From: lina <lin...@gm...> - 2011-09-16 15:45:22
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Hi, a quick question, how can update the ss for all states, not check one by one, and run dssp and update ... Thanks for any advice, -- Best Regards, lina |
From: Thomas H. <sp...@us...> - 2011-09-16 17:24:26
Attachments:
dssp.py
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Hi Lina, as far as I know the secondary structure atom property is not state specific, so you cannot assign per state. But you can split states to individual objects. The DSSP plugin (I guess you are talking about http://www.pymolwiki.org/index.php/DSSP) however does not deal well with multiple objects (Hongbo, can you fix that?). The build-in command "dss" does, maybe you can use that? Example: fetch 1d7q, async=0 as cartoon split_states 1d7q delete 1d7q dss all rebuild http://pymolwiki.org/index.php/Split_States http://pymolwiki.org/index.php/Dss I can also offer you my own dssp script which works with multiple objects, see attachment. It provides the PyMOL commands "dssp" and "stride". Check "help dssp". Cheers, Thomas lina wrote, On 09/16/11 17:45: > Hi, > > a quick question, > > how can update the ss for all states, not check one by one, > > and run dssp and update ... > > Thanks for any advice, > > -- > Best Regards, > > lina -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: lina <lin...@gm...> - 2011-09-16 17:31:53
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On Sat, Sep 17, 2011 at 1:01 AM, Thomas Holder < sp...@us...> wrote: > Hi Lina, > Hi Thomas, Thanks for your answering. > > as far as I know the secondary structure atom property is not state > specific, so you cannot assign per state. But you can split states to > individual objects. The DSSP plugin (I guess you are talking about > http://www.pymolwiki.org/**index.php/DSSP<http://www.pymolwiki.org/index.php/DSSP>) > however does not deal well with multiple objects (Hongbo, can you fix > that?). The build-in command "dss" does, maybe you can use that? > dss did not share the same criteria as the dssp, so sometimes if I choose the dssp criteria, lots of residues need alter. > > Example: > > fetch 1d7q, async=0 > as cartoon > split_states 1d7q > Haha... my case got 51 states there. kinda of splendid. delete 1d7q > dss all > rebuild > > http://pymolwiki.org/index.**php/Split_States<http://pymolwiki.org/index.php/Split_States> > http://pymolwiki.org/index.**php/Dss <http://pymolwiki.org/index.php/Dss> > > I can also offer you my own dssp script which works with multiple objects, > see attachment. It provides the PyMOL commands "dssp" and "stride". Check > "help dssp". > Thanks, I tried, PyMOL>dssp all, /home/lina/dssp, raw=text_type Traceback (most recent call last): File "/usr/local/lib/python2.6/dist-packages/pymol/parser.py", line 254, in parse self.result=apply(layer.kw[0],layer.args,layer.kw_args) File "dssp.py", line 70, in dssp process = Popen([exe, '-na', tmpfilepdb], stdout=PIPE) File "/usr/lib/python2.6/subprocess.py", line 623, in __init__ errread, errwrite) File "/usr/lib/python2.6/subprocess.py", line 1141, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory I am not experienced to fix it, can you provide me some clue. $ python python python2.7-config python3.2mu python2.5 python3 python3.2mu-config python2.5-config python3.1 python3-config python2.6 python3.1-config python-config python2.6-config python3.2 python2.7 python3.2-config > > Cheers, > Thomas > > lina wrote, On 09/16/11 17:45: > > Hi, >> >> a quick question, >> >> how can update the ss for all states, not check one by one, >> >> and run dssp and update ... >> >> Thanks for any advice, >> >> -- >> Best Regards, >> >> lina >> > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > -- Best Regards, lina |
From: Thomas H. <sp...@us...> - 2011-09-16 21:00:01
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Hi Lina, >> I can also offer you my own dssp script which works with multiple objects, see >> attachment. It provides the PyMOL commands "dssp" and "stride". Check "help dssp". > > Thanks, I tried, > > PyMOL>dssp all, /home/lina/dssp, raw=text_type > Traceback (most recent call last): > File "/usr/local/lib/python2.6/dist-packages/pymol/parser.py", line 254, in parse > self.result=apply(layer.kw[0],layer.args,layer.kw_args) > File "dssp.py", line 70, in dssp > process = Popen([exe, '-na', tmpfilepdb], stdout=PIPE) > File "/usr/lib/python2.6/subprocess.py", line 623, in __init__ > errread, errwrite) > File "/usr/lib/python2.6/subprocess.py", line 1141, in _execute_child > raise child_exception > OSError: [Errno 2] No such file or directory does /home/lina/dssp point to your dssp executable? Cheers, Thomas PS: I just realized that there is a new dssp-2 and it does not understand the -na option, thus will fail with my script without modifying it. -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: lina <lin...@gm...> - 2011-09-17 02:40:54
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On Sat, Sep 17, 2011 at 4:03 AM, Thomas Holder < sp...@us...> wrote: > Hi Lina, > > >> I can also offer you my own dssp script which works with multiple > objects, see > >> attachment. It provides the PyMOL commands "dssp" and "stride". Check > "help dssp". > > > > Thanks, I tried, > > > > PyMOL>dssp all, /home/lina/dssp, raw=text_type > > Traceback (most recent call last): > > File "/usr/local/lib/python2.6/dist-packages/pymol/parser.py", line > 254, in parse > > self.result=apply(layer.kw[0],layer.args,layer.kw_args) > > File "dssp.py", line 70, in dssp > > process = Popen([exe, '-na', tmpfilepdb], stdout=PIPE) > > File "/usr/lib/python2.6/subprocess.py", line 623, in __init__ > > errread, errwrite) > > File "/usr/lib/python2.6/subprocess.py", line 1141, in _execute_child > > raise child_exception > > OSError: [Errno 2] No such file or directory > > does /home/lina/dssp point to your dssp executable? > Yes. Later I also tried to keep the dsspcmbi name, still not work. > > Cheers, > Thomas > > PS: I just realized that there is a new dssp-2 and it does not > understand the -na option, thus will fail with my script without > modifying it. > Thanks for your script. > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > -- Best Regards, lina |
From: lina <lin...@gm...> - 2011-09-17 16:48:12
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Hi, Is it possible to output the sequence roughly following the skeleton of protein structure? Or are there some other good way handling it. I tried aline (seem this name) before and also manually. It's headache to arrange large molecules. Thanks for any suggestions. Lina |
From: Jason V. <jas...@sc...> - 2011-09-19 04:50:14
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Hi Lina, First, download the one-letter and three-letter amino acid converters (http://www.pymolwiki.org/index.php/Aa_codes) and run it or copy/paste it into PyMOL. It's nice to have these in your ~/.pymolrc. Then, try something like this: # fetch a protein fetch 1rx1, async=0 # hide all hide # show ball-and-stick for the main chain preset.ball_and_stick("n. C+O+N+CA") # hide the solvent hide everything, solvent # show the labels label vis, one_letter[resn] Cheers, -- Jason On Sat, Sep 17, 2011 at 12:48 PM, lina <lin...@gm...> wrote: > Hi, > > Is it possible to output the sequence roughly following the skeleton of protein structure? > > Or are there some other good way handling it. > > I tried aline (seem this name) before and also manually. It's headache to arrange large molecules. > > Thanks for any suggestions. > > Lina > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > http://p.sf.net/sfu/rim-devcon-copy2 > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: lina <lin...@gm...> - 2011-09-19 05:17:52
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On Mon, Sep 19, 2011 at 12:41 PM, Jason Vertrees < jas...@sc...> wrote: > Hi Lina, > > First, download the one-letter and three-letter amino acid converters > (http://www.pymolwiki.org/index.php/Aa_codes) and run it or copy/paste > it into PyMOL. It's nice to have these in your ~/.pymolrc. Then, try > something like this: > Hi Jason, Thanks for your answering. Another question here, can I show the whole residue as a ball, and different residues connect by (virtual) bonds. Just curious. Thanks again for your help, > > # fetch a protein > > fetch 1rx1, async=0 > > # hide all > > hide > > # show ball-and-stick for the main chain > > preset.ball_and_stick("n. C+O+N+CA") > > # hide the solvent > > hide everything, solvent > > # show the labels > > label vis, one_letter[resn] > > Cheers, > > -- Jason > > > On Sat, Sep 17, 2011 at 12:48 PM, lina <lin...@gm...> wrote: > > Hi, > > > > Is it possible to output the sequence roughly following the skeleton of > protein structure? > > > > Or are there some other good way handling it. > > > > I tried aline (seem this name) before and also manually. It's headache to > arrange large molecules. > > > > Thanks for any suggestions. > > > > Lina > > > ------------------------------------------------------------------------------ > > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > > http://p.sf.net/sfu/rim-devcon-copy2 > > _______________________________________________ > > PyMOL-users mailing list (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... > > > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > -- Best Regards, lina |
From: Thomas H. <sp...@us...> - 2011-09-19 07:56:21
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Hi Lina, > Another question here, > > can I show the whole residue as a ball, and different residues connect > by (virtual) bonds. combine ribbon and CA spheres: hide everything show ribbon show spheres, name CA set sphere_scale, 0.5 set ribbon_width, 5 Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: lina <lin...@gm...> - 2011-09-19 08:10:46
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On Mon, Sep 19, 2011 at 3:56 PM, Thomas Holder < sp...@us...> wrote: > Hi Lina, > > > Another question here, >> >> can I show the whole residue as a ball, and different residues connect by >> (virtual) bonds. >> > > combine ribbon and CA spheres: > > hide everything > show ribbon > show spheres, name CA > set sphere_scale, 0.5 > set ribbon_width, 5 > Ha ... Cool. Thanks. > > Cheers, > Thomas > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > -- Best Regards, lina |
From: Hongbo Z. <hon...@bi...> - 2011-10-19 11:14:54
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I just ran dssp plugin for an NMR structure (randomly chosen, 2LE0). In my case, secondary structures are calculated for all the 10 states of 2LE0. The plugin can also update color and secondary structures for all the 10 states of the NMR structure. I did not have to choose one state and run, and the next state. I tested the plugin under both Ubuntu and Windows 7. Maybe I misunderstood your question? regards, hongbo On 16.09.2011 5:45, lina wrote: > Hi, > > a quick question, > > how can update the ss for all states, not check one by one, > > and run dssp and update ... > > Thanks for any advice, > > -- > Best Regards, > > lina > > > > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > http://p.sf.net/sfu/rim-devcon-copy2 > > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |
From: lina <lin...@gm...> - 2011-10-19 14:15:52
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On Wed, Oct 19, 2011 at 6:43 PM, Hongbo Zhu <hon...@bi...> wrote: > I just ran dssp plugin for an NMR structure (randomly chosen, 2LE0). In my > case, secondary structures are calculated for all the 10 states of 2LE0. The > plugin can also update color and secondary structures for all the 10 states > of the NMR structure. I did not have to choose one state and run, and the > next state. might my pdb file reason? you may try: https://docs.google.com/leaf?id=0B93SVRfpVVg3NGY4MzkwZTQtNmIzMC00ZjkzLTkxMzEtZWIyMmNlYmE0OWQ0&hl=en_GB > I tested the plugin under both Ubuntu and Windows 7. > Maybe I misunderstood your question? > regards, Thanks, > hongbo > > On 16.09.2011 5:45, lina wrote: > > Hi, > > a quick question, > > how can update the ss for all states, not check one by one, > > and run dssp and update ... > > Thanks for any advice, > > -- > Best Regards, > > lina > > > > > ------------------------------------------------------------------------------ > BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA > http://p.sf.net/sfu/rim-devcon-copy2 > > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > > ------------------------------------------------------------------------------ > 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. > http://p.sf.net/sfu/splunk-d2d-oct > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: Hongbo Z. <hon...@bi...> - 2011-10-19 22:28:19
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Hi, Lina, I did not understand your question correctly. Now it is fixed. Try the new version on my page. It works for me for 2LE0 and your try.pse. You still have to use "split_state" to split your structure into different objects. Then you can specify these objects using wildcard to the DSSP plugin. The plugin will invoke DSSP to assign secondary structures for each object in your specified input. hongbo zhu On 19.10.2011 4:15, lina wrote: > On Wed, Oct 19, 2011 at 6:43 PM, Hongbo Zhu > <hon...@bi...> wrote: >> I just ran dssp plugin for an NMR structure (randomly chosen, 2LE0). In my >> case, secondary structures are calculated for all the 10 states of 2LE0. The >> plugin can also update color and secondary structures for all the 10 states >> of the NMR structure. I did not have to choose one state and run, and the >> next state. > might my pdb file reason? > > you may try: > > https://docs.google.com/leaf?id=0B93SVRfpVVg3NGY4MzkwZTQtNmIzMC00ZjkzLTkxMzEtZWIyMmNlYmE0OWQ0&hl=en_GB > >> I tested the plugin under both Ubuntu and Windows 7. >> Maybe I misunderstood your question? >> regards, > Thanks, >> hongbo >> >> On 16.09.2011 5:45, lina wrote: >> >> Hi, >> >> a quick question, >> >> how can update the ss for all states, not check one by one, >> >> and run dssp and update ... >> >> Thanks for any advice, >> >> -- >> Best Regards, >> >> lina >> >> >> >> >> ------------------------------------------------------------------------------ >> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA >> http://p.sf.net/sfu/rim-devcon-copy2 >> >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> >> ------------------------------------------------------------------------------ >> 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. >> http://p.sf.net/sfu/splunk-d2d-oct >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > ------------------------------------------------------------------------------ > 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. > http://p.sf.net/sfu/splunk-d2d-oct > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... |