[PyMOL] mutagenesis wizard and ignore_case
Dear PyMol users, The mutagenesis wizard does not seem to work if ignore_case is set to 0. I can reproduce this on an older incentive build and on the OS X compiled version from svn revision 4007. Thanks, Marius -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Write vector graphics of session
Hello, +1 for svg. It would be easier to add/remove stuff from them with a vector drawing program like Inkscape. Also .svg is also an open format. Not sure about .eps. All the best, Marius On Tue, Jan 15, 2013 at 1:32 PM, Martin Hediger ma@bluewin.ch wrote: I'm no expert but I guess my favorite would be EPS. Converting to PDF, if required, is easy on the Mac. Best regards Martin On 14.01.13 23:53, Jason Vertrees wrote: Martin, That would be a nice feature. Which format would you and the others prefer: SVG, PDF, or EPS? Cheers, -- Jason On Sat, Jan 12, 2013 at 6:31 AM, Martin Hediger ma@bluewin.ch wrote: Hi PyMOL users Can PyMOL write a vector based picture of a session? Does not require to be very fancy, but vector based would be cool. Something like in the old days with molscript. Best regards Martin -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122912 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Can't compile latest svn
I've reported this last week. http://sourceforge.net/tracker/?func=detailaid=3523770group_id=4546atid=104546 For the moment is not assigned. Marius On Mon, May 14, 2012 at 10:22 AM, Boris Kheyfets kheyfbo...@gmail.com wrote: I use PyMOL 1.4.1 which I have compiled myself. Now I'd like to switch to the latest version, so I checked out the latest svn, have enabled VMD plugins (and have also increased the fonts). I get the following error during compilation: contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function ‘read_basis_metadata’: contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:208:11: error: ‘molfile_qm_metadata_t’ has no member named ‘have_esp’ contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:209:11: error: ‘molfile_qm_metadata_t’ has no member named ‘have_npa’ contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:211:11: error: ‘molfile_qm_metadata_t’ has no member named ‘have_internals’ error: command 'gcc' failed with exit status 1 I attach my setup.py if it can be of any help. With great respect, Boris. -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Improved Plugin Manager
Hi Jason, I'll do that. The problem is that the new open-source branch does not compile with the vmd plugins. I've open a bug on the bug tracker on SourceForge. Thank you, Marius On Sun, May 6, 2012 at 3:31 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Marius, Just use the new open-source code in PyMOL. The plugin system is now built-in. If you try to integrate the plugin code yourself, it might take a little work. Cheers, -- Jason On Sat, May 5, 2012 at 4:24 PM, Marius Retegan marius.s.rete...@gmail.com wrote: Maybe I'm doing something wrong... I started by cloning the code from github, set the PYTHONPATH variable to it, but it does not seem to be taken into account by Pymol. python import sys print sys.path python end ['', '/Applications/MacPyMOL.app/pymol/modules', '/Applications/MacPyMOL.app/Contents/MacOS', '/Applications/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg', '/Applications/MacPyMOL.app/pymol/modules', '/Applications/MacPyMOL.app/pymol/ext/lib/python27.zip', '/Applications/MacPyMOL.app/pymol/ext/lib/python2.7', '/Applications/MacPyMOL.app/pymol/ext/lib/python2.7/plat-darwin', '/Applications/MacPyMOL.app/pymol/ext/lib/python2.7/plat-mac', '/Applications/MacPyMOL.app/pymol/ext/lib/python2.7/plat-mac/lib-scriptpackages', '/Applications/MacPyMOL.app/pymol/ext/lib/python2.7/lib-tk', '/Applications/MacPyMOL.app/pymol/ext/lib/python2.7/lib-old', '/Applications/MacPyMOL.app/pymol/ext/lib/python2.7/lib-dynload', '/Applications/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages', '/Applications/MacPyMOL.app/pymol/ext/lib/python2.7/site-packages/PIL', '/Applications/MacPyMOL.app/pymol/freemol/libpy'] On Sat, May 5, 2012 at 7:00 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Marius, The new plugin code was built and tested on Mac OS X before release. It worked just as well as on other platforms. Please let us know if you discover any issues. Cheers, -- Jason On Sat, May 5, 2012 at 4:49 AM, Marius Retegan marius.s.rete...@gmail.com wrote: Hello, Was the plugin manager tested with the incentive builds on mac osx? Is the setup procedure similar? Thank you Marius On Wed, May 2, 2012 at 3:43 PM, Michael Banck mba...@debian.org wrote: Hi, On Wed, May 02, 2012 at 09:39:59AM -0400, Jason Vertrees wrote: Thanks for this feedback. Since the inception the Script Library on the PyMOLWiki the policy is that all deposited scripts are open-source: http://pymolwiki.org/index.php/Category_talk:Script_Library#Policy. This link is Policy from the PyMOLWiki Scripts page. Awesome! (also about the meta-information in the plugin manager) Michael -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Improved Plugin Manager
Hello, Was the plugin manager tested with the incentive builds on mac osx? Is the setup procedure similar? Thank you Marius On Wed, May 2, 2012 at 3:43 PM, Michael Banck mba...@debian.org wrote: Hi, On Wed, May 02, 2012 at 09:39:59AM -0400, Jason Vertrees wrote: Thanks for this feedback. Since the inception the Script Library on the PyMOLWiki the policy is that all deposited scripts are open-source: http://pymolwiki.org/index.php/Category_talk:Script_Library#Policy. This link is Policy from the PyMOLWiki Scripts page. Awesome! (also about the meta-information in the plugin manager) Michael -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)
Hello, The latest revision 3971 compiles without problems with gcc 4.5.1 on Fedora 14. I usually install all the dependencies with yum. My suggestion would be to try compiling with gcc4.5. Marius On Fri, Dec 2, 2011 at 8:19 AM, grantaka36 grantak...@gmail.com wrote: Referring the following, I'm trying to install PyMOL 1.4.1 with attached 'compile_pymol.sh', but no success. Would you please help to finish installation, or give me some advices? If information inadequate, please contact me. http://www.pymolwiki.org/index.php/Linux_Install - Requirements - Get latest Source from SVN - Compile and install - Problems - gcc-4.5 is broken for pymol install, use gcc-4.4 -- My distribution has gcc4.5, so installed /usr/bin/gcc44, /usr/bin/g++44. Attached 'install_error.txt' gathers some information: - Original module files are in $HOME/install_module/pymol-archive - Intends to install in $HOME/pymol-svn - Original log has some Japanese messages so I added /* means ... */ Regards, Masataka -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)
Could you please specified what exactly did the gcc 4.5 broke in Pymol? Maybe this is not the case for every linux distribution. Cheers, Marius 2011/12/2 Troels Emtekær Linnet tlin...@gmail.com: Try Following this script. http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support Please report if you are successful. It would be interesting to see how it works on CentOS /T 2011/12/2 grantaka36 grantak...@gmail.com Referring the following, I'm trying to install PyMOL 1.4.1 with attached 'compile_pymol.sh', but no success. Would you please help to finish installation, or give me some advices? If information inadequate, please contact me. http://www.pymolwiki.org/index.php/Linux_Install - Requirements - Get latest Source from SVN - Compile and install - Problems - gcc-4.5 is broken for pymol install, use gcc-4.4 -- My distribution has gcc4.5, so installed /usr/bin/gcc44, /usr/bin/g++44. Attached 'install_error.txt' gathers some information: - Original module files are in $HOME/install_module/pymol-archive - Intends to install in $HOME/pymol-svn - Original log has some Japanese messages so I added /* means ... */ Regards, Masataka -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Movie to export
I used this a long time ago, but after googling for the error from bgra to yuv420p I guess that is a problem with the color space conversion that memcoder tries to enforce by default. Maybe you could try imposing the color space by adding -vf format=bgra, but I think that the video codec is not going to be happy about that. Try looking around for other options... Marius 2011/11/9 Troels Emtekær Linnet tlin...@gmail.com: What codec do I need to install?? MEncoder 1.0rc4-4.5.2 (C) 2000-2010 MPlayer Team Option x264encopts: Unknown suboption nodct_decimat success: format: 16 data: 0x0 - 0x0 MF file format detected. [mf] search expr: *.png [mf] number of files: 537 (4296) [demux_mf] file type was not set! trying 'type=png'... VIDEO: [MPNG] 0x0 24bpp 25.000 fps 0.0 kbps ( 0.0 kbyte/s) [V] filefmt:16 fourcc:0x474E504D size:0x0 fps:25.000 ftime:=0.0400 Opening video filter: [expand osd=1] Expand: -1 x -1, -1 ; -1, osd: 1, aspect: 0.00, round: 1 == Opening video decoder: [ffmpeg] FFmpeg's libavcodec codec family Selected video codec: [ffpng] vfm: ffmpeg (FFmpeg PNG) == Could not find matching colorspace - retrying with -vf scale... Opening video filter: [scale] Movie-Aspect is undefined - no prescaling applied. [swscaler @ 0x7f2555cc0620]BICUBIC scaler, from bgra to yuv420p using MMX2 FATAL: Cannot initialize video driver. Movie-Aspect is undefined - no prescaling applied. FATAL: Cannot initialize video driver. Exiting... 2011/11/9 Marius Retegan marius.s.rete...@gmail.com On a Linux system you can use the following commands to stick them all together mencoder mf://*.png -mf fps=25 -ovc x264 -x264encopts bitrate=3000:threads=auto:frameref=8:bframes=0:nob_adapt:direct_pred=auto:subq=7:mixed_refs:nodct_decimat:no_psnr:me=umh:keyint=25 -ofps 25 -nosound -noskip -of rawvideo -o movieLQ.264 This will create a x264 compressed file which you will have to put in a mp4 container using the following command. You can modify the bitrate which is now set to 3000 and the framerate 25 fps. MP4Box -fps 25 -add movieLQ.264 movieLQ.mp4 Best regards, Marius -- Département de Chimie Moléculaire Université Joseph Fourier 301 Rue de la Chimie BP 53, 38041 Grenoble Cedex 9, France Tel +33 (0) 4 76 63 44 03 GnuPG http://db.tt/rr7Hd0Y 2011/11/8 Jason Vertrees jason.vertr...@schrodinger.com: Hi Troels, One benefit of the Incentive version of PyMOL is the Files Save Movie as ... MPEG feature. If you don't have that or you want to use a different compressor that's cool. In the past I had great luck with mencoder (http://www.pymolwiki.org/index.php/Making_Movies)-- but I think everyone's using VLC (http://www.videolan.org/) or ffmpeg (http://ffmpeg.org/) now. If the PyMOLWiki's out of date, please feel free to update it. Cheers, -- Jason 2011/11/8 Troels Emtekær Linnet tlin...@gmail.com: Hi. I have made a nice little movie in Pymol. 1500 frames. So now I am wondering what is the best method to export? At the moment I do export to .png with ray tracing each image. set ray_trace_frames = 1 That takes a long time. And what program should I use to pack them together? The easy wasy? Can it be done faster with the MPEG method? Best Troels Troels Emtekær Linnet Slotsvej 2 4300 Holbæk Mobil: +45 60210234 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how can quickly make a fractional atoms into one
Dear Lina,
I don't want to be rude, but you should read this part of a document
on how to ask questions on a mailing list
http://catb.org/~esr/faqs/smart-questions.html#before.
Some of the question that you posted on this mailing list could have
been solved by a simple Google search.
Best regards,
Marius
--
Département de Chimie Moléculaire
Université Joseph Fourier
301 Rue de la Chimie
BP 53, 38041 Grenoble Cedex 9, France
Tel: +33 (0) 4 76 63 44 03
GnuPG http://db.tt/rr7Hd0Y
On Tue, Oct 11, 2011 at 10:37 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Lina,
That's best done following Thomas' approach, but using chain=X in
stead of segi=''
set pdb_retain_ids
load input.pdb
alter selection, chain='X'
save output.pdb
Cheers,
Tsjerk
On Tue, Oct 11, 2011 at 10:33 AM, lina lina.lastn...@gmail.com wrote:
On Tue, Oct 11, 2011 at 4:24 PM, Thomas Holder
spel...@users.sourceforge.net wrote:
On 10/11/2011 10:16 AM, Tsjerk Wassenaar wrote:
Not really a Pymol question, is it?
well, it's the segment identifier column, so you can do with PyMOL:
set pdb_retain_ids
load input.pdb
alter all, segi=''
save output.pdb
Thanks,
a bit further question, how to add chain identifier in pymol?
Here the situation is the 6 small ligands shared the same resn and even same
resi,
Cheers,
Thomas
On linux you can use sed:
sed '/^\(ATOM\|HETA\)/s/^\(.\{72\}\)/\1 /' filein.pdb
fileout.pdb
That means:
/^\(ATOM\|HETA\)/ :: Match lines starting with ATOM or with HETA, and
on those lines execute:
s/^\(.\{72\}\)/\1 / :: Subsitute the first 72 characters and
the following four by the first 72 and four spaces. '\1' refers to the
72 stored characters: \(.\{72\}\}
Hope it helps,
Tsjerk
On Tue, Oct 11, 2011 at 9:59 AM, linalina.lastn...@gmail.com wrote:
Hi,
I wish to change
ATOM 822 H01 PDB 1 32.103 36.531 -0.203 -0.11 0.02
.296
H
ATOM 823 C12 PDB 1 34.140 35.147 -0.218 -0.18 -0.01
.122
C
to:
ATOM 822 H01 PDB 1 32.103 36.531 -0.203 -0.11
0.02 H
ATOM 823 C12 PDB 1 34.140 35.147 -0.218 -0.18
-0.01 C
only the last field.
How can I quickly achieve it.
Thanks,
--
Thomas Holder
MPI for Developmental Biology
--
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post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
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--
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
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Re: [PyMOL] how to change atom name
Google search lead me to this http://www.pymolwiki.org/index.php/Atom_name_wildcard I think this should to the job in you case alter all, name=string.replace(name,H0,H) Best regards, Marius -- Dr. Marius Retegan Postdoctoral Fellow Département de Chimie Moléculaire Université Joseph Fourier 301 Rue de la Chimie BP 53, 38041 Grenoble Cedex 9, France Tel: +33 (0) 4 76 63 44 03 GnuPG http://db.tt/rr7Hd0Y On Tue, Sep 6, 2011 at 5:28 PM, lina lina.lastn...@gmail.com wrote: Hi, such as the atom name as H01, H03 How can I change it to H1, H3, Thanks for any suggestions (except modifying the .pdb file). -- Best Regards, lina -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free Love Thy Logs t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free Love Thy Logs t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] pymolrc file on Windows7
That variable (ray_trace_mode) dows not accept logical values. http://www.pymolwiki.org/index.php/Ray_trace_mode#Modes GnuPG http://db.tt/rr7Hd0Y On Tue, Aug 23, 2011 at 2:44 PM, Tatyana Sysoeva tatyanasyso...@gmail.com wrote: Hi Tsjerk, I am attaching the file and the terminal text. This Executable Build integrates and extends Open-Source PyMOL 1.3. Traceback (most recent call last): File C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parser.py, line 338, in parse parsing.run_file(path,self.pymol_names,self.pymol_names) File C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parsing.py, line 455, in run_file execfile(file,global_ns,local_ns) File C:\Users\Tanya\pymolrc.py, line 1 set ray_trace_mode, on ^ SyntaxError: invalid syntax + Thanks, Tanya On Tue, Aug 23, 2011 at 12:18 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Tanya, Does it say more than syntax error? Can you send the whole output? (copy crom the grey screen). In addition, can you send the pymolrc file as attachment? There might be something to do with line endings; so don't paste it in the mail, but attach the actual file that fails. Cheers, Tsjerk On Tue, Aug 23, 2011 at 2:03 AM, Tatyana Sysoeva tatyanasyso...@gmail.com wrote: Dear all, I have quite silly question but I could not find an answer so far. I am trying to use Pymol in a Power point presentation. For that I would like to change the default setting in Pymol - set security, off I have created a file pymolrc and put it in C:/Program Files/PyMol/PyMol/. When I am launching Pymol, it reads the file, but respond with syntax error. I checked and the same command is working properly if I type it directly into the Pymol prompt. I would appreciate any corrections or advices! Thank you very much, Tanya -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] pymolrc file on Windows7
What error to you get this time? These all work for me set security, 0 set security, off set security=off Marius GnuPG http://db.tt/rr7Hd0Y On Tue, Aug 23, 2011 at 2:53 PM, Tatyana Sysoeva tatyanasyso...@gmail.com wrote: true, my bad, but it does not work with 0,1,2 etc, as well as set security, off or set security = 0 I am sorry for the wrong file I sent. On Tue, Aug 23, 2011 at 8:51 AM, Marius Retegan marius.s.rete...@gmail.com wrote: That variable (ray_trace_mode) dows not accept logical values. http://www.pymolwiki.org/index.php/Ray_trace_mode#Modes GnuPG http://db.tt/rr7Hd0Y On Tue, Aug 23, 2011 at 2:44 PM, Tatyana Sysoeva tatyanasyso...@gmail.com wrote: Hi Tsjerk, I am attaching the file and the terminal text. This Executable Build integrates and extends Open-Source PyMOL 1.3. Traceback (most recent call last): File C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parser.py, line 338, in parse parsing.run_file(path,self.pymol_names,self.pymol_names) File C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parsing.py, line 455, in run_file execfile(file,global_ns,local_ns) File C:\Users\Tanya\pymolrc.py, line 1 set ray_trace_mode, on ^ SyntaxError: invalid syntax + Thanks, Tanya On Tue, Aug 23, 2011 at 12:18 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Tanya, Does it say more than syntax error? Can you send the whole output? (copy crom the grey screen). In addition, can you send the pymolrc file as attachment? There might be something to do with line endings; so don't paste it in the mail, but attach the actual file that fails. Cheers, Tsjerk On Tue, Aug 23, 2011 at 2:03 AM, Tatyana Sysoeva tatyanasyso...@gmail.com wrote: Dear all, I have quite silly question but I could not find an answer so far. I am trying to use Pymol in a Power point presentation. For that I would like to change the default setting in Pymol - set security, off I have created a file pymolrc and put it in C:/Program Files/PyMol/PyMol/. When I am launching Pymol, it reads the file, but respond with syntax error. I checked and the same command is working properly if I type it directly into the Pymol prompt. I would appreciate any corrections or advices! Thank you very much, Tanya -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Get a FREE DOWNLOAD! and learn more about uberSVN rich system, user administration capabilities and model configuration. Take the hassle out of deploying and managing Subversion and the tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] pymolrc file on Windows7
I've never tried to use pymol in a powerpoint presentation and I have
no idea what disabling security is suppose to do.
Did you try to call pymol with the -o argument. This supposedly
disables the security of session files.
http://www.pymolwiki.org/index.php/Command_Line_Options
Marius
GnuPG http://db.tt/rr7Hd0Y
On Tue, Aug 23, 2011 at 3:03 PM, Tatyana Sysoeva
tatyanasyso...@gmail.com wrote:
the same one:
Traceback (most recent call last):
File C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parser.py, line
338, in parse
parsing.run_file(path,self.pymol_names,self.pymol_names)
File C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parsing.py, line
455, in run_file
execfile(file,global_ns,local_ns)
File C:\Users\Tanya\pymolrc.py, line 1
set security, off
^
SyntaxError: invalid syntax
Tanya
On Tue, Aug 23, 2011 at 8:58 AM, Marius Retegan marius.s.rete...@gmail.com
wrote:
What error to you get this time?
These all work for me
set security, 0
set security, off
set security=off
Marius
GnuPG http://db.tt/rr7Hd0Y
On Tue, Aug 23, 2011 at 2:53 PM, Tatyana Sysoeva
tatyanasyso...@gmail.com wrote:
true, my bad, but it does not work with 0,1,2 etc, as well as set
security,
off or set security = 0
I am sorry for the wrong file I sent.
On Tue, Aug 23, 2011 at 8:51 AM, Marius Retegan
marius.s.rete...@gmail.com
wrote:
That variable (ray_trace_mode) dows not accept logical values.
http://www.pymolwiki.org/index.php/Ray_trace_mode#Modes
GnuPG http://db.tt/rr7Hd0Y
On Tue, Aug 23, 2011 at 2:44 PM, Tatyana Sysoeva
tatyanasyso...@gmail.com wrote:
Hi Tsjerk,
I am attaching the file and the terminal text.
This Executable Build integrates and extends Open-Source PyMOL 1.3.
Traceback (most recent call last):
File C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parser.py,
line
338, in parse
parsing.run_file(path,self.pymol_names,self.pymol_names)
File C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parsing.py,
line
455, in run_file
execfile(file,global_ns,local_ns)
File C:\Users\Tanya\pymolrc.py, line 1
set ray_trace_mode, on
^
SyntaxError: invalid syntax
+
Thanks,
Tanya
On Tue, Aug 23, 2011 at 12:18 AM, Tsjerk Wassenaar
tsje...@gmail.com
wrote:
Hi Tanya,
Does it say more than syntax error? Can you send the whole output?
(copy crom the grey screen). In addition, can you send the pymolrc
file as attachment? There might be something to do with line
endings;
so don't paste it in the mail, but attach the actual file that
fails.
Cheers,
Tsjerk
On Tue, Aug 23, 2011 at 2:03 AM, Tatyana Sysoeva
tatyanasyso...@gmail.com wrote:
Dear all,
I have quite silly question but I could not find an answer so far.
I am trying to use Pymol in a Power point presentation. For that I
would
like to change the default setting in Pymol -
set security, off
I have created a file pymolrc and put it in C:/Program
Files/PyMol/PyMol/.
When I am launching Pymol, it reads the file, but respond with
syntax
error.
I checked and the same command is working properly if I type it
directly
into the Pymol prompt.
I would appreciate any corrections or advices!
Thank you very much,
Tanya
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Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
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Re: [PyMOL] loading gro files
Maybe this can help you http://sourceforge.net/mailarchive/message.php?msg_id=19472192 Cheers, Marius On Tue, Aug 16, 2011 at 2:19 AM, Michael Daily mdaily.w...@gmail.com wrote: Hi all, Is there a direct way to load a gromacs structure file (.gro) in PyMOL? I know it's simple to convert them to pdb using editconf, but I want to load gro files directly (as you can in vmd) because they permit higher max. atom and residue numbers (100K vs. 10K for pdb) and permit longer residue names (4 chars vs. 3 for vmd). Thanks, Mike -- Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison) -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] load multiple pdb files in pdb
You could try something like this in a terminal for i in $(seq 1 1 100); do pymol $i.pdb; done if your file name are 1.pdb, 2.pdb ... 100.pdb Marius On Fri, Jul 15, 2011 at 9:00 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey Ram, It's scriptable, but not very doable on this Android :p The best solution would involve a generator funtion that takes a file pattern and a number, using glob to expand the file list, and using yield at each cycle. For a pythonista that should make sense ;) I may take it up when I'm typing with two hands again :) Cheers, Tsjerl On Jul 15, 2011 7:40 PM, r n ramm...@yahoo.com wrote: Hi I wanted to load 100 pdbs from 2000 pdb files. also is there way to load first 100 then second 200 etc.,? Is there any command that could control the number of PDB to load to pymol or script? I did downloaded PDBDIR from pymol wiki, but not much help. It did hang up for long time. Is there any commands like pymol c*.pdb, number=10 or file=10? any immediate help will be appreciated. thanks ram -- AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on Lean Startup Secrets Revealed. This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on Lean Startup Secrets Revealed. This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on Lean Startup Secrets Revealed. This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how to load two separate pdb files simultaneously
Hello Have you tried load A.pdb load B.pdb If this does not work for you, could you please define the what simultaneous means to you, i.e what exactly are you trying to do that requires simultaneous loading of two files? Marius On Wed, Jun 29, 2011 at 3:36 PM, leila karami karami.lei...@gmail.com wrote: Dear Hongbo very thanks for your attention. None of fetch 1A00 or 1A07 or 1A08 and fetch 1A00; fetch 1A07 does not help me. I need to load two separate pdb files simultaneously. -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] MacPyMOL touch pad control
This depends on how you touch pad is configured and what mode you selected froum the Mouse menu. I would suggest a trial and error approach to your problem. Try doing something and see what it does. Also Google is your friend. http://www.google.fr/search?q=pymol+mouse Marius On Thu, Jun 23, 2011 at 4:25 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi PyMol users, How can be I friendly with PyMol using the touch pad (MacBook Pro). What are the touch pad controls. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- Simplify data backup and recovery for your virtual environment with vRanger. Installation's a snap, and flexible recovery options mean your data is safe, secure and there when you need it. Data protection magic? Nope - It's vRanger. Get your free trial download today. http://p.sf.net/sfu/quest-sfdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Simplify data backup and recovery for your virtual environment with vRanger. Installation's a snap, and flexible recovery options mean your data is safe, secure and there when you need it. Data protection magic? Nope - It's vRanger. Get your free trial download today. http://p.sf.net/sfu/quest-sfdev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] global illumination, volume representation and ipython
Hello, There's been quite a while since I wanted to ask this on the list, but would it be possible to have in Pymol some kind of technique to emulate realistic lighting (global illumination) in a rendered scene? The next point is related to the new volume representation. For example after loading a cube file which contains the electrostatic potential of a small molecule, Pymol does not show the whole range in the volume representation. My data spans from -0.08 to 172.6. I haven't looked at how that scale is build, but would it be possible to let the user specify the range and build intermediate values from that. Also, while I understand that this feature was especially developed for the representation of electron density maps for proteins, not everyone is doing that and standard deviation or histograms on the volume representation should not be there by default. A simple scale should suffice. Also right clicking on the volume representation raises the following error Error: 2 type 'exceptions.TypeError' Exception in Tk callback Function: bound method Volume.editPoint of pmg_tk.skins.normal.volume.Volume instance at 0x2c556b90 (type: type 'instancemethod') Args: (Tkinter.Event instance at 0x2c7277a0,) Event type: ButtonPress (type num: 4) Traceback (innermost last): File /usr/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line 1747, in __call__ return apply(self.func, args) File /usr/lib64/python2.7/site-packages/pmg_tk/skins/normal/volume.py, line 369, in editPoint event.x = self.active_ramp.getPoint(pt) + self.padX type 'exceptions.TypeError': unsupported operand type(s) for +: 'NoneType' and 'int' Finally is it possible to use Pymol from within iPython? For example I wanted recently to see the properties of a C object. That would have been extremly easy in iPython import pymol cube = pymol.cmd.load(my.cube) cube.[TAB] [TAB] Thanks Marius -- Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] global illumination, volume representation and ipython
Hello, On Fri, Apr 8, 2011 at 6:49 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Marius, There's been quite a while since I wanted to ask this on the list, but would it be possible to have in Pymol some kind of technique to emulate realistic lighting (global illumination) in a rendered scene? So, you're looking for something like ambient occlusion? If so, try this (taken from the gallery at the PyMOLWiki): load $TUT/1hpv.pdb set_color oxygen, [1.0,0.4,0.4] set_color nitrogen, [0.5,0.5,1.0] remove solvent as spheres util.cbaw bg white set light_count,10 set spec_count,1 set shininess, 10 set specular, 0.25 set ambient,0 set direct,0 set reflect,1.5 set ray_shadow_decay_factor, 0.1 set ray_shadow_decay_range, 2 unset depth_cue ray PyMOL can simulate this, but not do it numerically perfectly. With the addition of shaders and us working on modernizing the code, this might be properly doable in the future. I knew about the solution from the wiki, but as you mentioned there are better ways to do this :). The next point is related to the new volume representation. For example after loading a cube file which contains the electrostatic potential of a small molecule, Pymol does not show the whole range in the volume representation. My data spans from -0.08 to 172.6. I haven't looked at how that scale is build, but would it be possible to let the user specify the range and build intermediate values from that. Also, while I understand that this feature was especially developed for the representation of electron density maps for proteins, not everyone is doing that and standard deviation or histograms on the volume representation should not be there by default. A simple scale should suffice. Thanks for trying this out and offering your feedback. Currently, the vast majority of volumes users are crystallographers with very well defined ranges for data. We tried to make the common case easy for them, while still allowing not-common use cases possible. We do plan to improve the UI in the future. Context aside, here's your fix: set volume_data_range, X where X is the number (or fraction) of +/- sigma-levels PyMOL should map out on the X axis. The default is 5. After you change this value, please reload the Volume editor, by clicking on the Volume button (twice). For your data if you need to hit 30 sigma levels to get to 172.6, then set volume_data_range to 30. Again, this was for statistically normalized crystallographic data and your data may not be normal and thus not have sigma levels with meaning. In that case, just try the numbers and see what works for you. You can also use fractional values to focus on a narrow portion of the data (around the mean). I'm going to give that a try. Maybe if I find some time I'm going to write the volume class closer to my need and post somewhere the code. For this I would really like to be able to see what gets passed thru it interactively (the reason why I've asked about iPyton). Also right clicking on the volume representation raises the following error Error: 2 type 'exceptions.TypeError' Exception in Tk callback Function: bound method Volume.editPoint of pmg_tk.skins.normal.volume.Volume instance at 0x2c556b90 (type: type 'instancemethod') Args: (Tkinter.Event instance at 0x2c7277a0,) Event type: ButtonPress (type num: 4) Traceback (innermost last): File /usr/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line 1747, in __call__ return apply(self.func, args) File /usr/lib64/python2.7/site-packages/pmg_tk/skins/normal/volume.py, line 369, in editPoint event.x = self.active_ramp.getPoint(pt) + self.padX type 'exceptions.TypeError': unsupported operand type(s) for +: 'NoneType' and 'int' This is a bug. We'll fix this. In the meantime, please right-click closer to color points. Right-clicking a point will allow you to edit it. Right-clicking the background will bring up that exception. You can delete points with the middle mouse button. Finally is it possible to use Pymol from within iPython? For example I wanted recently to see the properties of a C object. That would have been extremly easy in iPython import pymol cube = pymol.cmd.load(my.cube) cube.[TAB] [TAB] This is what I get in iPython In [4]: cube = pymol.cmd.load(my_cube.cube) --- AttributeErrorTraceback (most recent call last) /home/marius/ipython console in module() /usr/lib64/python2.7/site-packages/pymol/importing.pyc in load(filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial, mimic, _self) 870 discrete,quiet,multiplex,zoom,mimic,_self=_self) 871 finally: -- 872 _self.unlock(r,_self) 873 if go_to_first_scene: 874
Re: [PyMOL] Center of mass
Enter editing mode, select the 2 points, press Ctrl + t or type bond on the cli. Cheers, Marius On Thu, Mar 31, 2011 at 11:36 AM, kanika sharma ksharma...@gmail.comwrote: I have two points corresponding to center of masses of 2 proteins. I have to draw a line between both. Is there a feature that can do this? -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] installation of pymol V1.3r2 problem
Dear Edith, You have overwritten the python that comes with the system with that from a mgltools install. That particular install is 32 bit, your system is 64 bit. Look in your shell configuration file (.bashrc most probably) for something like export PYTHON_PATH and comment it temporally. Rerun the instalation http://www.pymolwiki.org/index.php/Linux_Install#Generic_Linux Best regards, Marius On Mon, Mar 21, 2011 at 5:04 PM, Edith Gincel edith.gin...@parisdescartes.fr wrote: I am working on Linux 2.6.18-8.el5 x86_64 GNU/Linux I had problem with the 0,99 version of pymol (it was working but with very strange behaviour thant no one could explain), so I am trying to install the 1.3r2 version I download it and then followed the instructions : I untarred and dezipped and then : python setup.py build install I get this error message which I don't understand at all. Could someone help me please? running build running build_py package init file 'modules/web/javascript/__init__.py' not found (or not a regular file) package init file 'modules/web/javascript/__init__.py' not found (or not a regular file) running build_ext building 'pymol._cmd' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Imodules/cealign/src -Imodules/cealign/src/tnt -I/home/edith/logiciels/mgltools_i86Linux2_1.5.4/include/python2.5 -c modules/cealign/src/ccealignmodule.cpp -o build/temp.linux-x86_64-2.5/modules/cealign/src/ccealignmodule.o -ffast-math -funroll-loops -O3 cc1plus: attention : l'option de la ligne de commande -Wstrict-prototypes est valide pour Ada/C/ObjC mais pas pour C++ Dans le fichier inclus à partir de /home/edith/logiciels/mgltools_i86Linux2_1.5.4/include/python2.5/Python.h:57, à partir de layer0/os_python.h:30, à partir de modules/cealign/src/ccealignmodule.H:57, à partir de modules/cealign/src/ccealignmodule.cpp:32: /home/edith/logiciels/mgltools_i86Linux2_1.5.4/include/python2.5/pyport.h:734:2: erreur: #error LONG_BIT definition appears wrong for platform (bad gcc/glibc config?). modules/cealign/src/ccealignmodule.cpp: In function ‘PyObject* findBest(cePoint*, cePoint*, afp**, int, int, int)’: modules/cealign/src/ccealignmodule.cpp:553: attention : comparaison entre des expressions entières signée et non signée modules/cealign/src/ccealignmodule.cpp: In function ‘TNT::Array2Ddouble transpose(const TNT::Array2Ddouble)’: modules/cealign/src/ccealignmodule.cpp:628: attention : comparaison entre des expressions entières signée et non signée modules/cealign/src/ccealignmodule.cpp:629: attention : comparaison entre des expressions entières signée et non signée error: command 'gcc' failed with exit status 1 -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] hbs
Hello Maia, Does this work? color black, hb* Marius On Tue, Mar 15, 2011 at 5:40 PM, Maia Cherney ch...@ualberta.ca wrote: Hi, Can anybody advise me what is the right command for selecting or coloring many hbs? Instead of color black, hb1 color black, hb2 etc I want something like color black, hb1+hb2+hb3 etc. Maia -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] FYI: Compiling Pymol 1.3 (svn trunk) on Mac OS X Snow Leopard
Did you try the macports (http://www.macports.org/) version? Marius On Fri, Jul 9, 2010 at 10:10 PM, Paul Rigor (uci) paul.ri...@uci.eduwrote: Hi gang, Actually, I spoke too soon! I attempted this compilation to address another user's problems with an external script. But as you can see from the attachment, the main control window is not being rendered properly. Am missing other libraries? Thanks, Paul On Fri, Jul 9, 2010 at 12:53 PM, Paul Rigor (uci) paul.ri...@uci.eduwrote: Hi gang, Just wanted to share some notes on compiling and getting Pymol 1.3.x running on OS X Snow Leopard. Before proceeding, you'll of course need the XCode SDK which comes supplied with the OS X cd's or downloaded through apple's developer site. (1) Compilation: For some reason, the included freetype2 library is insufficient even though the compilation flags correctly point to the library's path (ext/include/freetype2). The compilation fails with the following message (truncated): In file included from layer1/TypeFace.c:25: /usr/X11R6/include/ft2build.h:56:38: error: freetype/config/ftheader.h: No such file or directory The fix is to prepend the build step with the following CFLAGS environment variable like so which points to the system default X11 library: CFLAGS=-I/usr/X11R6/include/freetype2 python setup.py build You can then proceed with the installation, followed by the secondary setup2.py commend as noted at the end of the build step. (2) Additional library: A required library, Pmw, isn't included with the SVN trunk, so you'll need to download it from the following site: http://sourceforge.net/projects/pmw/files/ Unpack; dive into the src folder and issue python setup.py build python setup.py install All should work. Cheers, Paul -- Paul Rigor http://www.ics.uci.edu/~prigor http://www.ics.uci.edu/%7Eprigor -- Paul Rigor http://www.ics.uci.edu/~prigor http://www.ics.uci.edu/%7Eprigor -- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] FYI: Compiling Pymol 1.3 (svn trunk) on Mac OS X Snow Leopard
This usually means that tk or tcl is not installed correctly. You could try to google the error. This gives you an idea about the problem 99% of the cases. Also you can double check that everything is installed. $ port installed tk tcl pymol. On a macosx 10.5.8 I get: pymol @1.3_0 (active) tcl @8.5.8_0+darwin (active) tk @8.5.8_0+darwin (active) Ultimately you could file a bug report with macports or ask on their mailing list. Marius On Sat, Jul 10, 2010 at 3:10 AM, Paul Rigor (uci) paul.ri...@uci.eduwrote: Hi Marius, So I grabbed Pymol through macports, but now the main control window isn't being rendered. I also receive the following error message. I've truncated the error message. I know that macports resolved the tk/tcl dependencies, so I'm not sure what's up? Has anyone else run into this problem? Thanks, Paul === Error log below === OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: NVIDIA GeForce 320M OpenGL Engine GL_VERSION: 2.1 NVIDIA-1.6.16 Traceback (most recent call last): File /opt/local/lib/pymol/modules/pmg_tk/__init__.py, line 35, in run PMGApp(pymol_instance,skin).run(poll) File /opt/local/lib/pymol/modules/pmg_tk/PMGApp.py, line 389, in __init__ self.root = Tk() # creates the root window for the application File /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/lib-tk/Tkinter.py, line 1643, in __init__ self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) TclError: Can't find a usable tk.tcl in the following directories: On Fri, Jul 9, 2010 at 2:03 PM, Marius Retegan marius.s.rete...@gmail.com wrote: Did you try the macports (http://www.macports.org/) version? Marius On Fri, Jul 9, 2010 at 10:10 PM, Paul Rigor (uci) paul.ri...@uci.eduwrote: Hi gang, Actually, I spoke too soon! I attempted this compilation to address another user's problems with an external script. But as you can see from the attachment, the main control window is not being rendered properly. Am missing other libraries? Thanks, Paul On Fri, Jul 9, 2010 at 12:53 PM, Paul Rigor (uci) paul.ri...@uci.eduwrote: Hi gang, Just wanted to share some notes on compiling and getting Pymol 1.3.x running on OS X Snow Leopard. Before proceeding, you'll of course need the XCode SDK which comes supplied with the OS X cd's or downloaded through apple's developer site. (1) Compilation: For some reason, the included freetype2 library is insufficient even though the compilation flags correctly point to the library's path (ext/include/freetype2). The compilation fails with the following message (truncated): In file included from layer1/TypeFace.c:25: /usr/X11R6/include/ft2build.h:56:38: error: freetype/config/ftheader.h: No such file or directory The fix is to prepend the build step with the following CFLAGS environment variable like so which points to the system default X11 library: CFLAGS=-I/usr/X11R6/include/freetype2 python setup.py build You can then proceed with the installation, followed by the secondary setup2.py commend as noted at the end of the build step. (2) Additional library: A required library, Pmw, isn't included with the SVN trunk, so you'll need to download it from the following site: http://sourceforge.net/projects/pmw/files/ Unpack; dive into the src folder and issue python setup.py build python setup.py install All should work. Cheers, Paul -- Paul Rigor http://www.ics.uci.edu/~prigor http://www.ics.uci.edu/%7Eprigor -- Paul Rigor http://www.ics.uci.edu/~prigor http://www.ics.uci.edu/%7Eprigor -- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Paul Rigor http://www.ics.uci.edu/~prigor http://www.ics.uci.edu/%7Eprigor -- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] color an isosurface
Hello With help from Jason I've managed to solve my problem. As a result I've updated the wiki page for the ramp_new command to include my particular case (see bottom of the page) http://pymolwiki.org/index.php/Ramp_New Marius On Mon, Jun 28, 2010 at 10:32 PM, Marius Retegan marius.s.rete...@gmail.com wrote: Hello, Take the following scenario. I have two cube files, the first one holds some values of a function (electron localization function), while in the second cube for each value in the first cube file i can have either one of the numbers from 0 to 6. After loading the first cube file in Pymol, I create an isosurface of a given value for the contour level, lets say 0.8 a.u. Next I want to color this isosurface based on the values in the second cube file, e.g. all points that have a value of 3 in the second cube should be colored red etc. Any ideas on how to accomplish this? If needed, I could provide the two cube files for a simple test case Thank you Marius -- 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 (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] scripts with fetch
Just a wild guess fetch 1htr, async=0 Marius On Tue, May 4, 2010 at 10:58 PM, Michael Zimmermann micha...@iastate.eduwrote: Dear PyMOL users, I was just making a script to selectively download sections of PDB files using fetch. When I run the pml from the GUI I see that all of the commands are executed and then the structure called by fetch is loaded. Is there any way to force the other commands to wait until fetch is finished getting the PDB file? Interestingly, if I run the script a second time, then it behaves as I would have expected it to. If multiple PDB files are fetched and downloaded the pattern is similar; the first time the script is run all of the commands are processed, and then all of the structures are fetched but the second time the script is run the structures are fetched and then the next lines of code are run. I would like to do this for hundreds of structures based on PFam domains, so it would be nice if this would work reliably. I am executing the file with PyMOL.exe -c -k -u myscript.pml --PML-File -- fetch 1htr remove not (alt ''+A) alter all, alt='' select prot, (chain P and resi 2-30) save PF_1htr.pdb, prot delete all -- --PYMOL-output-after-first-run- PyMOL@Fetch_PF07966.pml PyMOLcd C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation cd: now in C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation PyMOLfetch 1htr PyMOLremove not (alt ''+A) PyMOLalter all, alt='' Alter: modified 0 atoms. PyMOLselect prot, (chain P and resi 2-30) Selector: selection prot defined with 0 atoms. PyMOLsave C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation\PF07966\PF_1htr.pdb, prot Save: wrote C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation\PF07966\PF_1htr.pdb. PyMOLdelete all HEADERASPARTYL PROTEASE 21-OCT-94 1HTR TITLE CRYSTAL AND MOLECULAR STRUCTURES OF HUMAN PROGASTRICSIN AT TITLE2 1.62 ANGSTROMS RESOLUTION COMPNDMOL_ID: 1; COMPND 2 MOLECULE: PROGASTRICSIN (PRO SEGMENT); COMPND 3 CHAIN: P; COMPND 4 EC: 3.4.23.3; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: GASTRICSIN; COMPND 8 CHAIN: B; COMPND 9 EC: 3.4.23.3; COMPND 10 ENGINEERED: YES ObjectMolecule: Read secondary structure assignments. ObjectMolecule: Read crystal symmetry information. Symmetry: Found 8 symmetry operators. CmdLoad: .\1htr.pdb loaded as 1htr. - --PYMOL-output-after-second-run- PyMOLfetch 1htr PyMOLremove not (alt ''+A) HEADERASPARTYL PROTEASE 21-OCT-94 1HTR TITLE CRYSTAL AND MOLECULAR STRUCTURES OF HUMAN PROGASTRICSIN AT TITLE2 1.62 ANGSTROMS RESOLUTION COMPNDMOL_ID: 1; COMPND 2 MOLECULE: PROGASTRICSIN (PRO SEGMENT); COMPND 3 CHAIN: P; COMPND 4 EC: 3.4.23.3; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: GASTRICSIN; COMPND 8 CHAIN: B; COMPND 9 EC: 3.4.23.3; COMPND 10 ENGINEERED: YES ObjectMolecule: Read secondary structure assignments. ObjectMolecule: Read crystal symmetry information. CmdLoad: .\1htr.pdb appended into object 1htr, state 2. Remove: eliminated 16 atoms in model 1htr. PyMOLalter all, alt='' Alter: modified 3113 atoms. PyMOLselect prot, (chain P and resi 2-30) Selector: selection prot defined with 239 atoms. PyMOLsave C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation\PF07966\PF_1htr.pdb, prot Save: wrote C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation\PF07966\PF_1htr.pdb. PyMOLdelete all - -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] scripts with fetch
I guess this is a general thing in pymol, i.e. if async is 1 your command is going to be spawned in another thread, so you keep working while it's executed. With async = 0 things are executed in the main thread. On Tue, May 4, 2010 at 11:24 PM, Michael Zimmermann micha...@iastate.eduwrote: Thank you Marius, that does appear to do the job. I guess this tip is sortof present on the wiki page for fetch, but I didn't understand it as written. Sincerely, Mike On Tue, May 4, 2010 at 4:13 PM, Marius Retegan marius.s.rete...@gmail.com wrote: Just a wild guess fetch 1htr, async=0 Marius On Tue, May 4, 2010 at 10:58 PM, Michael Zimmermann micha...@iastate.edu wrote: Dear PyMOL users, I was just making a script to selectively download sections of PDB files using fetch. When I run the pml from the GUI I see that all of the commands are executed and then the structure called by fetch is loaded. Is there any way to force the other commands to wait until fetch is finished getting the PDB file? Interestingly, if I run the script a second time, then it behaves as I would have expected it to. If multiple PDB files are fetched and downloaded the pattern is similar; the first time the script is run all of the commands are processed, and then all of the structures are fetched but the second time the script is run the structures are fetched and then the next lines of code are run. I would like to do this for hundreds of structures based on PFam domains, so it would be nice if this would work reliably. I am executing the file with PyMOL.exe -c -k -u myscript.pml --PML-File -- fetch 1htr remove not (alt ''+A) alter all, alt='' select prot, (chain P and resi 2-30) save PF_1htr.pdb, prot delete all -- --PYMOL-output-after-first-run- PyMOL@Fetch_PF07966.pml PyMOLcd C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation cd: now in C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation PyMOLfetch 1htr PyMOLremove not (alt ''+A) PyMOLalter all, alt='' Alter: modified 0 atoms. PyMOLselect prot, (chain P and resi 2-30) Selector: selection prot defined with 0 atoms. PyMOLsave C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation\PF07966\PF_1htr.pdb, prot Save: wrote C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation\PF07966\PF_1htr.pdb. PyMOLdelete all HEADERASPARTYL PROTEASE 21-OCT-94 1HTR TITLE CRYSTAL AND MOLECULAR STRUCTURES OF HUMAN PROGASTRICSIN AT TITLE2 1.62 ANGSTROMS RESOLUTION COMPNDMOL_ID: 1; COMPND 2 MOLECULE: PROGASTRICSIN (PRO SEGMENT); COMPND 3 CHAIN: P; COMPND 4 EC: 3.4.23.3; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: GASTRICSIN; COMPND 8 CHAIN: B; COMPND 9 EC: 3.4.23.3; COMPND 10 ENGINEERED: YES ObjectMolecule: Read secondary structure assignments. ObjectMolecule: Read crystal symmetry information. Symmetry: Found 8 symmetry operators. CmdLoad: .\1htr.pdb loaded as 1htr. - --PYMOL-output-after-second-run- PyMOLfetch 1htr PyMOLremove not (alt ''+A) HEADERASPARTYL PROTEASE 21-OCT-94 1HTR TITLE CRYSTAL AND MOLECULAR STRUCTURES OF HUMAN PROGASTRICSIN AT TITLE2 1.62 ANGSTROMS RESOLUTION COMPNDMOL_ID: 1; COMPND 2 MOLECULE: PROGASTRICSIN (PRO SEGMENT); COMPND 3 CHAIN: P; COMPND 4 EC: 3.4.23.3; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: GASTRICSIN; COMPND 8 CHAIN: B; COMPND 9 EC: 3.4.23.3; COMPND 10 ENGINEERED: YES ObjectMolecule: Read secondary structure assignments. ObjectMolecule: Read crystal symmetry information. CmdLoad: .\1htr.pdb appended into object 1htr, state 2. Remove: eliminated 16 atoms in model 1htr. PyMOLalter all, alt='' Alter: modified 3113 atoms. PyMOLselect prot, (chain P and resi 2-30) Selector: selection prot defined with 239 atoms. PyMOLsave C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation\PF07966\PF_1htr.pdb, prot Save: wrote C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\Motion_conservation\PF07966\PF_1htr.pdb. PyMOLdelete all - -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department of Biochemistry, Biophysics and Molecular Biology Iowa State University -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Zimmermann Ph.D. student in Bioinformatics and Computational Biology Department
Re: [PyMOL] Whitespacing?
Try the expand command on linux or google for sed tab to space
replacement.
Marius
On Tue, Jan 26, 2010 at 5:48 PM, Michael Zimmermann micha...@iastate.eduwrote:
If you have a lot of files to do this to, I would suggest learning at
least a little bit of perl. It might not be as nice an option as a
python tab manager (depending on your point of view), though.
Perl uses regular expressions. In case you'd like to see how to do
your tab-space replacement, the following bit of code would convert
tabs to 4 spaces.
Take care,
Mike Z
#--
use strict;
use warnings;
my $file = $ARGV[0];
open(IN,$file) or die $!;
open(OUT,.$file.notab) or die $!;
while(IN){
$_ =~ s/\t//g;
print OUT $_;
}
close(IN);
close(OUT);
exit;
#--
On Tue, Jan 26, 2010 at 9:09 AM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
David,
Oh, the joys of open-source. Here's my solution for you:
(1) load your file in your favorite editor
(2) determine user-desired tab stop setting
(3) convert all tabs to spaces in your editor (or search replace tabs
with X-spaces)
(4) save your file
One warning though, I have seen some interpreters crash when they
encounter spaces over tabs.
-- Jason
On Tue, Jan 26, 2010 at 9:12 AM, David Hall li...@cowsandmilk.net
wrote:
During my editing of dynoplot.py, I noticed that there were some
whitespace issues. Normally I consider whitespace a bikeshedding
topic, but in python, it is significant, so it matters. When tabs and
spaces are mixed, our own personal settings for how tabs are displayed
in an editor makes a huge difference in whether the script is
understandable.
I checked out the git repo of pymol scripts (
http://github.com/jlec/Pymol-script-repo/ ) and did some analysis
First, these files switch between some lines where all indenting is
tabs to lines where all indenting is spaces:
Objects_and_Selections/color_objects.py has 8 tab lines and 34 space
lines
ThirdParty_Scripts/WFMesh.py has 52 tab lines and 21 space lines
biochemical_scripts/pucker.py has 167 tab lines and 5 space lines
math_geo_cgo/modevectors.py has 160 tab lines and 2 space lines
structural_biology_scripts/DynoPlot.py has 82 tab lines and 27 space
lines
structural_biology_scripts/Rotamers.py has 86 tab lines and 22 space
lines
structural_biology_scripts/kabsch.py has 51 tab lines and 4 space lines
Second, there are files where the indenting inside a line switches
back and forth (numbers are the counts of lines that have both tabs
and spaces in indenting):
Objects_and_Selections/color_objects.py: 19
ThirdParty_Scripts/WFMesh.py: 29
ThirdParty_Scripts/transform_odb.py: 6
math_geo_cgo/modevectors.py: 12
structural_biology_scripts/DynoPlot.py: 83
structural_biology_scripts/Rotamers.py: 86
structural_biology_scripts/kabsch.py: 1
I've tried using pindent.py (
http://svn.python.org/projects/python/trunk/Tools/scripts/pindent.py )
and PythonTidy ( http://pypi.python.org/pypi/PythonTidy/ ) to
generally fix these, but they both run into problems. Is there a
general solution out in the python world to automatically fix this? I
don't care whether it produces tabs or spaces. I just want one or the
other. If someone points me to something, I'm more than willing to
run it on these scripts, push them back to github and copy them back
onto the wiki.
-David
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Archives:
Re: [PyMOL] 3D Stereo Problem
On Wed, Jan 20, 2010 at 9:35 AM, Jesper Lykkegaard Karlsen je...@bioxray.au.dk wrote: Hi Deepangi, 1. OS: Windows 7 2. Monitor:Samsung Syncmaster 2233RZ 22in 3D Gaming LCD 3. Card: EVGA GeForce 9800 GTX+ 512MB PCIe w/Dual Link DVI 4. Glasses: NVIDIA 3D Vision Glasses Wrong graphics card: http://www.nvidia.com/object/quadro_pro_graphics_boards.html No according to this http://www.nvidia.com/object/3D_Vision_Requirements.html and an old post from the list http://bit.ly/61Lwbn. /Jesper -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PyMOL Blender
Thank you for the nice tutorial. On Tue, Dec 22, 2009 at 8:17 PM, Shiven Shandilya shiven.shandi...@gmail.com wrote: Hello List, An initial attempt at a PyMOL + Blender tutorial is now on the pymolwiki: http://pymolwiki.org/index.php/Blender Hope some of you will find it useful. Fellow Blenderheads, crits are welcome. Also, please help improve/add to the tutorial. Best, Shiven Shivender Shandilya, Graduate Student, Schiffer Lab, Dept. of Biochemistry Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01604. -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Slightly off topic
In my opinion CentOS is not made for a desktop environment. If you are confortable with the rpm system package, try switching to Fedora and install the rpmforge repository (https://rpmrepo.org/RPMforge). Marius On Tue, Dec 15, 2009 at 4:33 AM, Joel Tyndall joel.tynd...@otago.ac.nzwrote: Hi folks, Sorry for the off topic post. I have just got a new whizz bang laptop and I’m wondering whether I have gone too high spec. It is 64 bit LED ASUS ul50v series. I am running linux centos 5.4 but can’t get the nvidia driver going (LED screen perhaps) and I just had an initial problem with pymol. (I want to run modeler, sybyl and gold also ) This is not to mention the fact that the kernel doesn’t have wireless or Ethernet drivers. Should I “downgrade” or persist. Many thanks for comments _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] selecting multiple, non-adjacent chains
Try this one select allothers, chain 0:4 or chain C:J or chain L:Z Marius On Thu, Oct 15, 2009 at 3:34 PM, Sean Moore semo...@mail.ucf.edu wrote: Hello, I am trying to find an easier way to select multiple chains at once in a large file with many chains (PDB 2i2t). The chain assignments exceed z and start again at 0 at the beginning of the chain list. In an effort to select chain 0-4, skip chain A+B, select chain C-J, skip chain K, and select the remaining L-Z, I have tried (among other things): select allothers, chain 0-4 and C-J and L-Z (the dashes don't seem to work for select) select allothers, chain 0:4 and C:J and L:Z select allothers, chain 0:4 and chain C:J and chain L:Z select allothers, (chain 0:4) and (chain C:J) and (chain L:Z) selecting chain 0+4 works, and selecting chain 0:4 works. As it stands I have to click all of the chains then rename the selection which leads to mistakes. Any help is appreciated. -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Change location of measurement label
I don't know if this is version dependent, but in my case (version 1.2r2) you have to enter in editing mode (Mouse - 3 Buttons Editing) and Ctrl+left click the label and drag. Hope this helps Marius On Wed, Oct 14, 2009 at 11:55 AM, Per Larsson per.lars...@sbc.su.se wrote: Hi! I need to make some pictures of very simple di-peptide systems, and need to include values (from wizard-measurement-dihedrals) of certain dihedral angles. However, the two labels end up very close, with the values almost on top of each other making them un-readable. Is there a way to change the location of the measurement labels? Thanks! /Per -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] load dcd files problem
I've just update my source code. So what you need to do is uncomment lines 126, 127, 146 and change the zero on line 293 with a 1. Let me now if this works. I don't have a dcd trajectory in order to test this. Marius On Tue, Sep 15, 2009 at 3:45 PM, Hugo G. de Teran hugo.te...@usc.es wrote: I did that now, run again pymol setup.py build install pymol setup2.py install but still the same error ... Hugo Marius Retegan wrote: Did you uncomment in setup.py the lines related to VMD support? On Tue, Sep 15, 2009 at 3:07 PM, Hugo G. de Teran hugo.te...@usc.es wrote: Hi, I am trying to use the load_traj command to load dcd files. Holever, I get the following error: PyMOLload_traj ../../1bwb/dc1.dcd, initial, ObjectMolecule-Error: sorry, VMD Molfile Plugins not compiled into this build. I have installed pymol from source with the default method (i.e., python install scripts) on my opensuse11.1 x86_64 Thanks for help, Hugo -- Hugo G. de Teran, PhD. Parga Pondal Research fellow Fundación Pública Galega de Medicina Xenómica - SERGAS Santiago de Compostela (SPAIN) Phone +34 981563100 ext 13873 e-mail:hugo.te...@usc.es e-mail%3ahugo.te...@usc.es e-mail%3ahugo.te...@usc.es e-mail%253ahugo.te...@usc.es http://web.usc.es/~hugogdt http://web.usc.es/%7Ehugogdt http://web.usc.es/%7Ehugogdt -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net --0016e6db2dbbff30f304739dc03a Content-Type: text/html; charset=O-8859-1 Content-Transfer-Encoding: quoted-printable Did you uncomment in setup.py the lines related to VMD support?brbrdiv class=gmail_quoteOn Tue, Sep 15, 2009 at 3:07 PM, Hugo G. de Teran span dir=ltrlt;a href=mailto:hugo.te...@usc.es;hDelivered-To: hugo...@gmail.com Received: by 10.103.221.10 with SMTP id y10cs111217muq; Tue, 15 Sep 2009 06:29:04 -0700 (PDT) Received: by 10.211.171.14 with SMTP id y14mr8459245ebo.58.1253021301179; Tue, 15 Sep 2009 06:28:21 -0700 (PDT) Return-Path: marius.s.rete...@gmail.com Received: from rojo2.usc.es (rojo2.usc.es [193.144.75.10]) by mx.google.com with ESMTP id 25si5396218ewy.39.2009.09.15.06.28.19; Tue, 15 Sep 2009 06:28:20 -0700 (PDT) Received-SPF: neutral (google.com: 193.144.75.10 is neither permitted nor denied by domain of marius.s.rete...@gmail.com) client-ip 3.144.75.10; Authentication-Results: mx.google.com; spf=utral (google.com: 193.144.75.10 is neither permitted nor denied by domain of marius.s.rete...@gmail.com) smtp.mail=marius.s.rete...@gmail.com; dkim=pass (test mode) header...@gmail.com Received: from localhost (rojo2 [127.0.0.1]) by rojo2.usc.es (Postfix) with ESMTP id 2291E464A5F for hugo...@gmail.com; Tue, 15 Sep 2009 15:28:16 +0200 (CEST) X-Virus-Scanned: amavisd-new at usc.es Received: from rojo2.usc.es ([127.0.0.1]) by localhost (rojo2.usc.es [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 6KotJbBytw00 for hugo...@gmail.com; Tue, 15 Sep 2009 15:28:16 +0200 (CEST) Received: from oro1.usc.es (oro1.usc.es [193.144.75.8]) by rojo2.usc.es (Postfix) with ESMTP id F357A464A3D for hugo...@gmail.com; Tue, 15 Sep 2009 15:28:15 +0200 (CEST) Received: by oro1.usc.es (Postfix, from userid 100) id 712C23A02D; Tue, 15 Sep 2009 15:28:19 +0200 (CEST) Received: from oro1.usc.es ([unix socket]) by oro1 (Cyrus v2.1.18-IPv6-Debian-2.1.18-1+sarge2) with LMTP; Tue, 15 Sep 2009 15:28:19 +0200 X-Sieve: CMU Sieve 2.2 Received: from rojo3.usc.es (rojo3.usc.es [193.144.75.13]) by oro1.usc.es (Postfix) with ESMTP id 4F4023A02B for hugo.te...@usc.es; Tue, 15 Sep 2009 15:28:19 +0200 (CEST) Received: from localhost (localhost.localdomain [127.0.0.1]) by rojo3.usc.es (Postfix) with ESMTP id E285C3C184 for hugo.te...@usc.es; Tue, 15 Sep 2009 15:28:18 +0200 (CEST) X-Virus-Scanned: amavisd-new at usc.es X-Spam-Score: 1.44 X-Spam-Level: * X-Spam-Status: No, score=44 tagged_above=-999 required=5 tests=[DNS_FROM_RFC_POST=1.44, HTML_MESSAGE=0.001, SPF_PASS=-0.001] Received: from rojo3.usc.es ([127.0.0.1]) by localhost (rojo3.usc.es [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 9yKch60LhdRg for hugo.te...@usc.es; Tue, 15 Sep 2009 15:28:12 +0200 (CEST) Received
Re: [PyMOL] where to find a 64 bit Linux version?
Hi Tom, On Wed, Mar 18, 2009 at 12:03 AM, Thomas Evangelidis te8...@mbg.duth.gr wrote: Dear Pymol users, does anyone know where I can find a 64 bit version for my Fedora 10. The package from the repositories works fine but when it comes to install new plugins it yields error messages. As a matter of fact I What error message and what plugin? can't even figure out where the whole program is installed (used locate command but still remains unclear). On the other hand when I The database used by locate is updated once a day. To update it try updatedb as root. install the 32 bit version and try to resolve those i386 library-dependencies I end up getting the error message: /home/thomas/Documents/pymol/pymol.exe: error while loading shared libraries: libstdc++.so.5: wrong ELF class: ELFCLASS64 Why do you have a pymol.exe on Fedora? libstdc++.so.5 is in the correct directory (/usr/lib/), cannot imagine what's going wrong. Anyway, I think a 64 bit version (if does exist) would solve all the afore-mentioned problems. thanks in advance, Tom -- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] keyboard shortcuts
Hello, While I am in editing mode, there is a keyboard shortcut to display the distance between to selected atoms, but I cant remember it. I would appreciate if someone could refresh my memory. Another related question would be where I can find a list of shortcuts currently available in Pymol? And finally, I recall seeing a feature request related to displaying the default values for all the available commands in Pymol, for example what is default value for specular. Was this feature implemented? Thank you. Marius
Re: [PyMOL] label with arbitrary string
Hello Leo,
You could use Unicode to get the special characters you were taking about.
angstrom = u\u00C5
angstrom_utf8 = angstrom.encode ('utf-8')
label (residue 200 and name ca), Distance: 8+angstrom_utf8
To see the label bigger use set label_size, 20
You can get the unicode charts from here http://www.unicode.org/charts
On Wed, Jul 30, 2008 at 11:18 AM, Tsjerk Wassenaar tsje...@gmail.comwrote:
Hi Leo,
AFAIK you can't do it with Pymol, as it would require additional
fonts. Also, it seems tough to me to position to label properly with
respect to the camera. But you have plenty control with
convert/imagemagick (see
http://www.imagemagick.org/Usage/annotating/). That will allow you to
process your images script-wise, I think even using whatever font you
want (although copyright 2008 or (c)2008 will probably also do ;) see
the examples).
Hope it helps,
Tsjerk
On Wed, Jul 30, 2008 at 10:27 AM, Chavas Leo pymolhnaa...@gmail.com
wrote:
Dear all --
On 30 Jul 2008, at 01:03, DeLano Scientific wrote:
Richard,
label (residue 200 and name ca), My favorite C_alpha
The command you provided works as written, so what are you asking
exactly?
Is is that you want us to add a GUI way of doing this?
Related to labeling, I was wondering how to insert symbol labels such as
angstrom, or alpha etc., even the copyright symbol?
I've tried in the past, without much success. I know it will be easier to
do
it via an external program such as Gimp, but I'm asking in the idea to
generate a line at the bottom of the picture for copyright purpose, when
I'm
generating hundreds of pictures for building a movie... Do I have to link
the font library to the library I've got on my computer?
Kind regards.
-- Leo --
Chavas Leonard, Ph.D. @ home
Research Associate
Faculty of Life Sciences
The University of Manchester
The Michael Smith Building
Oxford Road
Manchester Lancashire
M13 9PT
Tel: +44(0)161-275-1586
e-mail: leonard.cha...@manchester.ac.uk
http://personalpages.manchester.ac.uk/staff/leonard.chavas/
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[PyMOL] writing selection to a external file
Hi All, I'm using pymol to select (by residue) all the atoms around 10 angstroms from a certain atom. Now I would like to write the residue id's of my selection to an external file, so that I can integrated in the ndx file from Gromacs. Do you have any idea how I could do that? Thanks, Marius Retegan
Re: [PyMOL] writing selection to a external file
Hi, It seems that I run into a little problem. When I try to write a large selection I get only a partial list of ID. If for example I print ID after the iterate command, all the list is printed into pymol window. Do you have any idea why? I run Pymol 1.1pre5 under Fedora 8. On Fri, Jun 27, 2008 at 1:36 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi, This should've gone to the list... (isn't there an option send replies to list rather than to poster to the mailing list?) Tsjerk On Fri, Jun 27, 2008 at 1:34 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Marius, You want iterate. You do have to make sure though that the numbering of your atoms in the structure file is correct. Than you can do: ndx=open(index.ndx,w) ndx.write([ MyIndex ]\n) iterate selection, ndx.write(%d\n % ID) ndx.close() I did make the assumption that you wanted the atom id's rather than the residue id's, since the latter are of no use to Gromacs. Hope it helps, Tsjerk On Fri, Jun 27, 2008 at 1:17 PM, Marius Retegan marius.s.rete...@gmail.com wrote: Hi All, I'm using pymol to select (by residue) all the atoms around 10 angstroms from a certain atom. Now I would like to write the residue id's of my selection to an external file, so that I can integrated in the ndx file from Gromacs. Do you have any idea how I could do that? Thanks, Marius Retegan - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
