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From: leila k. <kar...@gm...> - 2010-07-31 14:03:52
|
Hi pymol users I want to generate an initial model structure (PDB file) for the PRH homeodomain-DNA complex for doing md simulation calculation. There is PDB file for my PRH homeodomain protein (PDB ID code: 2E1O), but there isn't PDB file for PRH homeodomain-DNA complex. also, there are PDB files for other homeodomain protein-DNA complexes as template. Is it possible to make this using pymol? I am beginner in pymol. please guide me |
|
From: Disha T. <dis...@gm...> - 2010-07-30 16:31:01
|
Hello all, I have to perform virtual screening for which I installed the autodock plugin in Pymol(1.2 evaluation versiom)[Python 2.5 and Numpy 1.3]. Configuration settings and grid box settings are fine, but i m facing problems when it comes to accepting the receptor and the ligands. e.g.- I got an error when I tried loading ligands: os.symlink=os(....) <type exceptions.atTribute error> Object 'module' has no attribute named 'symlink' Please help me out with this. I suspect some pathway problem, but yet haven't figured out any. regards, Disha Tandon |
|
From: Thomas H. <sp...@us...> - 2010-07-29 07:47:08
|
use the `alter` command to set `formal_charge`: alter sele, formal_charge=0 alter sele, formal_charge=1 alter sele, formal_charge=-1 Cheers, Thomas On Mon, Jul 26, 2010 at 7:34 PM, Davide Cruz <dav...@gm...> wrote: > Hello there, > > Is there a command to change the charge of a picked/selected atom? I want to > write a script that adds different protonation states to each molecule of a > (large) library, and the best method I know is changing the charge of a > picked atom, and then using h_fill to add the hydrogen atoms. But I don't > know the command to change the charge and now I'm stuck. > > Please help > > Thanks > > Davide Cruz |
|
From: Angelo R. <ang...@gm...> - 2010-07-28 18:34:15
|
Hello: I always receiving a segmentation fault with pymol-v1.3-Linux-x86_64-TclTk8.5.tar.bz2. It also happens with pymol-v1.3-Linux-x86-TclTk8.5.tar.bz2 but not all the time. Here is how the segmentation fault happens. 1) read in a molecule ... a small one for testing purposes ... one that should have double bonds. 2) set valence, 0.1 3) click on editing mode. 4) with mouse, cntl-right click on bond, this is ok. 5) with mouse, cntl-w to get the a double bond; left click with mouse, and segmentation fault may occur. 6) repeat step 5 with a second bond, and segmentation fault will definitely occur. I am a subscriber. Kind regards, Angelol |
|
From: Jason V. <jas...@sc...> - 2010-07-26 22:27:05
|
Vitaly,
The documentation says that
select myRes, i. 10, state=4
should just select residue 10 from state 4, but that doesn't seem to
work in practice (or I'm doing something wrong).
You can also try,
m = cmd.get_model("myProtein", 4)
to select the protein in state 4. Then you can do
m.get_coord_list([3]) to get the 4th atom's location, or
m.get_residues() to get the atom list for each residue.
There should be an easier way, though.
Cheers,
-- Jason
On Sun, Jul 25, 2010 at 11:25 PM, Vitaly Vostrikov <vv...@ua...> wrote:
> Hello,
>
> Is it possible to select a residue only within a given state? Suppose I have an NMR ensemble, and I want to select the first residue in the first model, i.e. something like "select N-term, resi 1 and state 1".
>
> Thank you,
> Vitaly
>
> ------------------------------------------------------------------------------
> The Palm PDK Hot Apps Program offers developers who use the
> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> of $1 Million in cash or HP Products. Visit us here for more details:
> http://ad.doubleclick.net/clk;226879339;13503038;l?
> http://clk.atdmt.com/CRS/go/247765532/direct/01/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120
|
|
From: Davide C. <dav...@gm...> - 2010-07-26 17:34:40
|
Hello there, Is there a command to change the charge of a picked/selected atom? I want to write a script that adds different protonation states to each molecule of a (large) library, and the best method I know is changing the charge of a picked atom, and then using h_fill to add the hydrogen atoms. But I don't know the command to change the charge and now I'm stuck. Please help Thanks Davide Cruz |
|
From: Vitaly V. <vv...@ua...> - 2010-07-26 03:25:20
|
Hello, Is it possible to select a residue only within a given state? Suppose I have an NMR ensemble, and I want to select the first residue in the first model, i.e. something like "select N-term, resi 1 and state 1". Thank you, Vitaly |
|
From: Bradley H. <bra...@ag...> - 2010-07-23 16:03:16
|
I'm writing a manuscript and just need clarification.
Does "cmd.iterate('all and n. ca', 'stored.stored_ss.append([ss])')"
use pymol's DSS to assign secondary structure? If not, how is this
command assigning secondary structure?
Thanks,
Bradley
On Tue, Jun 22, 2010 at 7:37 PM, Jason Vertrees
<jas...@sc...> wrote:
> Hi Bradley,
>
> PyMOL uses its own internal routine for secondary structure
> classification. The iterator token is "ss". Check out
> http://pymolwiki.org/index.php/Ss and
> http://pymolwiki.org/index.php/Iterate_sses and
> http://pymolwiki.org/index.php/WriteSS.
>
> Cheers,
>
> -- Jason
>
> On Tue, Jun 22, 2010 at 4:04 PM, Bradley Hintze
> <bra...@ag...> wrote:
>> Hi all,
>>
>> Is there a way to get an output from PyMol's DSS command (like a dssp output)?
>>
>> --
>> Bradley J. Hintze
>> Graduate Student
>> Duke University
>> School of Medicine
>> 801-712-8799
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit. See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>
--
Bradley J. Hintze
Graduate Student
Duke University
School of Medicine
801-712-8799
|
|
From: Jason V. <jas...@sc...> - 2010-07-23 15:59:08
|
Hi Bradley,
> Does "cmd.iterate('all and n. ca', 'stored.stored_ss.append([ss])')"
'ss' in this usage just reads from the current model of the molecule
in memory. PyMOL can read secondary structure from the PDB files if
it's present or determine it by itself using dss. PyMOL defaults to
the former, but can do the latter if you explicitly call 'dss' on your
structure. To illustrate this, in the following snippet you'll get
two different lists of secondary structure:
# grab a protein
fetch 1wld
from pymol import stored
stored.a = []
stored.b = []
iterate *, stored.a.append(ss)
dss
iterate *, stored.b.append(ss)
You will see that the list in stored.a does not equal the list in
stored.b. The first is read from the file, the 2nd from the results
of dss.
Cheers,
-- Jason
On Fri, Jul 23, 2010 at 11:35 AM, Bradley Hintze
<bra...@ag...> wrote:
> I'm writing a manuscript and just need clarification.
>
> Does "cmd.iterate('all and n. ca', 'stored.stored_ss.append([ss])')"
> use pymol's DSS to assign secondary structure? If not, how is this
> command assigning secondary structure?
>
> Thanks,
> Bradley
>
>
> On Tue, Jun 22, 2010 at 7:37 PM, Jason Vertrees
> <jas...@sc...> wrote:
>> Hi Bradley,
>>
>> PyMOL uses its own internal routine for secondary structure
>> classification. The iterator token is "ss". Check out
>> http://pymolwiki.org/index.php/Ss and
>> http://pymolwiki.org/index.php/Iterate_sses and
>> http://pymolwiki.org/index.php/WriteSS.
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Tue, Jun 22, 2010 at 4:04 PM, Bradley Hintze
>> <bra...@ag...> wrote:
>>> Hi all,
>>>
>>> Is there a way to get an output from PyMol's DSS command (like a dssp output)?
>>>
>>> --
>>> Bradley J. Hintze
>>> Graduate Student
>>> Duke University
>>> School of Medicine
>>> 801-712-8799
>>>
>>> ------------------------------------------------------------------------------
>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> lucky parental unit. See the prize list and enter to win:
>>> http://p.sf.net/sfu/thinkgeek-promo
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) Jas...@sc...
>> (o) +1 (603) 374-7120
>>
>
>
>
> --
> Bradley J. Hintze
> Graduate Student
> Duke University
> School of Medicine
> 801-712-8799
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120
|
|
From: Thomas H. <sp...@us...> - 2010-07-22 19:26:16
|
Hi pymol users, there is a new script on the wiki that does arbitrary gradient coloring, it's called "spectrumany". http://pymolwiki.org/index.php/Spectrumany Cheers, Thomas |
|
From: Jason V. <jas...@sc...> - 2010-07-22 18:38:01
|
Bradley, set dash_gap, 0, distName where distName is the name of the distance object from the distance command. Cheers, -- Jason On Thu, Jul 22, 2010 at 2:02 PM, Bradley Hintze <bra...@ag...> wrote: > I have measurements in my figure so set dash_gap, 0 is not desirable > (unless i can specify a particular object??) > I tried looking at CGO but all I can find on the wiki is how to draw > text and circles. Is there a page I'm not seeing that explaining > cmd.load_cgo in detail?? > > On Thu, Jul 22, 2010 at 12:22 PM, Jason Vertrees > <jas...@sc...> wrote: >> Bradley, >> >> The fastest way is to create two pseudoatoms and measure the distance >> between them. For an arrow, see Modevectors >> (http://www.pymolwiki.org/index.php/Modevectors). >> >> pseudoatom pt1, pos=[x1, y1, z1] >> pseudoatom pt2, pos=[x2, y2, z2] >> distance /pt1, /pt2 >> set dash_gap, 0 >> >> You can also create CGO lines between two points, if you want. >> >> Cheers, >> >> -- Jason >> >> On Thu, Jul 22, 2010 at 11:58 AM, Bradley Hintze >> <bra...@ag...> wrote: >>> Hi all, >>> >>> Can I draw a vector if I give two XYZ coords in pymol? >>> >>> e.g. >>> draw_vector(x1, y1, z1, x2, y2, z2) >>> >>> Thanks, >>> Bradley >>> >>> -- >>> Bradley J. Hintze >>> Graduate Student >>> Duke University >>> School of Medicine >>> 801-712-8799 >>> >>> ------------------------------------------------------------------------------ >>> This SF.net email is sponsored by Sprint >>> What will you do first with EVO, the first 4G phone? >>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >>> _______________________________________________ >>> PyMOL-users mailing list (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >>> >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) Jas...@sc... >> (o) +1 (603) 374-7120 >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > Bradley J. Hintze > Graduate Student > Duke University > School of Medicine > 801-712-8799 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
|
From: Bradley H. <bra...@ag...> - 2010-07-22 18:25:22
|
I have measurements in my figure so set dash_gap, 0 is not desirable (unless i can specify a particular object??) I tried looking at CGO but all I can find on the wiki is how to draw text and circles. Is there a page I'm not seeing that explaining cmd.load_cgo in detail?? On Thu, Jul 22, 2010 at 12:22 PM, Jason Vertrees <jas...@sc...> wrote: > Bradley, > > The fastest way is to create two pseudoatoms and measure the distance > between them. For an arrow, see Modevectors > (http://www.pymolwiki.org/index.php/Modevectors). > > pseudoatom pt1, pos=[x1, y1, z1] > pseudoatom pt2, pos=[x2, y2, z2] > distance /pt1, /pt2 > set dash_gap, 0 > > You can also create CGO lines between two points, if you want. > > Cheers, > > -- Jason > > On Thu, Jul 22, 2010 at 11:58 AM, Bradley Hintze > <bra...@ag...> wrote: >> Hi all, >> >> Can I draw a vector if I give two XYZ coords in pymol? >> >> e.g. >> draw_vector(x1, y1, z1, x2, y2, z2) >> >> Thanks, >> Bradley >> >> -- >> Bradley J. Hintze >> Graduate Student >> Duke University >> School of Medicine >> 801-712-8799 >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 |
|
From: Jason V. <jas...@sc...> - 2010-07-22 16:23:04
|
Bradley, The fastest way is to create two pseudoatoms and measure the distance between them. For an arrow, see Modevectors (http://www.pymolwiki.org/index.php/Modevectors). pseudoatom pt1, pos=[x1, y1, z1] pseudoatom pt2, pos=[x2, y2, z2] distance /pt1, /pt2 set dash_gap, 0 You can also create CGO lines between two points, if you want. Cheers, -- Jason On Thu, Jul 22, 2010 at 11:58 AM, Bradley Hintze <bra...@ag...> wrote: > Hi all, > > Can I draw a vector if I give two XYZ coords in pymol? > > e.g. > draw_vector(x1, y1, z1, x2, y2, z2) > > Thanks, > Bradley > > -- > Bradley J. Hintze > Graduate Student > Duke University > School of Medicine > 801-712-8799 > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
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From: Bradley H. <bra...@ag...> - 2010-07-22 15:59:04
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Hi all, Can I draw a vector if I give two XYZ coords in pymol? e.g. draw_vector(x1, y1, z1, x2, y2, z2) Thanks, Bradley -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 |
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From: Michael L. <mgl...@gm...> - 2010-07-22 14:59:51
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Hi Daniel, The version on the wiki (http://pymolwiki.org/index.php/User:Mglerner) should handle the fink (apbs-mpi-openmpi and apbs-mpi-lammpi) and macports (apbs-mpi) versions of MPI-enabled APBS. Please note that the PyMOL-APBS plugin doesn't go out of its way to take advantage of parallel features; it just calls the MPI-enabled versions of APBS. Because I test the non-parallel versions more frequently, it checks for the normal APBS first. If you want it to find the MPI by default, you can 1) uninstall the non-MPI version, 2) set the APBS_BINARY variable in the plugin directly, or 3) set the APBS_BINARY_DIR environment variable. It's worth noting that the environment variables weren't working in some previous versions of the plugin. Cheers, -Michael On Wed, Jul 21, 2010 at 2:56 PM, Michael Lerner < mgl...@gm... <mglerner%2Bs...@gm...>> wrote: > Hi Daniel, > > Sorry for the delay! I wasn't actually aware of that talk page; you'll get > a faster response if you email the PyMOL list. > > The version that you can download from pymolwiki.org will fix the problems > you had with the temp path. I've never used the openmpi version of APBS on > the mac before, so I want to do a few more tests before I put up a version > of the plugin that finds it by default. In the meantime, you can type the > binary location into the APBS Location box and it should work. You don't > need to worry about APBS's psize.py for the vast majority of systems. > > I'll let you know when I've updated the plugin fully deal with this. > > Note that the plugin will still run things using the same input files it > would with a single-processor APBS. > > -Michael > > > On Tue, Jul 20, 2010 at 7:15 PM, RaDaniel Christian 성준 < > ren...@gm...> wrote: > >> I want to bring to your attention the wiki entry I posted in pymolwiki >> regarding the default loading paths for apbs: >> After installing with fink, none of the default paths work. >> >> >> http://pymolwiki.org/index.php/Talk:APBS#Making_the_default_paths_to_work.3F >> >> If someone knows what is going on, please drop a line! >> Many thanks in advance, >> Daniel Ra >> >> ---------- Forwarded message ---------- >> From: RaDaniel Christian 성준 <ren...@gm...> >> Date: Mon, Jun 7, 2010 at 7:07 PM >> Subject: Help setting apbs tools2 on Mac >> To: su...@de... >> >> >> Can I get help with setting configuration files on pymol (cvs fink >> version1.2r3pre)? >> [ snip ] > > -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) |
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From: R. B. F. <rob...@ir...> - 2010-07-21 14:27:48
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Hi, I would like to build an ideal beta-sheet fold. Can anyone suggest how to do this with pymol or any other program. I have already tried with the build command, however I am not sure how to proceed once the first strand is built. Many thanks, Bryn |
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From: Vitaly V. <vv...@ua...> - 2010-07-21 00:08:44
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Hi Bradley, If you have one of the latest builds, you can use this approach: http://www.mail-archive.com/pym...@li.../msg07754.html Hope it helps. Vitaly ----- Original Message ----- From: Bradley Hintze <bra...@ag...> Date: Tuesday, July 20, 2010 5:37 pm Subject: [PyMOL] get coordinates To: pymol-users <pym...@li...> > Hi all, > > Is there an easy way to get coordinates of a given atom? > > e.g. 'get_coordinates /model//A/ALA`76/CA' > for the CA coordinates of resi 76 > > All the examples on the wiki use "iterate" to get the coordinates > of a > selection. Is there a simple way to get one coordinate of a given > atom? > > -- > Bradley J. Hintze > Graduate Student > Duke University > School of Medicine > 801-712-8799 > > -------------------------------------------------------------------- > ---------- > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol- > us...@li... |
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From: RaDaniel C. 성준 <ren...@gm...> - 2010-07-20 23:17:33
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Edited the subject. Thanks! On Tue, Jul 20, 2010 at 6:15 PM, RaDaniel Christian 성준 <ren...@gm...> wrote: > I want to bring to your attention the wiki entry I posted in pymolwiki > regarding the default loading paths for apbs: > After installing with fink, none of the default paths work. > > http://pymolwiki.org/index.php/Talk:APBS#Making_the_default_paths_to_work.3F > > If someone knows what is going on, please drop a line! > Many thanks in advance, > Daniel Ra > > ---------- Forwarded message ---------- > From: RaDaniel Christian 성준 <ren...@gm...> > Date: Mon, Jun 7, 2010 at 7:07 PM > Subject: Help setting apbs tools2 on Mac > To: su...@de... > > > Can I get help with setting configuration files on pymol (cvs fink > version1.2r3pre)? > > I modified the apbsplugin.py to have the following default locations > (taken from http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol#TOC-Visualization-through-the-new-APBS- > OR http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py) > : > > APBS_BINARY_LOCATION = '/sw64/bin/apbs-mpi-openmpi' > APBS_PSIZE_LOCATION = '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py' > APBS_PDB2PQR_LOCATION = '/sw64/bin/pdb2pqr' > TEMPORARY_FILE_DIR = '/apbstemp' > but after installing by running xpymol as root, I still get this error: > > Search dirs ['/sw64/lib/pymol-py26/ext/bin', > '/sw64/lib/pymol-py26/freemol/bin', > '/sw64/lib/pymol-py26/freemol/share/apbs', > '/sw64/lib/pymol-py26/freemol/share/pdb2pqr', > '/sw64/bin/apbs-mpi-openmpi', > '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py', > '/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr', > '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', > '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', > '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', > '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', > '/sw64/share/xtal/ccp4-6.1.3/bin', > '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', > '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', > '/opt/local/bin', '/sw/bin'] > get_default_location will search the following: > ['/sw64/lib/pymol-py26/ext/bin', '/sw64/lib/pymol-py26/freemol/bin', > '/sw64/lib/pymol-py26/freemol/share/apbs', > '/sw64/lib/pymol-py26/freemol/share/pdb2pqr', > '/sw64/bin/apbs-mpi-openmpi', > '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py', > '/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr', > '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', > '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', > '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', > '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', > '/sw64/share/xtal/ccp4-6.1.3/bin', > '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', > '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', > '/opt/local/bin', '/sw/bin'] > trying /sw64/lib/pymol-py26/ext/bin/psize.py > trying /sw64/lib/pymol-py26/ext/bin/psize > trying /sw64/lib/pymol-py26/freemol/bin/psize.py > trying /sw64/lib/pymol-py26/freemol/bin/psize > trying /sw64/lib/pymol-py26/freemol/share/apbs/psize.py > trying /sw64/lib/pymol-py26/freemol/share/apbs/psize > trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/psize.py > trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/psize > trying /sw64/bin/apbs-mpi-openmpi/psize.py > trying /sw64/bin/apbs-mpi-openmpi/psize > trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/psize.py > trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/psize > trying /sw64/bin/pdb2pqr/psize.py > trying /sw64/bin/pdb2pqr/psize > trying /sw/share/pdb2pqr/psize.py > trying /sw/share/pdb2pqr/psize > trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/psize.py > trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/psize > trying /sw64/bin/psize.py > trying /sw64/bin/psize > trying /sw64/sbin/psize.py > trying /sw64/sbin/psize > trying /usr/bin/psize.py > trying /usr/bin/psize > trying /bin/psize.py > trying /bin/psize > trying /usr/sbin/psize.py > trying /usr/sbin/psize > trying /sbin/psize.py > trying /sbin/psize > trying /usr/local/bin/psize.py > trying /usr/local/bin/psize > trying /usr/X11/bin/psize.py > trying /usr/X11/bin/psize > trying /usr/libexec/psize.py > trying /usr/libexec/psize > trying /Developer/Tools/psize.py > trying /Developer/Tools/psize > trying /usr/X11R6/bin/psize.py > trying /usr/X11R6/bin/psize > trying /sw64/share/xtal/ccp4-6.1.3/etc/psize.py > trying /sw64/share/xtal/ccp4-6.1.3/etc/psize > trying /sw64/share/xtal/ccp4-6.1.3/bin/psize.py > trying /sw64/share/xtal/ccp4-6.1.3/bin/psize > trying /sw64/share/xtal/ccp4-6.1.3/ccp4i/bin/psize.py > trying /sw64/share/xtal/ccp4-6.1.3/ccp4i/bin/psize > trying /sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin/psize.py > trying /sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin/psize > trying /sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications/psize.py > trying /sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications/psize > trying /usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/psize.py > trying /usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/psize > trying /usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386/psize.py > trying /usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386/psize > trying /usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications/psize.py > trying /usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications/psize > trying /usr/local/bin/psize.py > trying /usr/local/bin/psize > trying /opt/local/bin/psize.py > trying /opt/local/bin/psize > trying /sw/bin/psize.py > trying /sw/bin/psize > Could not find default location for file: psize.py > Search dirs ['/sw64/lib/pymol-py26/ext/bin', > '/sw64/lib/pymol-py26/freemol/bin', > '/sw64/lib/pymol-py26/freemol/share/apbs', > '/sw64/lib/pymol-py26/freemol/share/pdb2pqr', > '/sw64/bin/apbs-mpi-openmpi', > '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py', > '/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr', > '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', > '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', > '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', > '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', > '/sw64/share/xtal/ccp4-6.1.3/bin', > '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', > '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', > '/opt/local/bin', '/sw/bin'] > get_default_location will search the following: > ['/sw64/lib/pymol-py26/ext/bin', '/sw64/lib/pymol-py26/freemol/bin', > '/sw64/lib/pymol-py26/freemol/share/apbs', > '/sw64/lib/pymol-py26/freemol/share/pdb2pqr', > '/sw64/bin/apbs-mpi-openmpi', > '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py', > '/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr', > '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', > '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', > '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', > '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', > '/sw64/share/xtal/ccp4-6.1.3/bin', > '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', > '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', > '/opt/local/bin', '/sw/bin'] > trying /sw64/lib/pymol-py26/ext/bin/pdb2pqr.py > trying /sw64/lib/pymol-py26/ext/bin/pdb2pqr > trying /sw64/lib/pymol-py26/freemol/bin/pdb2pqr.py > trying /sw64/lib/pymol-py26/freemol/bin/pdb2pqr > trying /sw64/lib/pymol-py26/freemol/share/apbs/pdb2pqr.py > trying /sw64/lib/pymol-py26/freemol/share/apbs/pdb2pqr > trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/pdb2pqr.py > trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/pdb2pqr > trying /sw64/bin/apbs-mpi-openmpi/pdb2pqr.py > trying /sw64/bin/apbs-mpi-openmpi/pdb2pqr > trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/pdb2pqr.py > trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/pdb2pqr > trying /sw64/bin/pdb2pqr/pdb2pqr.py > trying /sw64/bin/pdb2pqr/pdb2pqr > trying /sw/share/pdb2pqr/pdb2pqr.py > trying /sw/share/pdb2pqr/pdb2pqr > trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/pdb2pqr.py > trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/pdb2pqr > trying /sw64/bin/pdb2pqr.py > trying /sw64/bin/pdb2pqr > Search dirs ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr', > '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', > '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', > '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', > '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', > '/sw64/share/xtal/ccp4-6.1.3/bin', > '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', > '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', > '/opt/local/bin', '/sw/bin'] > get_default_location will search the following: > ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr', > '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', > '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', > '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', > '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', > '/sw64/share/xtal/ccp4-6.1.3/bin', > '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', > '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', > '/opt/local/bin', '/sw/bin'] > Could not find default location for file: temp > Search dirs ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr', > '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', > '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', > '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', > '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', > '/sw64/share/xtal/ccp4-6.1.3/bin', > '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', > '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', > '/opt/local/bin', '/sw/bin'] > get_default_location will search the following: > ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr', > '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', > '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', > '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', > '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', > '/sw64/share/xtal/ccp4-6.1.3/bin', > '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', > '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', > '/opt/local/bin', '/sw/bin'] > Could not find default location for file: temp > Search dirs ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr', > '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', > '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', > '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', > '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', > '/sw64/share/xtal/ccp4-6.1.3/bin', > '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', > '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', > '/opt/local/bin', '/sw/bin'] > get_default_location will search the following: > ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr', > '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', > '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', > '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', > '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', > '/sw64/share/xtal/ccp4-6.1.3/bin', > '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', > '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', > '/opt/local/bin', '/sw/bin'] > Could not find default location for file: temp > Search dirs ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr', > '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', > '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', > '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', > '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', > '/sw64/share/xtal/ccp4-6.1.3/bin', > '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', > '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', > '/opt/local/bin', '/sw/bin'] > get_default_location will search the following: > ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr', > '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', > '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', > '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', > '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', > '/sw64/share/xtal/ccp4-6.1.3/bin', > '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', > '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', > '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', > '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', > '/opt/local/bin', '/sw/bin'] > Could not find default location for file: temp > > Also, the default locations are not read, and I get the following > values on the apbs tools2 plugin window: > > APBS_BINARY_LOCATION = /sw64/bin/apbs > APBS_PSIZE_LOCATION = blank > APBS_PDB2PQR_LOCATION = /sw64/bin/pdb2pqr > > TEMPORARY PQR FILE = pymol-generated.pqr > TEMPORARY PDB FILE = pymol-generated.pdb > TEMPORARY DX FILE = pymol-generated.dx > APBS INPUT FILE = pymol-generated.in > > Is there a fix for this? > > Thank you, > Daniel Ra > -- > Stop the ACTA. Row, row; fight the power! http://www.eff.org/ > > > > -- > Stop the ACTA. Row, row; fight the power! http://www.eff.org/ > > Choel Kim Structural Biology Laboratory > Department of Pharmacology, Baylor College of Medicine, > Alkek N510, One Baylor Plaza, Houston, TX 77030 > 713-798-8687 (Lab) > 713-798-3145 (Fax) > -- Stop the ACTA. Row, row; fight the power! http://www.eff.org/ Choel Kim Structural Biology Laboratory Department of Pharmacology, Baylor College of Medicine, Alkek N510, One Baylor Plaza, Houston, TX 77030 713-798-8687 (Lab) 713-798-3145 (Fax) |
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From: RaDaniel C. 성준 <ren...@gm...> - 2010-07-20 23:15:21
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I want to bring to your attention the wiki entry I posted in pymolwiki regarding the default loading paths for apbs: After installing with fink, none of the default paths work. http://pymolwiki.org/index.php/Talk:APBS#Making_the_default_paths_to_work.3F If someone knows what is going on, please drop a line! Many thanks in advance, Daniel Ra ---------- Forwarded message ---------- From: RaDaniel Christian 성준 <ren...@gm...> Date: Mon, Jun 7, 2010 at 7:07 PM Subject: Help setting apbs tools2 on Mac To: su...@de... Can I get help with setting configuration files on pymol (cvs fink version1.2r3pre)? I modified the apbsplugin.py to have the following default locations (taken from http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol#TOC-Visualization-through-the-new-APBS- OR http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py) : APBS_BINARY_LOCATION = '/sw64/bin/apbs-mpi-openmpi' APBS_PSIZE_LOCATION = '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py' APBS_PDB2PQR_LOCATION = '/sw64/bin/pdb2pqr' TEMPORARY_FILE_DIR = '/apbstemp' but after installing by running xpymol as root, I still get this error: Search dirs ['/sw64/lib/pymol-py26/ext/bin', '/sw64/lib/pymol-py26/freemol/bin', '/sw64/lib/pymol-py26/freemol/share/apbs', '/sw64/lib/pymol-py26/freemol/share/pdb2pqr', '/sw64/bin/apbs-mpi-openmpi', '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py', '/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr', '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', '/sw64/share/xtal/ccp4-6.1.3/bin', '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] get_default_location will search the following: ['/sw64/lib/pymol-py26/ext/bin', '/sw64/lib/pymol-py26/freemol/bin', '/sw64/lib/pymol-py26/freemol/share/apbs', '/sw64/lib/pymol-py26/freemol/share/pdb2pqr', '/sw64/bin/apbs-mpi-openmpi', '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py', '/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr', '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', '/sw64/share/xtal/ccp4-6.1.3/bin', '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] trying /sw64/lib/pymol-py26/ext/bin/psize.py trying /sw64/lib/pymol-py26/ext/bin/psize trying /sw64/lib/pymol-py26/freemol/bin/psize.py trying /sw64/lib/pymol-py26/freemol/bin/psize trying /sw64/lib/pymol-py26/freemol/share/apbs/psize.py trying /sw64/lib/pymol-py26/freemol/share/apbs/psize trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/psize.py trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/psize trying /sw64/bin/apbs-mpi-openmpi/psize.py trying /sw64/bin/apbs-mpi-openmpi/psize trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/psize.py trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/psize trying /sw64/bin/pdb2pqr/psize.py trying /sw64/bin/pdb2pqr/psize trying /sw/share/pdb2pqr/psize.py trying /sw/share/pdb2pqr/psize trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/psize.py trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/psize trying /sw64/bin/psize.py trying /sw64/bin/psize trying /sw64/sbin/psize.py trying /sw64/sbin/psize trying /usr/bin/psize.py trying /usr/bin/psize trying /bin/psize.py trying /bin/psize trying /usr/sbin/psize.py trying /usr/sbin/psize trying /sbin/psize.py trying /sbin/psize trying /usr/local/bin/psize.py trying /usr/local/bin/psize trying /usr/X11/bin/psize.py trying /usr/X11/bin/psize trying /usr/libexec/psize.py trying /usr/libexec/psize trying /Developer/Tools/psize.py trying /Developer/Tools/psize trying /usr/X11R6/bin/psize.py trying /usr/X11R6/bin/psize trying /sw64/share/xtal/ccp4-6.1.3/etc/psize.py trying /sw64/share/xtal/ccp4-6.1.3/etc/psize trying /sw64/share/xtal/ccp4-6.1.3/bin/psize.py trying /sw64/share/xtal/ccp4-6.1.3/bin/psize trying /sw64/share/xtal/ccp4-6.1.3/ccp4i/bin/psize.py trying /sw64/share/xtal/ccp4-6.1.3/ccp4i/bin/psize trying /sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin/psize.py trying /sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin/psize trying /sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications/psize.py trying /sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications/psize trying /usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/psize.py trying /usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/psize trying /usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386/psize.py trying /usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386/psize trying /usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications/psize.py trying /usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications/psize trying /usr/local/bin/psize.py trying /usr/local/bin/psize trying /opt/local/bin/psize.py trying /opt/local/bin/psize trying /sw/bin/psize.py trying /sw/bin/psize Could not find default location for file: psize.py Search dirs ['/sw64/lib/pymol-py26/ext/bin', '/sw64/lib/pymol-py26/freemol/bin', '/sw64/lib/pymol-py26/freemol/share/apbs', '/sw64/lib/pymol-py26/freemol/share/pdb2pqr', '/sw64/bin/apbs-mpi-openmpi', '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py', '/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr', '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', '/sw64/share/xtal/ccp4-6.1.3/bin', '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] get_default_location will search the following: ['/sw64/lib/pymol-py26/ext/bin', '/sw64/lib/pymol-py26/freemol/bin', '/sw64/lib/pymol-py26/freemol/share/apbs', '/sw64/lib/pymol-py26/freemol/share/pdb2pqr', '/sw64/bin/apbs-mpi-openmpi', '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py', '/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr', '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', '/sw64/share/xtal/ccp4-6.1.3/bin', '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] trying /sw64/lib/pymol-py26/ext/bin/pdb2pqr.py trying /sw64/lib/pymol-py26/ext/bin/pdb2pqr trying /sw64/lib/pymol-py26/freemol/bin/pdb2pqr.py trying /sw64/lib/pymol-py26/freemol/bin/pdb2pqr trying /sw64/lib/pymol-py26/freemol/share/apbs/pdb2pqr.py trying /sw64/lib/pymol-py26/freemol/share/apbs/pdb2pqr trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/pdb2pqr.py trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/pdb2pqr trying /sw64/bin/apbs-mpi-openmpi/pdb2pqr.py trying /sw64/bin/apbs-mpi-openmpi/pdb2pqr trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/pdb2pqr.py trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/pdb2pqr trying /sw64/bin/pdb2pqr/pdb2pqr.py trying /sw64/bin/pdb2pqr/pdb2pqr trying /sw/share/pdb2pqr/pdb2pqr.py trying /sw/share/pdb2pqr/pdb2pqr trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/pdb2pqr.py trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/pdb2pqr trying /sw64/bin/pdb2pqr.py trying /sw64/bin/pdb2pqr Search dirs ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr', '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', '/sw64/share/xtal/ccp4-6.1.3/bin', '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] get_default_location will search the following: ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr', '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', '/sw64/share/xtal/ccp4-6.1.3/bin', '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] Could not find default location for file: temp Search dirs ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr', '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', '/sw64/share/xtal/ccp4-6.1.3/bin', '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] get_default_location will search the following: ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr', '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', '/sw64/share/xtal/ccp4-6.1.3/bin', '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] Could not find default location for file: temp Search dirs ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr', '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', '/sw64/share/xtal/ccp4-6.1.3/bin', '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] get_default_location will search the following: ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr', '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', '/sw64/share/xtal/ccp4-6.1.3/bin', '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] Could not find default location for file: temp Search dirs ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr', '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', '/sw64/share/xtal/ccp4-6.1.3/bin', '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] get_default_location will search the following: ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr', '/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin', '/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin', '/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools', '/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc', '/sw64/share/xtal/ccp4-6.1.3/bin', '/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin', '/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test', '/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386', '/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin', '/opt/local/bin', '/sw/bin'] Could not find default location for file: temp Also, the default locations are not read, and I get the following values on the apbs tools2 plugin window: APBS_BINARY_LOCATION = /sw64/bin/apbs APBS_PSIZE_LOCATION = blank APBS_PDB2PQR_LOCATION = /sw64/bin/pdb2pqr TEMPORARY PQR FILE = pymol-generated.pqr TEMPORARY PDB FILE = pymol-generated.pdb TEMPORARY DX FILE = pymol-generated.dx APBS INPUT FILE = pymol-generated.in Is there a fix for this? Thank you, Daniel Ra -- Stop the ACTA. Row, row; fight the power! http://www.eff.org/ -- Stop the ACTA. Row, row; fight the power! http://www.eff.org/ Choel Kim Structural Biology Laboratory Department of Pharmacology, Baylor College of Medicine, Alkek N510, One Baylor Plaza, Houston, TX 77030 713-798-8687 (Lab) 713-798-3145 (Fax) |
|
From: Jason V. <jas...@sc...> - 2010-07-20 23:13:17
|
Hi Bradley,
print cmd.get_atom_coords("76/CA")
Cheers,
-- Jason
On Tue, Jul 20, 2010 at 5:39 PM, Bradley Hintze
<bra...@ag...> wrote:
> Hi all,
>
> Is there an easy way to get coordinates of a given atom?
>
> e.g. 'get_coordinates /model//A/ALA`76/CA'
> for the CA coordinates of resi 76
>
> All the examples on the wiki use "iterate" to get the coordinates of a
> selection. Is there a simple way to get one coordinate of a given
> atom?
>
> --
> Bradley J. Hintze
> Graduate Student
> Duke University
> School of Medicine
> 801-712-8799
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120
|
|
From: Bradley H. <bra...@ag...> - 2010-07-20 22:36:53
|
Hi all, Is there an easy way to get coordinates of a given atom? e.g. 'get_coordinates /model//A/ALA`76/CA' for the CA coordinates of resi 76 All the examples on the wiki use "iterate" to get the coordinates of a selection. Is there a simple way to get one coordinate of a given atom? -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 |
|
From: Andreas K. <and...@ac...> - 2010-07-20 19:36:35
|
[[
Get your papers in.
The deadline for abstracts and proposals is
less than two weeks away.
]]
17th Annual Tcl/Tk Conference (Tcl'2010)
http://www.tcl.tk/community/tcl2010/
October 11 - 15, 2010
Hilton Suites/Conference Center
Chicago/Oakbrook Terrace, Illinois, USA
Important Dates:
Abstracts and proposals due August 1, 2010
Notification to authors August 15, 2010
WIP and BOF reservations open August 1, 2010
Author materials due October 1, 2010
Tutorials Start October 11, 2010
Conference starts October 13, 2010
Email Contact: tcl...@go...
Submission of Summaries
Tcl/Tk 2010 will be held in Chicago/Oakbrook Terrace, Illinois USA
from October 11 - 15, 2010. The program committee is asking for papers
and presentation proposals from anyone using or developing with Tcl/Tk
(and extensions). Past conferences have seen submissions covering a
wide variety of topics including:
* Scientific and engineering applications
* Industrial controls
* Distributed applications and Network Managment
* Object oriented extensions to Tcl/Tk
* New widgets for Tk
* Simulation and application steering with Tcl/Tk
* Tcl/Tk-centric operating environments
* Tcl/Tk on small and embedded devices
* Medical applications and visualization
* Use of different programming paradigms in Tcl/Tk and proposals for new
directions.
* New areas of exploration for the Tcl/Tk language
This year is the third year that the Tcl community is participating in
the Google Summer of Code. The conference program committee would
like to encourage submissions that report on the Tcl projects selected
for Google SoC 2010.
Submissions should consist of an abstract of about 100 words and a
summary of not more than two pages, and should be sent as plain text
to <tclconference AT googlegroups DOT com> no later than August 15,
2010. Authors of accepted abstracts will have until October 1, 2010 to
submit their final paper for the inclusion in the conference
proceedings. The proceedings will be made available on digital media,
so extra materials such as presentation slides, code examples, code
for extensions etc. are encouraged.
Printed proceedings will be produced as an on-demand book at lulu.com
The authors will have 25 minutes to present their paper at the
conference.
The program committee will review and evaluate papers according to the
following criteria:
* Quantity and quality of novel content
* Relevance and interest to the Tcl/Tk community
* Suitability of content for presentation at the conference
Proposals may report on commercial or non-commercial systems, but
those with only blatant marketing content will not be accepted.
Application and experience papers need to strike a balance between
background on the application domain and the relevance of Tcl/Tk to
the application. Application and experience papers should clearly
explain how the application or experience illustrates a novel use of
Tcl/Tk, and what lessons the Tcl/Tk community can derive from the
application or experience to apply to their own development efforts.
Papers accompanied by non-disclosure agreements will be returned to
the author(s) unread. All submissions are held in the highest
confidentiality prior to publication in the Proceedings, both as a
matter of policy and in accord with the U. S. Copyright Act of 1976.
The primary author for each accepted paper will receive registration
to the Technical Sessions portion of the conference at a reduced rate.
Other Forms of Participation
The program committee also welcomes proposals for panel discussions of
up to 90 minutes. Proposals should include a list of confirmed
panelists, a title and format, and a panel description with position
statements from each panelist. Panels should have no more than four
speakers, including the panel moderator, and should allow time for
substantial interaction with attendees. Panels are not presentations
of related research papers.
Slots for Works-in-Progress (WIP) presentations and Birds-of-a-Feather
sessions (BOFs) are available on a first-come, first-served basis
starting in August 1, 2010. Specific instructions for reserving WIP
and BOF time slots will be provided in the registration information
available in June 2010. Some WIP and BOF time slots will be held open
for on-site reservation. All attendees with an interesting work in
progress should consider reserving a WIP slot.
Registration Information
More information on the conference is available the conference Web
site (http://www.tcl.tk/community/tcl2010/) and will be published on
various Tcl/Tk-related information channels.
Reservations for hotel suites and $25 airport shuttle rides can be
made at
http://www.hilton.com/en/hi/groups/personalized/CHIOTHS-TCL-20101010/index.jhtml?WT.mc_id=POG
To keep in touch with news regarding the conference and Tcl events in
general, subscribe to the tcl-announce list. See:
http://aspn.activestate.com/ASPN/Mail/ to subscribe to the
tcl-announce mailing list.
Special Social Activites
October 15, 2010 - Friday afternoon -- Tour of Fermilab
Fermi National Accelerator Laboratory, http://www.fnal.gov/
A tour lasts about two hours and begins in Wilson Hall. Visitors view
the Laboratory from the 15th floor windows and visit various displays
located there. The tour moves to the Linear Accelerator building where
visitors see the Cockcroft-Walton, the components in the linear
accelerator gallery and the Main Control Room. There is a docent for
every 20 people. Registration required since tours must be arranged in
advance.
October 15, 2010 - Friday evening
Dinner-theater at the award winning Drury Lane theater located next to
our hotel. .
Special package price for dinner and theater at $44.00 per
person. Regularly $64 per person.
"Seven Brides for Seven Brothers" http://www.drurylaneoakbrook.com/
Bill Jenkins is one of the newest and most exciting new directors on
the Chicago scene. As Chairman of the Department of Theatre and Dance
at Ball State University, he heads one of the nation's largest theatre
programs. After admiring his work with other Chicago area theatres, we
are very pleased for this opportunity to showcase his talent at Drury
Lane. Once Bill shared some of the fresh ideas and insights he had for
ÂSeven Brides for Seven BrothersÂ, we knew we would have a great
show for the holidays.
Conference Committee
Clif Flynt Noumena Corp General Chair, Website Admin
Andreas Kupries ActiveState Software Inc. Program Chair
Cyndy Lilagan Iomas Research, LLC Facilities Coordination
Brian Griffin Mentor Graphics
Ron Fox NSCL/FRIB Michigan State University
Arjen Markus Deltares
Mike Doyle Iomas Research, LLC
Gerald Lester KnG Consulting, LLC
Donal Fellows University of Manchester
Jeffrey Hobbs ActiveState Software Inc.
Steve Landers Digital Smarties
Kevin Kenny GE Global Research Center
Larry Virden Tcl FAQ Maintainer
Steve Redler IV SR Technology
Contact Information tcl...@go...
Tcl'2010 would like to thank those who are sponsoring the conference:
ActiveState Software Inc.
Buonacorsi Foundation
Mentor Graphics
Noumena Corp.
SR Technology
Tcl Community Association
|
|
From: Marius R. <mar...@gm...> - 2010-07-20 15:14:56
|
Are you using cyrillic characters for your file names? If yes try changing that and see what happens. On Tue, Jul 20, 2010 at 4:35 PM, Павел Кудрявцев <pa...@gm...> wrote: > Hi, > I'm installed Pymol version 1.2 from repository on Mandriva Linux and > I'm constantly getting following errors when trying to open/save files > > Error: 1 > <type 'exceptions.UnicodeEncodeError'> Exception in Tk callback > Function: <bound method Normal.file_open of > <pmg_tk.skins.normal.Normal instance at 0x7f2c67cc55a8>> (type: <type > 'instancemethod'>) > Args: () > Traceback (innermost last): > File "/usr/lib/python2.6/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", > line 1747, in __call__ > return apply(self.func, args) > File "/usr/lib64/python2.6/site-packages/pmg_tk/skins/normal/__init__.py", > line 544, in file_open > self.cmd.load(ofile,quiet=0) > File "/usr/lib64/python2.6/site-packages/pymol/importing.py", line > 869, in load > _self.unlock(r,_self) > File "/usr/lib64/python2.6/site-packages/pymol/locking.py", line 99, in > unlock > _self.lock_api.release() > File "/usr/lib64/python2.6/threading.py", line 135, in release > if self.__owner is not current_thread(): > File "/usr/lib64/python2.6/threading.py", line 803, in currentThread > return _active[_get_ident()] > <type 'exceptions.UnicodeEncodeError'>: 'ascii' codec can't encode > characters in position 12-20: ordinal not in range(128) > > after this error Pymol stop responding > > I tried to reinstall Python, Tk and Pymol but it does not help. > Does somebody know how to fix it? I'd be very grateful for help. > > thanks in advance > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
|
From: Павел К. <pa...@gm...> - 2010-07-20 15:06:25
|
Hi,
I'm installed Pymol version 1.2 from repository on Mandriva Linux and
I'm constantly getting following errors when trying to open/save files
Error: 1
<type 'exceptions.UnicodeEncodeError'> Exception in Tk callback
Function: <bound method Normal.file_open of
<pmg_tk.skins.normal.Normal instance at 0x7f2c67cc55a8>> (type: <type
'instancemethod'>)
Args: ()
Traceback (innermost last):
File "/usr/lib/python2.6/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
return apply(self.func, args)
File "/usr/lib64/python2.6/site-packages/pmg_tk/skins/normal/__init__.py",
line 544, in file_open
self.cmd.load(ofile,quiet=0)
File "/usr/lib64/python2.6/site-packages/pymol/importing.py", line
869, in load
_self.unlock(r,_self)
File "/usr/lib64/python2.6/site-packages/pymol/locking.py", line 99, in unlock
_self.lock_api.release()
File "/usr/lib64/python2.6/threading.py", line 135, in release
if self.__owner is not current_thread():
File "/usr/lib64/python2.6/threading.py", line 803, in currentThread
return _active[_get_ident()]
<type 'exceptions.UnicodeEncodeError'>: 'ascii' codec can't encode
characters in position 12-20: ordinal not in range(128)
after this error Pymol stop responding
I tried to reinstall Python, Tk and Pymol but it does not help.
Does somebody know how to fix it? I'd be very grateful for help.
thanks in advance
|
|
From: Jovine L. <Luc...@ki...> - 2010-07-19 11:12:24
|
On Jul 19, 2010, at 12:29 PM, José Ignacio Sánchez Gallego wrote: > Hi everybody, > I have to make a 3D structure of my protein, I mutated some aminoacids in order to add some N-linked glycans, does anyone know is it possible to show the glycosilation on the surface of the 3D structure?? It would be a nice picture. > Thanks in advance, > Greetings Hi José, You can use GlyProt to *model* your glycan chains: http://www.glycosciences.de/modeling/glyprot/php/main.php HTH, Luca ---------------------------------------------------------------- Luca Jovine, Ph.D. Group Leader & EMBO Young Investigator Karolinska Institutet Department of Biosciences and Nutrition & Center for Biosciences Hälsovägen 7, SE-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6081-501 E-mail: luc...@ki... W3: http://jovinelab.org ---------------------------------------------------------------- |
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