the models in a biounit file. for example, ftp://ftp.rcsb.org/pub/pdb/data/biounit/coordinates/divided/ky/1kyw.pdb2.gz has two models. so, i - load it - split_states on it - save everything into a pdb file but .. the pdb file ends up empty (it's just an END line). am i doing something wrong? is there a workaround? 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 | / \ | mlerner@umich |
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From: Warren D. <wa...@de...> - 2005-01-28 21:06:31
|
Eiza, This isn't possible yet -- first someone needs to chemical recognition patterns, atom names, atom types, formal charges, partial charges and radii for nucliec acids to the dictionaries in the files: PyMOL/modules/chempy/champ/amber99.py and PyMOL/modules/chempy/champ/formal_charges.py Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of Eiza Yu > Sent: Tuesday, January 25, 2005 3:39 PM > To: pym...@li... > Subject: [PyMOL] vacuum electrostatics for nucleic acids? > > hi! > > Is there a way to (qualitatively) visualize electrostatics of > nucleic acids with Pymol? I know this can be done for > proteins already. Thanks. > > Eiza Yu > graduate student > |
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From: Warren D. <wa...@de...> - 2005-01-28 19:37:28
|
Andreas, It's not a stupid question -- its just a year or more ahead of its time. Right now "aligment" objects currently don't do anything other than show you which atoms were aligned in the 3D viewer. In time however, those objects will integrate with the sequence-viewer... Cheers, Warren > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of > Andreas Henschel > Sent: Friday, January 28, 2005 9:18 AM > To: pym...@li... > Subject: [PyMOL] Alignment objects > > Dear PyMOL community, > > I am trying to use the align command (from within python) > and want to evaluate the pairwise matches. > the command > > cmd.align(sel1, sel2, object="alignment") > > should do. Sorry for this stupid question, but how do I get > hold of the "alignment" object, and what is its functionality? > Ie which methods/values does it provide? > > Many thanks. > Andreas > > -- > Andreas Henschel > Bioinformatics Group > TU Dresden > Tatzberg 47-51 > 01307 Dresden, Germany > > Phone: +49 351 463 40063 > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IntelliVIEW -- Interactive > Reporting Tool for open source databases. Create drag-&-drop > reports. Save time by over 75%! Publish reports on the web. > Export to DOC, XLS, RTF, etc. > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
|
From: Andreas H. <ah...@bi...> - 2005-01-28 18:22:51
|
Dear PyMOL community, I am trying to use the align command (from within python) and want to evaluate the pairwise matches. the command cmd.align(sel1, sel2, object="alignment") should do. Sorry for this stupid question, but how do I get hold of the "alignment" object, and what is its functionality? Ie which methods/values does it provide? Many thanks. Andreas -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 |
|
From: Robert C. <rl...@po...> - 2005-01-28 16:04:47
|
Hi, * Lisa Craig <li...@sf...> [2005-01-27 20:43] wrote: > > How do I select side chains without selecting the backbone atoms? > Add "&! n. n+ca+c+o" or in long form "and not name n+ca+c+o" to your selection. So to colour all arginine and lysine side chains blue: color blue, r. arg+lys &! n. n+ca+c+o Cheers, Rob -- Robert L. Campbell, Ph.D. <rl...@po...> Senior Research Associate phone: 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 |
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From: dieter b. <die...@un...> - 2005-01-28 09:19:02
|
Thanx Warren, perfect! But when entering: "> load map1.dsn6 > slice_new slice1,map1 I get the message: Syntax Error: invalid syntax with a ^ pointing to the "1" in slice1 I have tried several permutations of the syntax, but always receive an error message! On 27 Jan 2005 at 22:51, Warren DeLano wrote: > > 1/ can I make a solid surface? > > Solid (opaque) surface with isosurface command (just like isomesh) > > > 2/ can I make volume slices? > > Slices are possible: > > load map1.dsn6 > slice_new slice1,map1 > ramp_new ramp1,map1 > color ramp1, slice1 > > Then ctrl-middle-click and drag to change slice contour coloring > > > 3/ can I load the map in the same way I load pdb files > > without command line input and manipulate the parameters with > > the mouse? > > Not yet. > > > is it O.K. to answer in this way or should I send the mail to > > the mailing list? > > The mailing list is preferable. > > Cheers, > Warren > > > -- > Warren L. DeLano, Ph.D. > Principal Scientist > > . DeLano Scientific LLC > . 400 Oyster Point Blvd., Suite 213 > . South San Francisco, CA 94080 > . Biz:(650)-872-0942 Tech:(650)-872-0834 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:wa...@de... > > > > -----Original Message----- > > From: dieter blaas [mailto:die...@un...] > > Sent: Thursday, January 27, 2005 9:20 PM > > To: Warren DeLano > > Subject: RE: [PyMOL] electron density map manipulation > > > > Thanx a lot, this works! I have three additional questions: > > 1/ can I make a solid surface? > > 2/ can I make volume slices? > > 3/ can I load the map in the same way I load pdb files > > without command line input and manipulate the parameters with > > the mouse? > > > > is it O.K. to answer in this way or should I send the mail to > > the mailing list? > > Dieter > > > > > > On 27 Jan 2005 at 16:49, Warren DeLano wrote: > > > > > Dieter, > > > > > > Have you tried the isomesh and isosurf commands? > > > > > > load map1.dsn6, map1 > > > isomesh mesh1, map1, 1.0 > > > > > > Cheers, > > > Warren > > > > > > -- > > > Warren L. DeLano, Ph.D. > > > Principal Scientist > > > > > > . DeLano Scientific LLC > > > . 400 Oyster Point Blvd., Suite 213 > > > . South San Francisco, CA 94080 > > > . Biz:(650)-872-0942 Tech:(650)-872-0834 > > > . Fax:(650)-872-0273 Cell:(650)-346-1154 > > > . mailto:wa...@de... > > > > > > > > > > -----Original Message----- > > > > From: pym...@li... > > > > [mailto:pym...@li...] On Behalf Of > > > > Dieter Blaas > > > > Sent: Monday, January 24, 2005 6:54 AM > > > > To: pym...@li... > > > > Subject: [PyMOL] electron density map manipulation > > > > > > > > Hi, I have been trying to visualize a DN6 electron density > > > > map. Although it is read in apparently correctly nothing > > > > shows on the screen. Are there any particular parameters to > > > > be set? I can visualize it in SwisspdbViewer but I was unable > > > > to produce surface rendering. Can Pymol produce a surface at > > > > a particular cut-off value as can Amira? > > > > Thanx for hints, Dieter > > > > > > > > > > > > ------------------------------------------------------- > > > > This SF.Net email is sponsored by: IntelliVIEW -- Interactive > > > > Reporting Tool for open source databases. Create drag-&-drop > > > > reports. Save time by over 75%! Publish reports on the web. > > > > Export to DOC, XLS, RTF, etc. > > > > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > > > > _______________________________________________ > > > > PyMOL-users mailing list > > > > PyM...@li... > > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > > > > > > > > > > |
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From: Lisa C. <li...@sf...> - 2005-01-28 04:44:27
|
Hi, How do I select side chains without selecting the backbone atoms? Cheers, Lisa. |
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From: Jonathan E. <je...@di...> - 2005-01-28 01:30:41
|
Hello Pymol Users/Developers, I am developing a wxpython application for windows that is essentially a fancy multiple sequence alignment viewer. I have linked this to pymol. I would like to be able to launch multiple instances of pymol with different molecules from a single parent process. =20 The current solution I am using is as follows: I execute pymol as a separate asynchronous process and then redirect stdin, stdout, and stderr. Pymol is launched with the external GUI disabled. Commands are sent to pymol on stdin. This works reasonably well for sending commands to multiple instances of pymol but there are two problems. =20 1: When pymol is closed using the X in the top right corner of the opengl frame pymol freezes and is unrecoverable. Pymol will close clean if I exit from the command prompt but not from the frame. This seems to be an artifact of the way it is launched and does not occur when I launch pymol with -ix directly from a command prompt rather then a wxpython program. If there is a solution for this, all is well, it is a bit hackish but it works. 2: This is not as much of a problem but pymol somehow manages to consume the command window that launches the wxpython application. I find this remarkably confusing, I am not an expert developer but I thought launching as an asynchronous process would prevent that from occurring. =09 I'm a pymol newbie and am not sure if this is the best way to do this. I have tried a few other approaches from mail lists. 1: Control through greg landrum's xmlrpc listener. This exhibits the same exit issues if I launch pymol form the parent application. 2: Launching pymol on start up and communicating through a pymol cmd object. This consumes the parent thread and I am unable to determine how to launch multiple instances. Consumption of the parent thread causes the main application to exit when pymol exits. This is a bit of a show stopper. =09 Any advice/suggestions would be greatly appreciated. Thank you Jonathan Eads je...@di... |
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From: Warren D. <wa...@de...> - 2005-01-26 21:53:30
|
> > Actually when you > > build the slide in PPT 2004 in edit mode the preview of the movie > > plays fine but not in presentation mode!!! If anyone has > found a work > > round let me know! The only PC/Powerpoint workaround I've found is to buy a faster laptop and keep movie resolutions low (e.g. 640x480 for Cinepak). It is actually faster magnifying a low resolution movie than to playing a higher-resolution movie without scaling. For example, the g3w5 smoothly playing PowerPoint movie I've beeen able to generate is 960x720 scaled up to 1024x768 (full-screen) on a 2.2 Ghz Pentium 4M laptop with the MPEG4 V2 codec (compressed using Premiere on a PC). Cheers, Warren PS. If a Mac laptop is an option for you, they generally do better with video & animations. -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of > Nat Echols > Sent: Wednesday, January 26, 2005 11:00 AM > To: pym...@li... > Subject: Re: [PyMOL] animation format > > > There is a well documented bug in Powerpoint 2004 for mac regarding > > movie playback performance which seems to be the problem. > There are > > hundreds of posts on Microsoft's support forums. Actually when you > > build the slide in PPT 2004 in edit mode the preview of the movie > > plays fine but not in presentation mode!!! If anyone has > found a work > > round let me know! > > I suspect this is the same bug I've encountered on Windows in > PowerPoint 2003. (And on my boss's shiny new G4 with PPT > 2004. Oddly, his old G3 with PPT 98 plays the same movies > just fine in presentations.) For the jerkiness during > playback, reducing the framerate certainly helps on a PC. > (One of my coworkers pointed me to a Windows program called > VideoLan, which makes it ridiculously easy to assemble PNGs > into a variety of movie formats, with complete control over > framerate and compression. It's a pretty slick program- $25 > shareware I think.) > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IntelliVIEW -- Interactive > Reporting Tool for open source databases. Create drag-&-drop > reports. Save time by over 75%! Publish reports on the web. > Export to DOC, XLS, RTF, etc. > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
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From: Nat E. <ec...@uc...> - 2005-01-26 19:14:25
|
> There is a well documented bug in Powerpoint 2004 for mac regarding > movie playback performance which seems to be the problem. There are > hundreds of posts on Microsoft's support forums. Actually when you > build the slide in PPT 2004 in edit mode the preview of the movie plays > fine but not in presentation mode!!! If anyone has found a work round > let me know! I suspect this is the same bug I've encountered on Windows in PowerPoint 2003. (And on my boss's shiny new G4 with PPT 2004. Oddly, his old G3 with PPT 98 plays the same movies just fine in presentations.) For the jerkiness during playback, reducing the framerate certainly helps on a PC. (One of my coworkers pointed me to a Windows program called VideoLan, which makes it ridiculously easy to assemble PNGs into a variety of movie formats, with complete control over framerate and compression. It's a pretty slick program- $25 shareware I think.) |
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From: Martin M. <mg...@mr...> - 2005-01-26 11:39:41
|
I've used Keynote and it works well (have only tried version 1). My only gripe about it is writing text with superscript/subscript isn't easy like it is in PPT. There is a well documented bug in Powerpoint 2004 for mac regarding movie playback performance which seems to be the problem. There are hundreds of posts on Microsoft's support forums. Actually when you build the slide in PPT 2004 in edit mode the preview of the movie plays fine but not in presentation mode!!! If anyone has found a work round let me know! I've just made three movies of a simple rotation each one was saved using Macpymol 0.98 beta 27s Save movie as quicktime (more options) drop down. I selected best quality for all three but tried 12, 15 and 24 fps. Powerpoint 2004 for Mac gives either a jerky, stop/start rotation or (with a bit of fiddling of the "scale" settings) it gives a reasonable rotation but the image breaks up during playback. All three versions work well (an occaisional streaky line) in Powerpoint v.X and work perfectly in Keynote - smooth rotation and no image breakup. If you use a mac, use PPT v.X or Keynote! MGM On 25 Jan 2005, at 19:00, Nat Echols wrote: >> Thanks to the poewrful software I was able to create some protein >> animations using Python. As a mac user I have the option to save >> directly the animation for quick time player. From the options I have >> upom save, I tried 'movie' and 'animation' and both formats show a >> reduced performance when the files are launched from PowerPoint. Since > > Well, using MPEG encoding on a PC I've found that a normal 25fps > framerate > can involve too much data for PowerPoint to handle, thanks to some > idiotic "feature" used to scale movies in presentation mode. In the > past, I've been able to fix this occasionally using smaller movies, or > using a reduced framerate. I found that 20fps was quite reasonable and > the computer didn't choke. (Oddly, I was using lower compression and > the bitrate was actually higher with the slower movies!) > > Personally, I've found MPEGs to be extremely portable and (to the > extent > that anything does) they work well in PowerPoint. You just need to > fiddle > with the compression and framerate settings to get something > high-quality > that won't hiccup in presentations. Either Windows Media or Quicktime > can produce better movies but I think this involves more advanced > codecs > and you lose quite a bit of portability. You should have the same > control > over compression ratio and framerate, though. > > Has anyone used Keynote for anything like this, by the way? > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting > Tool for open source databases. Create drag-&-drop reports. Save time > by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
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From: Bond, I. \(UMKC-Student\) <ib...@um...> - 2005-01-26 01:25:52
|
I really need to know how to load 2 proteins and superimpose them.=20 =20 Thank you |
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From: Eiza Y. <e2...@um...> - 2005-01-25 23:39:03
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hi! Is there a way to (qualitatively) visualize electrostatics of nucleic = acids with Pymol? I know this can be done for proteins already. Thanks. Eiza Yu graduate student |
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From: Nat E. <ec...@uc...> - 2005-01-25 19:15:22
|
> Thanks to the poewrful software I was able to create some protein > animations using Python. As a mac user I have the option to save > directly the animation for quick time player. From the options I have > upom save, I tried 'movie' and 'animation' and both formats show a > reduced performance when the files are launched from PowerPoint. Since Well, using MPEG encoding on a PC I've found that a normal 25fps framerate can involve too much data for PowerPoint to handle, thanks to some idiotic "feature" used to scale movies in presentation mode. In the past, I've been able to fix this occasionally using smaller movies, or using a reduced framerate. I found that 20fps was quite reasonable and the computer didn't choke. (Oddly, I was using lower compression and the bitrate was actually higher with the slower movies!) Personally, I've found MPEGs to be extremely portable and (to the extent that anything does) they work well in PowerPoint. You just need to fiddle with the compression and framerate settings to get something high-quality that won't hiccup in presentations. Either Windows Media or Quicktime can produce better movies but I think this involves more advanced codecs and you lose quite a bit of portability. You should have the same control over compression ratio and framerate, though. Has anyone used Keynote for anything like this, by the way? |
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From: Kostas T. <ko...@nm...> - 2005-01-25 09:04:04
|
Hallo Pymolers Thanks to the poewrful software I was able to create some protein animations using Python. As a mac user I have the option to save directly the animation for quick time player. From the options I have upom save, I tried 'movie' and 'animation' and both formats show a reduced performance when the files are launched from PowerPoint. Since there is a dozen of other options I wonder if any of them produce better results for PowerPoint. I would also like to know which of them gives you the best quality appart from my previous request. cheers kostas -- ------------------------------------------------------------------------ Kostas Tripsianes, PhD student Bijvoet Center for Biomolecular Research NMR Spectroscopy, Utrecht University Padualaan 8, 3584 CH Utrecht, The Netherlands ko...@nm... phone: +31-30-2532875 fax: +31-30-2537623 :-) |
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From: Alexandra D. <de...@ma...> - 2005-01-25 06:14:40
|
Hello All, Is there a way to have the automatic secondary structure assignments output in the Pymol log-file explicitly (eg HELIX from resi 1-100, LOOP from 101-110 etc) much like MOLAUTO is able to do? I realize that secondary structure assignment in Pymol is not always correct, but I would to alter it to make a cartoon figure without having to write the entire script with all the secondary structure segments from scratch. Thank you very much, Alexandra |
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From: Dieter B. <die...@un...> - 2005-01-24 14:54:46
|
Hi, I have been trying to visualize a DN6 electron density map. Although it is read in apparently correctly nothing shows on the screen. Are there any particular parameters to be set? I can visualize it in SwisspdbViewer but I was unable to produce surface rendering. Can Pymol produce a surface at a particular cut-off value as can Amira? Thanx for hints, Dieter |