pymol-users Mailing List for PyMOL Molecular Graphics System

Warren,

The problem is with ray tracing a surface from an old_session.pse.   
Much better results if you retrace it with the version that created  
it.  Thanks for your help.

Mark
_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Biophysics Research Division, University of Michigan

On Feb 28, 2006, at 6:13 PM, Warren DeLano wrote:

> Hi Mark,
>
> Hmm.  PyMOL attempts to migrate old settings into the new model,  
> but it
> isn't perfect and one may need to fiddle with the various settings  
> after
> migration.  We'll need a new feature to reinitialize settings without
> deleting content so thanks for the suggestion!  In the meantime,  
> you can
> do something like this:
>
> from chempy import io
> sess=io.pkl.fromFile("old_session.pse")
> del sess['settings']
> io.pkl.toFile(sess,"new_session.pse")
>
> load new_session.pse
>
> which will load the old session with new default settings.
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . 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
>> Mark A Saper
>> Sent: Tuesday, February 28, 2006 11:12 AM
>> To: Pymol
>> Subject: [PyMOL] Set all settings to default
>>
>> 0.99 and 0.98 have different ray tracing and lighting models.
>>  When I read an old .pse file into .99, are the settings in
>> the old file converted to the new style?  Is there a way to
>> reset all of the settings to default values, without
>> modifying the objects themselves?
>>
>> Thanks,
>> Mark
>> _________________________________
>> Mark A. Saper, Ph.D.
>> Associate Professor of Biological Chemistry Biophysics
>> Research Division, University of Michigan Chemistry Building
>> Room 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A.
>>
>> sa...@um...        (734) 764-3353        fax (734) 764-3323
>> http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by xPML, a groundbreaking
>> scripting language that extends applications into web and
>> mobile media. Attend the live webcast and join the prime
>> developer group breaking into this new coding territory!
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&
>> dat=121642
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>>
>>
>
>

Hi Mark,

Hmm.  PyMOL attempts to migrate old settings into the new model, but it
isn't perfect and one may need to fiddle with the various settings after
migration.  We'll need a new feature to reinitialize settings without
deleting content so thanks for the suggestion!  In the meantime, you can
do something like this:

from chempy import io
sess=3Dio.pkl.fromFile("old_session.pse")
del sess['settings']
io.pkl.toFile(sess,"new_session.pse")

load new_session.pse

which will load the old session with new default settings.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Mark A Saper
> Sent: Tuesday, February 28, 2006 11:12 AM
> To: Pymol
> Subject: [PyMOL] Set all settings to default
>=20
> 0.99 and 0.98 have different ray tracing and lighting models.=20
>  When I read an old .pse file into .99, are the settings in=20
> the old file converted to the new style?  Is there a way to=20
> reset all of the settings to default values, without=20
> modifying the objects themselves?
>=20
> Thanks,
> Mark
> _________________________________
> Mark A. Saper, Ph.D.
> Associate Professor of Biological Chemistry Biophysics=20
> Research Division, University of Michigan Chemistry Building=20
> Room 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A.
>=20
> sa...@um...        (734) 764-3353        fax (734) 764-3323
> http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking=20
> scripting language that extends applications into web and=20
> mobile media. Attend the live webcast and join the prime=20
> developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Joel,

Not yet...in fact, we're still not able to show an alignment in the
sequence viewer.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Joel Tyndall
> Sent: Tuesday, February 28, 2006 12:25 PM
> To: pym...@li...
> Subject: [PyMOL] Sequence view print out
>=20
> Hi all,
>=20
> I'm not sure if this has been asked before and I'm not sure=20
> if its possible...but here goes anyway. Is there a way to=20
> print/export the sequences in the viewer window? It would be=20
> an easy way to translate actual secondary structure to a=20
> sequence alignment
>=20
> Thanks
>=20
> J
>=20
> --
> Joel Tyndall, PhD
>=20
> Lecturer
> National School of Pharmacy
> University of Otago
> PO Box 913 Dunedin
> New Zealand                    =20
>=20
> Pukenga
> Te Kura Taiwhanga Putaiao
> Te Whare Wananga o Otago
> Pouaka Poutapeta 913 Otepoti
> Aotearoa
>=20
> Ph / Waea               +64 3 4797293=20
> Fax / Waeawhakaahua     +64 3 4797034
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking=20
> scripting language that extends applications into web and=20
> mobile media. Attend the live webcast and join the prime=20
> developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Hi all,

I'm not sure if this has been asked before and I'm not sure if its 
possible...but here goes anyway. Is there a way to print/export the 
sequences in the viewer window? It would be an easy way to translate 
actual secondary structure to a sequence alignment

Thanks

J

-- 
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                     

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea               +64 3 4797293 
Fax / Waeawhakaahua     +64 3 4797034

Hi,
 
 I am using ver 0.99 and would like to install the castp plugin.
 i am not successful in installing under Linux/OSX. i am getting the following error.
 
 
 This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc1.
 Exception in plugin 'CASTpyMOL' -- Traceback follows...
 Traceback (most recent call last):
   File "/new-programs/pymol/modules/pmg_tk/PMGApp.py", line 156, in initialize_plugins
     __builtin__.__import__(mod_name)
 ImportError: Bad magic number in /new-programs/pymol/modules/pmg_tk/startup/CASTpyMOL.pyc
 Error: unable to initialize plugin 'CASTpyMOL'.
 
 
 any help would be appreciated.
 Thanks
 Raj

		
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0.99 and 0.98 have different ray tracing and lighting models.  When I  
read an old .pse file into .99, are the settings in the old file  
converted to the new style?  Is there a way to reset all of the  
settings to default values, without modifying the objects themselves?

Thanks,
Mark
_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Biophysics Research Division, University of Michigan
Chemistry Building Room 3040
930 N University Ave
Ann Arbor MI 48109-1055 U.S.A.

sa...@um...        (734) 764-3353        fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

Indraneel,

At present, wizards need to be located in the
$PYMOL_PATH/modules/pymol/wizard directory -- changing this would be
nontrivial, since all wizards are assumed to reside in the
"pymol.wizard" namespace.

FYI:  module-name.__path__ has a different meaning than sys.path.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: Indraneel Majumdar [mailto:ind...@sm...]=20
> Sent: Monday, February 27, 2006 5:51 PM
> To: pym...@li...
> Cc: Warren DeLano
> Subject: wizard path option
>=20
> Hi,
>=20
> I notice that imp.find_module() uses wizard.__path__ instead=20
> of the default sys.path. Is there a problem in using=20
> wizard.__path__+sys.path ?
> I guess changing wizard.__path__ is probably a bad idea.
>=20
> How should one run wizards not located in the pymol tree (eg=20
> during testing)?
>=20
> TIA,
> Indraneel
>=20
> --
> http://prodata.swmed.edu
>=20
>=20
>=20
>=20

I have been trying to build and install pymol-0.99rc from source because th=
e=20
binary version will not work on my system (there appears to be an=20
incompatibility in my recently updated python install and the provided pymo=
l=20
=2D rebuilding on my pentiumpro system worked fine).  I have managed to get=
=20
through the main build process but when I run "python setup.py install" I=20
get:

[root@stonekeep pymol-0.99]# python setup.py install
running install
running build
running build_py
running build_ext
building 'pymol._cmd' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe=20
=2DWp,-D_FORTIFY_SOURCE=3D2 -Wall -g -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE=
=20
=2DD_PYMOL_FREETYPE -D_HAVE_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ila=
yer3=20
=2DIlayer4 -Ilayer5 -I/usr/include/freetype2 -I/usr/include/python2.4 -c=20
layer0/Crystal.c -o build/temp.linux-x86_64-2.4/layer0/Crystal.o -ffast-mat=
h=20
=2Dfunroll-loops -O3
layer0/Crystal.c:314:1: error: unterminated argument list invoking macro=20
"sprintf"
layer0/Crystal.c: In function 'CrystalDump':
layer0/Crystal.c:201: error: syntax error at end of input
layer0/Crystal.c:201: warning: unused variable '_FBstr'
layer0/Crystal.c:199: warning: unused variable 'i'
layer0/Crystal.c:198: warning: unused variable 'G'
error: command 'gcc' failed with exit status 1

I am no programmer but my cursory examination of the "offending" portion of=
=20
Crystal.c above doesn't present any obvious problems that I can fix.  Anyon=
e=20
have any idea as to what is going on and how to fix it? =20

praedor
=2D-=20
The Reichstag fire is to Hitler as 9/11 is to Bush

Hi Michael,

simply load both molecules in the same frame, and change to Mouse/3 
Button Editing Mode.
You have to select the molecule you want to translate/rotate by left 
clicking on an atom of it.
Now, you have following options:
shift+LMB+mouse_movement := rotate this molecule around the selected atom

shift+MMB+mouse_movement := translate in x and y directions

shift+RMB+mouse_movement := translate in z direction.

Just play around with these combinations...
Greetz

Yusuf

Quoting Michael Weber <we...@st...>:

> Hello,
> how is it possible to independently rotate or translate two molecules 
> in pyMOL? I would like to display the interaction of two 
> macromolecules but to do so, I first have to adjust their position 
> relative to each other.
> Do I have to use different frames for loading, then positioning each 
> in the desired way and finally display as "all states" or is there a 
> more convenient way to achieve this apparently simple task that I 
> have obviously overlooked?
>
> Thanks a lot for your help,
> Michael.

Hello,
how is it possible to independently rotate or translate two molecules in =
pyMOL? I would like to display the interaction of two macromolecules but =
to do so, I first have to adjust their position relative to each other.
Do I have to use different frames for loading, then positioning each in =
the desired way and finally display as "all states" or is there a more =
convenient way to achieve this apparently simple task that I have =
obviously overlooked?

Thanks a lot for your help,
Michael.

Dear all,

   I made a PQR file by PDB2PQR, and then in PyMOL, I run apbs.

  I got an error. Help.


PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC.

  A current PyMOL Maintenance and/or Support Subscription may be required
  for legal use of this Build beyond a finite honor-system evaluation 
period.
  Please visit http://www.pymol.org/funding.html for more information.

  This PyMOL Executable Build incorporates Open-Source PyMOL 0.99beta37.
  OpenGL graphics engine:
   GL_VENDOR: NVIDIA Corporation
   GL_RENDERER: Quadro4 750 XGL/AGP/SSE2
   GL_VERSION: 1.5.2 NVIDIA 66.29
  Adapting to Quadro hardware.
  Detected 2 CPUs.  Enabled multithreaded rendering.
  CmdLoad: "pdb3929-out" loaded as "pdb3929-out".
  APBS Tools: set pqr file to 
/datadisk/people/syliu/Backup_Design/epodesign/EPO_DATA/Data_1mai/Charmmed/ReComputed/11410261472.pqr
cs [5, 7, 8]
finedim [71.384999990463257, 96.904001235961914, 116.09099578857422]
nlev 4
mult_fac 32
finegridpoints [161, 225, 257]
Maximum number of grid points exceeded.  Old grid dimensions were [161, 
225, 257]
Fine grid points rounded down from [81, 113, 129]
New grid dimensions are [65, 97, 129]
  APBS Tools: coarse grid: (87.354,130.737,163.355)
  APBS Tools: fine grid: (71.385,96.904,116.091)
  APBS Tools: center: (-22.203,10.832,100.751)
  APBS Tools: fine grid points (65,97,129)


     ----------------------------------------------------------------------
     APBS -- Adaptive Poisson-Boltzmann Solver
     Version 0.4.0

     Nathan A. Baker (ba...@bi...)
     Dept. Biochemistry and Molecular Biophysics
     Center for Computational Biology
     Washington University in St. Louis

     Additional contributing authors listed in the code documentation.

     Copyright (c) 2002-2005.  Washington University in St. Louis.
     All Rights Reserved.
     Portions Copyright (c) 1999-2002.  The Regents of the University of
     California.
     Portions Copyright (c) 1995.  Michael Holst.

     This program is free software; you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
     the Free Software Foundation; either version 2 of the License, or
     (at your option) any later version.

     This program is distributed in the hope that it will be useful,
     but WITHOUT ANY WARRANTY; without even the implied warranty of
     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     GNU General Public License for more details.

     You should have received a copy of the GNU General Public License
     along with this program; if not, write to the Free Software
     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 
USA
     ----------------------------------------------------------------------
     APBS uses PMG and FEtk to solve the Poisson-Boltzmann equation
     numerically.  FEtk and PMG are developed and maintained by the Holst
     Research Group at UC San Diego.  PMG is designed to solve the 
nonlinear
     Poisson-Boltzmann equation and similar problems with linear space and
     time complexity through the use of box methods, inexact Newton 
methods,
     and algebraic multilevel methods.  FEtk is designed to solve general
     coupled systems of nonlinear partial differential equations accurately
     and efficiently using adaptive multilevel finite element methods,
     inexact Newton methods, and algebraic multilevel methods.  More
     information about PMG and FEtk may be found at <http://www.FEtk.ORG>.
     ----------------------------------------------------------------------
     Please cite your use of APBS as:
        Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics 
of
        nanosystems: application to microtubules and the ribosome. Proc.
        Natl. Acad. Sci. USA 98, 10037-10041 2001.


This executable compiled on Feb 28 2006 at 10:10:21

Parsing input file pymol-generated.in...
Parsed input file.
Got PQR paths for 1 molecules
Reading PQR-format atom data from 
/datadisk/people/syliu/Backup_Design/epodesign/EPO_DATA/Data_1mai/Charmmed/ReComputed/11410261472.pqr.
Vio_ctor2: some error occurred.
Vio_ctor: Vio_ctor2() failed.
Problem opening virtual socket 
/datadisk/people/syliu/Backup_Design/epodesign/EPO_DATA/Data_1mai/Charmmed/ReComputed/11410261472.pqr!
Error reading molecules!
ObjectMapLoadDXFile-Error: Unable to open file!






On Thu, 23 Feb 2006 pym...@li... wrote:

> Send PyMOL-users mailing list submissions to
> 	pym...@li...
>
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
> 	pym...@li...
>
> You can reach the person managing the list at
> 	pym...@li...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
>
>
> Today's Topics:
>
>   1. running macpymol in the background from the terminal (Andrew Wollacott)
>   2. label positions, centered, left, or right (Seth Harris)
>   3. RE: label positions, centered, left, or right (Warren DeLano)
>
> --__--__--
>
> Message: 1
> Date: Wed, 22 Feb 2006 21:26:29 -0800
> From: "Andrew Wollacott" <sen...@gm...>
> To: pym...@li...
> Subject: [PyMOL] running macpymol in the background from the terminal
>
> ------=_Part_19022_27230051.1140672389773
> Content-Type: text/plain; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> Content-Disposition: inline
>
> hello,
>
> I'm running MacPyMol 0.99.  I typically open pymol from the terminal (
> terminal.app) using the "open" command.
>
>> open test.pdb
>
> I have .pdb files set to open with MacPyMol, so graphicConverter doesn't
> open when I do this.  The problem I have when doing this is that when
> entering the "pwd" command into pymol, I get the following:
>
> PyMOL> pwd
> /
>
> so pymol thinks it's running from the root directory.  This makes it tough
> for me to load more pdbfiles into pymol using the "load" command as I must
> first "cd" into the directory with pymol.  Just a note, that in version 0.9=
> 8,
> using the "open" command, pymol would recognize what directory it was opene=
> d
> from.
>
> Now, I can use the "pymol test.pdb" to open pdbfiles, but then the terminal
> gets the output from pymol.  I've tried to run pymol in the background so
> that I can continue to use this terminal window while stilll having pymol
> open.  Using "pymol test.pdb &" I still get pymol output to the terminal.  =
> I
> could use "pymol test.pdb >& /dev/null &" but that seems quite a bit more
> verbose compared to "open test.pdb"
>
> I guess I could alias pymol to essentially pipe it's output to /dev/null bu=
> t
> since version 0.98 worked fine, I was wondering if anyone has a workaround
> for this inconvenience.
>
> Thanks.
>
> - Andrew Wollacott
>
> ------=_Part_19022_27230051.1140672389773
> Content-Type: text/html; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> Content-Disposition: inline
>
> hello,<br><br>I'm running MacPyMol 0.99.&nbsp; I typically open pymol from =
> the terminal (terminal.app) using the &quot;open&quot; command.<br><br>&gt;=
> open test.pdb<br><br>I have .pdb files set to open with MacPyMol, so graph=
> icConverter doesn't open when I do this.&nbsp; The problem I have when doin=
> g this is that when entering the &quot;pwd&quot; command into pymol, I get =
> the following:
> <br><br>PyMOL&gt; pwd<br>/<br><br>so pymol thinks it's running from the roo=
> t directory.&nbsp; This makes it tough for me to load more pdbfiles into py=
> mol using the &quot;load&quot; command as I must first &quot;cd&quot; into =
> the directory with pymol.&nbsp; Just a note, that in version=20
> 0.98, using the &quot;open&quot; command, pymol would recognize what direct=
> ory it was opened from.<br><br>Now, I can use the &quot;pymol test.pdb&quot=
> ; to open pdbfiles, but then the terminal gets the output from pymol.&nbsp;=
> I've tried to run pymol in the background so that I can continue to use th=
> is terminal window while stilll having pymol open.&nbsp; Using &quot;pymol=
> =20
> test.pdb &amp;&quot; I still get pymol output to the terminal.&nbsp; I coul=
> d use &quot;pymol test.pdb &gt;&amp; /dev/null &amp;&quot; but that seems q=
> uite a bit more verbose compared to &quot;open test.pdb&quot;<br><br>I gues=
> s I could alias pymol to essentially pipe it's output to /dev/null but sinc=
> e version=20
> 0.98 worked fine, I was wondering if anyone has a workaround for this incon=
> venience.<br><br>Thanks.<br><br>- Andrew Wollacott<br><br><br>
>
> ------=_Part_19022_27230051.1140672389773--
>
>
> --__--__--
>
> Message: 2
> Date: Thu, 23 Feb 2006 10:39:32 -0800
> From: "Seth Harris" <se...@gm...>
> To: pym...@li...
> Subject: [PyMOL] label positions, centered, left, or right
>
> ------=_Part_8191_17923195.1140719972653
> Content-Type: text/plain; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> Content-Disposition: inline
>
> Hi all,
>
> Minor thing, but thought I'd ask...
>
> Labels now appear to be centered on whatever atom they are labeling.
> Previously, the left-hand side of the label was on the atom (left-anchored)=
> .
> Is there a way to choose whether the label is left-anchored, centered, or
> right-anchored?
>
> I find that it's hard to offset the label sufficiently with commands like:
>
> label myprot and name ca, "    %s%s" % (resn,resi)
>
> which used to get the label to float nicely just to the right of the atom.
> Now that the label is centered the spaces don't help push the labels over a=
> s
> much as they used to, and the obvious route of adding twice as many spaces
> somehow isn't getting me there. I thought there might be an anchor, align,
> or justification flag on the labels.
>
> I did also notice that in editing mode you can drag the labels to whatever
> position you wanted in recent betas.  Very nice!
>
> Cheers,
> Seth
>
> ------=_Part_8191_17923195.1140719972653
> Content-Type: text/html; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> Content-Disposition: inline
>
> Hi all,<br>
> <br>
> Minor thing, but thought I'd ask...<br>
> <br>
> Labels now appear to be centered on whatever atom they are labeling.
> Previously, the left-hand side of the label was on the atom
> (left-anchored). Is there a way to choose whether the label is
> left-anchored, centered, or right-anchored? <br>
> <br>
> I find that it's hard to offset the label sufficiently with commands like:<=
> br>
> <br>
> label myprot and name ca, &quot;&nbsp;&nbsp;&nbsp; %s%s&quot; % (resn,resi)=
> <br>
> <br>
> which used to get the label to float nicely just to the right of the atom. =
> <br>
> Now that the label is centered the spaces don't help push the labels
> over as much as they used to, and the obvious route of adding twice as
> many spaces somehow isn't getting me there. I thought there might be an
> anchor, align, or justification flag on the labels. <br>
> <br>
> I did also notice that in editing mode you can drag the labels to whatever =
> position you wanted in recent betas.&nbsp; Very nice!<br>
> <br>
> Cheers,<br>
> Seth<br>
>
> ------=_Part_8191_17923195.1140719972653--
>
>
> --__--__--
>
> Message: 3
> Subject: RE: [PyMOL] label positions, centered, left, or right
> Date: Thu, 23 Feb 2006 10:53:21 -0800
> From: "Warren DeLano" <wa...@de...>
> To: "Seth Harris" <se...@gm...>,
> 	<pym...@li...>
>
> Seth,
>
> Yes, via the "label_position" setting which specifies x,y, and z
> alignment of labels.
>
> Values in the range [-1,1] imply alignment.  Beyond that, it is a
> translation along camera axes in model-space dimensions. =20
>
> # for left alignment 0.75 A in front of atom
>
> set label_position, [-1,0,1.75]
>
> # for right alignment directly on atom
>
> set label_position, [1,0,0]
>
> # for left alignment 1 A to right of atom
>
> set label_position, [2,0,0]
>
> # for center alignment 2 A below atom
>
> set label_position, [0,-3,0]
>
> # centered 3 A in front of atom
>
> set label_position, [0,0,4]
>
> etc.
>
> Cheers,
> Waren
>
>
> --
> Warren L. DeLano, Ph.D.                    =20
> Principal Scientist
>
> . DeLano Scientific LLC =20
> . 400 Oyster Point Blvd., Suite 213          =20
> . South San Francisco, CA 94080 USA  =20
> . Biz:(650)-872-0942  Tech:(650)-872-0834    =20
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...     =20
> =20
>
>> -----Original Message-----
>> From: pym...@li...=20
>> [mailto:pym...@li...] On Behalf Of=20
>> Seth Harris
>> Sent: Thursday, February 23, 2006 10:45 AM
>> To: pym...@li...
>> Subject: [PyMOL] label positions, centered, left, or right
>> =20
>> Hi all,
>> =20
>> Minor thing, but thought I'd ask...
>> =20
>> Labels now appear to be centered on whatever atom they are=20
>> labeling. Previously, the left-hand side of the label was on=20
>> the atom (left-anchored). Is there a way to choose whether=20
>> the label is left-anchored, centered, or right-anchored?=20
>> =20
>> I find that it's hard to offset the label sufficiently with=20
>> commands like:
>> =20
>> label myprot and name ca, "    %s%s" % (resn,resi)
>> =20
>> which used to get the label to float nicely just to the right=20
>> of the atom.=20
>> Now that the label is centered the spaces don't help push the=20
>> labels over as much as they used to, and the obvious route of=20
>> adding twice as many spaces somehow isn't getting me there. I=20
>> thought there might be an anchor, align, or justification=20
>> flag on the labels.=20
>> =20
>> I did also notice that in editing mode you can drag the=20
>> labels to whatever position you wanted in recent betas.  Very nice!
>> =20
>> Cheers,
>> Seth
>> =20
>> =20
>
>
>
> --__--__--
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> End of PyMOL-users Digest
>

Hi,

I notice that imp.find_module() uses wizard.__path__ instead of the
default sys.path. Is there a problem in using wizard.__path__+sys.path ?
I guess changing wizard.__path__ is probably a bad idea.

How should one run wizards not located in the pymol tree (eg during
testing)?

TIA,
Indraneel

-- 
http://prodata.swmed.edu

I would like to draw the surface of a protein with the contribution of
each residue clearly shown. In other words when two adjacent triangles
are assigned to different residues, those and only those triangles should
be drawn in -say- black.

I have no idea how to do it.
Aldo
-- 

Hi all,
I'm using macPyMOL 0.99rc1 and found very useful the commands  
align&pair_fit to do superposition. I'm just wondering which specific  
algorithm they use, if somebody never used them to do superposition  
of Ca trace for publications, and if there is a specific reference to  
them.
Thanks in advance,
Enrico.

--
Enrico Malito
Dept. of Biochemistry and Molecular Genetics
University of Illinois at Chicago
900 S. Ashland Ave.
Molecular Biology Research Building, Room 1116
Chicago, IL 60607 - U.S.A.
Tel (312) 996-6299
Fax (312) 355-4535

You can call the executable inside an application and it will work in the 
normal unix way, eg

/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL

You might want to make an alias or a function or a symbolic link like

alias pymol=/Applications/Xtal/MacPyMOL.app/Contents/MacOS/MacPyMOL

or

pymol() { /Applications/Xtal/MacPyMOL.app/Contents/MacOS/MacPyMOL "$@" ; }

or

ln -s  /Applications/Xtal/MacPyMOL.app/Contents/MacOS/MacPyMOL 
/usr/local/bin/pymol


more here, on the wiki:

http://www.pymolwiki.org/index.php/Launching_PyMOL#MacOS_X:


HTH,

Bill



> From: "Andrew Wollacott" <sen...@gm...>
> To: pym...@li...
> Subject: [PyMOL] running macpymol in the background from the terminal
>
> ------=_Part_19022_27230051.1140672389773
> Content-Type: text/plain; charset=ISO-8859-1
> Content-Transfer-Encoding: quoted-printable
> Content-Disposition: inline
>
> hello,
>
> I'm running MacPyMol 0.99.  I typically open pymol from the terminal (
> terminal.app) using the "open" command.
>
>> open test.pdb
>
> I have .pdb files set to open with MacPyMol, so graphicConverter doesn't
> open when I do this.  The problem I have when doing this is that when
> entering the "pwd" command into pymol, I get the following:
>
> PyMOL> pwd
> /
>
> so pymol thinks it's running from the root directory.  This makes it tough
> for me to load more pdbfiles into pymol using the "load" command as I must
> first "cd" into the directory with pymol.  Just a note, that in version 0.9=
> 8,
> using the "open" command, pymol would recognize what directory it was opene=
> d
> from.
>
> Now, I can use the "pymol test.pdb" to open pdbfiles, but then the terminal
> gets the output from pymol.  I've tried to run pymol in the background so
> that I can continue to use this terminal window while stilll having pymol
> open.  Using "pymol test.pdb &" I still get pymol output to the terminal.  =
> I
> could use "pymol test.pdb >& /dev/null &" but that seems quite a bit more
> verbose compared to "open test.pdb"
>
> I guess I could alias pymol to essentially pipe it's output to /dev/null bu=
> t
> since version 0.98 worked fine, I was wondering if anyone has a workaround
> for this inconvenience.
>
> Thanks.
>
> - Andrew Wollacott

Seth,

Yes, via the "label_position" setting which specifies x,y, and z
alignment of labels.

Values in the range [-1,1] imply alignment.  Beyond that, it is a
translation along camera axes in model-space dimensions. =20

# for left alignment 0.75 A in front of atom

set label_position, [-1,0,1.75]

# for right alignment directly on atom

set label_position, [1,0,0]

# for left alignment 1 A to right of atom

set label_position, [2,0,0]

# for center alignment 2 A below atom

set label_position, [0,-3,0]

# centered 3 A in front of atom

set label_position, [0,0,4]

etc.

Cheers,
Waren


--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Seth Harris
> Sent: Thursday, February 23, 2006 10:45 AM
> To: pym...@li...
> Subject: [PyMOL] label positions, centered, left, or right
>=20
> Hi all,
>=20
> Minor thing, but thought I'd ask...
>=20
> Labels now appear to be centered on whatever atom they are=20
> labeling. Previously, the left-hand side of the label was on=20
> the atom (left-anchored). Is there a way to choose whether=20
> the label is left-anchored, centered, or right-anchored?=20
>=20
> I find that it's hard to offset the label sufficiently with=20
> commands like:
>=20
> label myprot and name ca, "    %s%s" % (resn,resi)
>=20
> which used to get the label to float nicely just to the right=20
> of the atom.=20
> Now that the label is centered the spaces don't help push the=20
> labels over as much as they used to, and the obvious route of=20
> adding twice as many spaces somehow isn't getting me there. I=20
> thought there might be an anchor, align, or justification=20
> flag on the labels.=20
>=20
> I did also notice that in editing mode you can drag the=20
> labels to whatever position you wanted in recent betas.  Very nice!
>=20
> Cheers,
> Seth
>=20
>=20

Hi all,

Minor thing, but thought I'd ask...

Labels now appear to be centered on whatever atom they are labeling.
Previously, the left-hand side of the label was on the atom (left-anchored)=
.
Is there a way to choose whether the label is left-anchored, centered, or
right-anchored?

I find that it's hard to offset the label sufficiently with commands like:

label myprot and name ca, "    %s%s" % (resn,resi)

which used to get the label to float nicely just to the right of the atom.
Now that the label is centered the spaces don't help push the labels over a=
s
much as they used to, and the obvious route of adding twice as many spaces
somehow isn't getting me there. I thought there might be an anchor, align,
or justification flag on the labels.

I did also notice that in editing mode you can drag the labels to whatever
position you wanted in recent betas.  Very nice!

Cheers,
Seth

hello,

I'm running MacPyMol 0.99.  I typically open pymol from the terminal (
terminal.app) using the "open" command.

> open test.pdb

I have .pdb files set to open with MacPyMol, so graphicConverter doesn't
open when I do this.  The problem I have when doing this is that when
entering the "pwd" command into pymol, I get the following:

PyMOL> pwd
/

so pymol thinks it's running from the root directory.  This makes it tough
for me to load more pdbfiles into pymol using the "load" command as I must
first "cd" into the directory with pymol.  Just a note, that in version 0.9=
8,
using the "open" command, pymol would recognize what directory it was opene=
d
from.

Now, I can use the "pymol test.pdb" to open pdbfiles, but then the terminal
gets the output from pymol.  I've tried to run pymol in the background so
that I can continue to use this terminal window while stilll having pymol
open.  Using "pymol test.pdb &" I still get pymol output to the terminal.  =
I
could use "pymol test.pdb >& /dev/null &" but that seems quite a bit more
verbose compared to "open test.pdb"

I guess I could alias pymol to essentially pipe it's output to /dev/null bu=
t
since version 0.98 worked fine, I was wondering if anyone has a workaround
for this inconvenience.

Thanks.

- Andrew Wollacott

Here's an example script that scratch-builds such an animation.  Note
that the "rotate" command seems broken in terms of the selections it
currently accepts -- selection macros don't currently work, so you'll
need to write them out long-hand as I have done below.

# create a 4 state molecule

fragment asp,mov
fragment asp,mov
fragment asp,mov
fragment asp,mov

# orient the camera parallel to the plane of motion

reset
turn x,-50
orient mov////CG+OD1+OD2

# get coordinates of the CG atom

crd =3D [0,0,0]

iterate_state 1,mov////CG, crd[0:3]=3D(x,y,z)

# now rotate atoms in states 2-4

frame 2
cmd.rotate("z",-4,"mov and name OD1",origin=3Dcrd)
cmd.rotate("z", 4,"mov and name OD2",origin=3Dcrd)

frame 3
cmd.rotate("z",-8,"mov and name OD1",origin=3Dcrd)
cmd.rotate("z", 8,"mov and name OD2",origin=3Dcrd)

frame 4
cmd.rotate("z",-4,"mov and name OD1",origin=3Dcrd)
cmd.rotate("z", 4,"mov and name OD2",origin=3Dcrd)

as sticks
set sphere_quality,2
set stick_radius, 0.1
show spheres
set sphere_scale, 0.25
mplay

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Sven Lammers
> Sent: Wednesday, February 22, 2006 5:05 AM
> To: pym...@li...
> Subject: [PyMOL] animate angle bending
>=20
> Dear pymol users,
>=20
> I'm struggling to figure out how to create an animation of an=20
> angle bending vibration with pymol, like this 
> http://www.ch.embnet.org/MD_tutorial/Images/Part2/a.gif
> My question is how do I correctly set the origin and axis so=20
> that I could use the rotate command to rotate one bond with=20
> respect to the other.
>=20
> Thanks a lot in advance and best regards, Sven
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Peter,

PyMOL does read the alpha, but it doesn't support compositition with the
software at present, so there is no practical use for this capability.

set show_alpha_checker
load transparent.png

Will demonstrate that the alpha is read by adding a checker pattern to
the background.  It sounds, you'd like it superimposed over the existing
scene for purposes of alignment. =20

Thanks for the suggestion!

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Peter Adrian Meyer
> Sent: Wednesday, February 22, 2006 7:43 AM
> To: pym...@li...
> Subject: [PyMOL] load_png doesn't support alpha (transparency)?
>=20
> Hi all,
>=20
> I noticed today that when reading a png file using load_png,=20
> the alpha channel does not appear to be respected (regions of=20
> the png that should be transparent are not transparent but=20
> show up as white).
>=20
> Does anyone know if this by design, a bug, or something I'm=20
> doing incorrectly setting my alpha channel in the png file?
>=20
> If you're wondering why I'm trying to do this; I'm attempting=20
> to generate two aligned figures from models that are in=20
> crystallographic origins.  The end goal is to have maps in=20
> each of these figures also aligned for comparison, so I can't=20
> just transform the models to get them aligned (use of the=20
> align command is out for similar reasons; unless there's a=20
> way to get the transformation matrix generated by model=20
> alignment and apply it to a map that I'm not aware of).
>=20
> Thanks,
>=20
> Pete
>=20
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
>=20
>=20
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Marc,

Not exactly, but you can get pretty close with something like this:

load protA.pdb
load protB.pdb

select siteA_res, byres (((protA & donors) within 3.45 of (protB &
acceptors)) or ((protA & acceptors) within 3.45 of (protB & donors)))

select siteB_res, byres (((protB & donors) within 3.45 of (protA &
acceptors)) or ((protB & acceptors) within 3.45 of (protA & donors)))

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Marc Bruning
> Sent: Wednesday, February 22, 2006 5:05 AM
> To: pym...@li...
> Subject: Re: [PyMOL] (kein Betreff)
>=20
> hello,
>=20
> is there a way to only select residues that are involved in=20
> polar contacts?
> thanks,
>=20
> marc
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Hi all,

I noticed today that when reading a png file using load_png, the alpha
channel does not appear to be respected (regions of the png that should be
transparent are not transparent but show up as white).

Does anyone know if this by design, a bug, or something I'm doing
incorrectly setting my alpha channel in the png file?

If you're wondering why I'm trying to do this; I'm attempting to generate
two aligned figures from models that are in crystallographic origins.  The
end goal is to have maps in each of these figures also aligned for
comparison, so I can't just transform the models to get them aligned (use
of the align command is out for similar reasons; unless there's a way to
get the transformation matrix generated by model alignment and apply it to
a map that I'm not aware of).

Thanks,

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Dear pymol users,

I'm struggling to figure out how to create an animation of an angle 
bending vibration
with pymol, like this one 
http://www.ch.embnet.org/MD_tutorial/Images/Part2/a.gif
My question is how do I correctly set the origin and axis so that I 
could use the rotate command
to rotate one bond with respect to the other.

Thanks a lot in advance and best regards,
Sven

hello,

is there a way to only select residues that are involved in polar contacts?
thanks,

marc