From: PAVAN P. <pav...@gm...> - 2011-12-26 18:45:47
|
Dear PyMol Users, I am using PyMol +v0.97 version on Windows XP .I have downloded super_all.py<http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/super_all.py> and tried to install the plugin by using install Plugin option menu. Then I got the message that the plugin was installed but after re-initialization I dont find the Plugin for the same in Plugin list,also was unable to run super command .So will you please help me to solve this problem.Is there any incompatibility issues for OS XP? Please help me in solving this problem.Or suggest the proper way of doing the same as I am new user . Pavan |
From: Jacob K. <j-k...@fs...> - 2011-12-26 20:47:47
|
You can try the "alignto" command as an alternative, if you want. JPK On Mon, Dec 26, 2011 at 12:45 PM, PAVAN PAYGHAN <pav...@gm...> wrote: > Dear PyMol Users, > > I am using PyMol +v0.97 version on Windows XP .I have downloded > super_all.py and tried to install the plugin by using install Plugin option > menu. > Then I got the message that the plugin was installed but after > re-initialization I dont find the Plugin for the same in Plugin list,also > was unable to run > super command .So will you please help me to solve this problem.Is there > any incompatibility issues for OS XP? > Please help me in solving this problem.Or suggest the proper way of doing > the same as I am new user . > > Pavan > > > > > > ------------------------------------------------------------------------------ > Write once. Port to many. > Get the SDK and tools to simplify cross-platform app development. Create > new or port existing apps to sell to consumers worldwide. Explore the > Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join > http://p.sf.net/sfu/intel-appdev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-k...@no... ******************************************* |
From: Robert C. <rob...@qu...> - 2011-12-26 20:48:41
|
Dear Pavan, On Tue, 27 Dec 2011 00:15:38 +0530, PAVAN PAYGHAN <pav...@gm...> wrote: > Dear PyMol Users, > > I am using PyMol +v0.97 version on Windows XP .I have downloded > super_all.py<http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/super_all.py> > and tried to install the plugin by using install Plugin option menu. > Then I got the message that the plugin was installed but after > re-initialization I dont find the Plugin for the same in Plugin list,also > was unable to run > super command .So will you please help me to solve this problem.Is there > any incompatibility issues for OS XP? > Please help me in solving this problem.Or suggest the proper way of doing > the same as I am new user . This is not a plugin that needs installing, but simply a script that you run. To use it, you just store the super_all.py file somewhere on your computer (I have a directory/folder dedicated to PyMOL scripts) and you load the script's function by using the "Run" function from the "File" menu. This has to be done once each time PyMOL starts. I load my commonly used scripts automatically via my .pymolrc file. Once the script loaded, then you can call the "super_all" function from the command line within PyMOL. You can see the options by typing super_all ? and you can get more information by typing help super_all I hope this helps. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |
From: PAVAN P. <pav...@gm...> - 2011-12-27 11:50:22
|
Dear , I want to install the plugins like super_all.py, align_all_to_all.py ,build_seq.py etc in the PyMol version +v0.97 but I am unable to do so . As I mentioned earlier also , even after getting the success message of plugin has been installed, please restart PyMol to begin use failed to use the commands . I got following error message - *AttributeError: 'NoneType' object has no attribute 'lower( for super_all.py ).* Also i want to know whether installing the plugin will add them to be displayed in plugin list compulsorily for the above mentioned or all the plugins. * * * * Pavan Payghan On Tue, Dec 27, 2011 at 2:17 AM, Jacob Keller < j-k...@fs...> wrote: > You can try the "alignto" command as an alternative, if you want. > > JPK > > On Mon, Dec 26, 2011 at 12:45 PM, PAVAN PAYGHAN <pav...@gm...> > wrote: > > Dear PyMol Users, > > > > I am using PyMol +v0.97 version on Windows XP .I have downloded > > super_all.py and tried to install the plugin by using install Plugin > option > > menu. > > Then I got the message that the plugin was installed but after > > re-initialization I dont find the Plugin for the same in Plugin list,also > > was unable to run > > super command .So will you please help me to solve this problem.Is there > > any incompatibility issues for OS XP? > > Please help me in solving this problem.Or suggest the proper way of doing > > the same as I am new user . > > > > Pavan > > > > > > > > > > > > > ------------------------------------------------------------------------------ > > Write once. Port to many. > > Get the SDK and tools to simplify cross-platform app development. Create > > new or port existing apps to sell to consumers worldwide. Explore the > > Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join > > http://p.sf.net/sfu/intel-appdev > > _______________________________________________ > > PyMOL-users mailing list (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... > > > > -- > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > email: j-k...@no... > ******************************************* > |
From: Thomas H. <sp...@us...> - 2011-12-27 12:11:45
|
Hi Pavan, > I want to install the plugins like super_all.py, align_all_to_all.py > ,build_seq.py etc in the PyMol version +v0.97 but I am unable to do so. > As I mentioned earlier also , even after getting the success message of > plugin has been installed, please restart PyMol to begin use failed to > use the commands . > I got following error message - AttributeError: 'NoneType' object has no > attribute 'lower( for super_all.py ). Provide the name of the reference object as first argument. All other arguments have default values. > Also i want to know whether installing the plugin will add them to be > displayed in plugin list compulsorily for the above mentioned or all the > plugins. The above mentioned scripts do not add plugin menu items, they only provide new commands. Cheers, Thomas > Pavan Payghan > > > On Tue, Dec 27, 2011 at 2:17 AM, Jacob Keller > <j-k...@fs... <mailto:j-k...@fs...>> > wrote: > > You can try the "alignto" command as an alternative, if you want. > > JPK > > On Mon, Dec 26, 2011 at 12:45 PM, PAVAN PAYGHAN <pav...@gm... > <mailto:pav...@gm...>> wrote: > > Dear PyMol Users, > > > > I am using PyMol +v0.97 version on Windows XP .I have downloded > > super_all.py and tried to install the plugin by using install > Plugin option > > menu. > > Then I got the message that the plugin was installed but after > > re-initialization I dont find the Plugin for the same in Plugin > list,also > > was unable to run > > super command .So will you please help me to solve this > problem.Is there > > any incompatibility issues for OS XP? > > Please help me in solving this problem.Or suggest the proper way > of doing > > the same as I am new user . > > > > Pavan > > > > > > -- > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > email: j-k...@no... <mailto:j-k...@no...> > ******************************************* -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: PAVAN P. <pav...@gm...> - 2011-12-27 12:27:44
|
Dear Mr. Thomas Holder , Thanks for the reply .According to you the plugin has been installed properly.Can you briefly mention 1.how to define the reference object for using super command 2.how to use super command with multiple structures to align with the suitable example. I have started using pymol recently so it will be worth working for me. Pavan Payghan On Tue, Dec 27, 2011 at 5:41 PM, Thomas Holder < sp...@us...> wrote: > Hi Pavan, > > > I want to install the plugins like super_all.py, align_all_to_all.py >> ,build_seq.py etc in the PyMol version +v0.97 but I am unable to do so. >> As I mentioned earlier also , even after getting the success message of >> plugin has been installed, please restart PyMol to begin use failed to use >> the commands . >> I got following error message - AttributeError: 'NoneType' object has no >> attribute 'lower( for super_all.py ). >> > > Provide the name of the reference object as first argument. All other > arguments have default values. > > > Also i want to know whether installing the plugin will add them to be >> displayed in plugin list compulsorily for the above mentioned or all the >> plugins. >> > > The above mentioned scripts do not add plugin menu items, they only > provide new commands. > > Cheers, > Thomas > > Pavan Payghan >> >> >> On Tue, Dec 27, 2011 at 2:17 AM, Jacob Keller < >> j-k...@fs...rthwestern.**edu <j-k...@fs...><mailto: >> j-keller2@fsm.**northwestern.edu <j-k...@fs...>>> >> wrote: >> >> You can try the "alignto" command as an alternative, if you want. >> >> JPK >> >> On Mon, Dec 26, 2011 at 12:45 PM, PAVAN PAYGHAN <pav...@gm... >> <mailto:pav...@gm...>> wrote: >> > Dear PyMol Users, >> > >> > I am using PyMol +v0.97 version on Windows XP .I have downloded >> > super_all.py and tried to install the plugin by using install >> Plugin option >> > menu. >> > Then I got the message that the plugin was installed but after >> > re-initialization I dont find the Plugin for the same in Plugin >> list,also >> > was unable to run >> > super command .So will you please help me to solve this >> problem.Is there >> > any incompatibility issues for OS XP? >> > Please help me in solving this problem.Or suggest the proper way >> of doing >> > the same as I am new user . >> > >> > Pavan >> > >> > >> >> -- >> ********************************************* >> Jacob Pearson Keller >> Northwestern University >> Medical Scientist Training Program >> email: j-k...@no... <mailto:j-keller2@**northwestern.edu<j-k...@no...> >> > >> ********************************************* >> > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > |
From: Thomas H. <sp...@us...> - 2011-12-27 14:07:44
|
Dear Pavan, PyMOL has a command line where you need to type in the commands which are provided by those scripts. Consider this example: # fetch some example structures fetch 1e4y 1ake 4ake 3hpq, async=0 remove chain B # use 1ake as reference for superpositioning super_all 1ake Not all script can be installed as "plugins". If installation as plugin fails please use "File > Run..." from the menu. PyMOL version 0.97 is quite old, please consider upgrading. Also have a look at http://pymolwiki.org where you can find lots of documentation and useful scripts. Cheers, Thomas PAVAN PAYGHAN wrote, On 12/27/11 13:27: > Dear Mr. Thomas Holder , > > Thanks for the reply .According to you the plugin has been installed > properly.Can you briefly mention > 1.how to define the reference object for using super command > 2.how to use super command with multiple structures to align with the > suitable example. > I have started using pymol recently so it will be worth working for me. > > Pavan Payghan > > > On Tue, Dec 27, 2011 at 5:41 PM, Thomas Holder > wrote: > > Hi Pavan, > > > I want to install the plugins like super_all.py, > align_all_to_all.py ,build_seq.py etc in the PyMol version > +v0.97 but I am unable to do so. > As I mentioned earlier also , even after getting the success > message of plugin has been installed, please restart PyMol to > begin use failed to use the commands . > I got following error message - AttributeError: 'NoneType' > object has no attribute 'lower( for super_all.py ). > > > Provide the name of the reference object as first argument. All > other arguments have default values. > > > Also i want to know whether installing the plugin will add them > to be displayed in plugin list compulsorily for the above > mentioned or all the plugins. > > > The above mentioned scripts do not add plugin menu items, they only > provide new commands. > > Cheers, > Thomas > > Pavan Payghan > > > On Tue, Dec 27, 2011 at 2:17 AM, Jacob Keller > <j-k...@fs...> wrote: > > You can try the "alignto" command as an alternative, if you want. > > JPK > > On Mon, Dec 26, 2011 at 12:45 PM, PAVAN PAYGHAN > <pav...@gm... <mailto:pav...@gm...> > <mailto:pav...@gm... <mailto:pav...@gm...>>> wrote: > > Dear PyMol Users, > > > > I am using PyMol +v0.97 version on Windows XP .I have > downloded > > super_all.py and tried to install the plugin by using install > Plugin option > > menu. > > Then I got the message that the plugin was installed but after > > re-initialization I dont find the Plugin for the same in > Plugin > list,also > > was unable to run > > super command .So will you please help me to solve this > problem.Is there > > any incompatibility issues for OS XP? > > Please help me in solving this problem.Or suggest the > proper way > of doing > > the same as I am new user . > > > > Pavan > > > > > > -- > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > email: j-k...@no... > ******************************************* -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: PAVAN P. <pav...@gm...> - 2011-12-28 06:14:33
|
Dear, While using super_all command I am getting following error message *valueError: list.remove(x): x not in list.* To mention how I have tried to use this command .. 1.I have loaded structures(say 4 pdb files) using file> load option. 2. Then super_all xyz.pdb after this I got the above mentioned valueError message. Pavan Payghan On Tue, Dec 27, 2011 at 7:37 PM, Thomas Holder < sp...@us...> wrote: > Dear Pavan, > > PyMOL has a command line where you need to type in the commands which are > provided by those scripts. Consider this example: > > # fetch some example structures > fetch 1e4y 1ake 4ake 3hpq, async=0 > remove chain B > > # use 1ake as reference for superpositioning > super_all 1ake > > Not all script can be installed as "plugins". If installation as plugin > fails please use "File > Run..." from the menu. > > PyMOL version 0.97 is quite old, please consider upgrading. Also have a > look at http://pymolwiki.org where you can find lots of documentation and > useful scripts. > > Cheers, > Thomas > > PAVAN PAYGHAN wrote, On 12/27/11 13:27: > >> Dear Mr. Thomas Holder , >> >> Thanks for the reply .According to you the plugin has been installed >> properly.Can you briefly mention 1.how to define the reference object for >> using super command 2.how to use super command with multiple structures to >> align with the suitable example. >> I have started using pymol recently so it will be worth working for me. >> Pavan Payghan >> >> >> On Tue, Dec 27, 2011 at 5:41 PM, Thomas Holder wrote: >> >> Hi Pavan, >> >> >> I want to install the plugins like super_all.py, >> align_all_to_all.py ,build_seq.py etc in the PyMol version >> +v0.97 but I am unable to do so. >> As I mentioned earlier also , even after getting the success >> message of plugin has been installed, please restart PyMol to >> begin use failed to use the commands . >> I got following error message - AttributeError: 'NoneType' >> object has no attribute 'lower( for super_all.py ). >> >> >> Provide the name of the reference object as first argument. All >> other arguments have default values. >> >> >> Also i want to know whether installing the plugin will add them >> to be displayed in plugin list compulsorily for the above >> mentioned or all the plugins. >> >> >> The above mentioned scripts do not add plugin menu items, they only >> provide new commands. >> >> Cheers, >> Thomas >> >> Pavan Payghan >> >> On Tue, Dec 27, 2011 at 2:17 AM, Jacob Keller >> <j-k...@fs...rthwestern.**edu <j-k...@fs...>> >> wrote: >> >> You can try the "alignto" command as an alternative, if you >> want. >> >> JPK >> >> On Mon, Dec 26, 2011 at 12:45 PM, PAVAN PAYGHAN >> <pav...@gm... <mailto:pav...@gm...> >> <mailto:pav...@gm... <mailto:pav...@gm...>>> >> wrote: >> > Dear PyMol Users, >> > >> > I am using PyMol +v0.97 version on Windows XP .I have >> downloded >> > super_all.py and tried to install the plugin by using >> install >> Plugin option >> > menu. >> > Then I got the message that the plugin was installed but >> after >> > re-initialization I dont find the Plugin for the same in >> Plugin >> list,also >> > was unable to run >> > super command .So will you please help me to solve this >> problem.Is there >> > any incompatibility issues for OS XP? >> > Please help me in solving this problem.Or suggest the >> proper way >> of doing >> > the same as I am new user . >> > >> > Pavan >> > >> > >> >> -- >> ********************************************* >> Jacob Pearson Keller >> Northwestern University >> Medical Scientist Training Program >> email: j-k...@no... >> ********************************************* >> > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > |
From: Thomas H. <sp...@us...> - 2011-12-28 07:44:47
|
Dear Pavan, > 2. Then super_all xyz.pdb Not the filename, but the name of the loaded object (by default this is the filename without .pdb suffix). super_all xyz Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: PAVAN P. <pav...@gm...> - 2011-12-29 10:24:43
|
Dear, Thanks a lot for the information. As you mentioned super is only for aligning two structures while with super_all to align the multiple structures, but the most important thing is to obtain the alignment file out of all this excercise, can it be possible with super, super_all? If not which option exist in Pymol wherein one can align 4-5 structures at a time (with low sequence identity). Pavan Payghan On Wed, Dec 28, 2011 at 6:11 PM, Thomas Holder < sp...@us...> wrote: > Hi Pavan, > > > Thank you very much for the modified script. >> >> Its working fine, only thing I am facing is that it can not be used for >> aligning more than two structures at a time(I want it for around 4 -5 >> structure alignment). The command used to do so is >> >> super abc,def,XYZ >> > > "super" is for two structures, "super_all" (from the script) is for many > structures. But the syntax is without comma in mobile selection: > > super_all abc, def ghi jkl > > for the third structure its giving error like ,ValueError: invalid >> literal for float (): XYZ. >> >> Apart form this could you please explain >> >> 1. Number of alignment residues should match exactly in all the >> structures. >> > > you can't influence this with super_all. > > 2. How to get alignment file for super, super_all command after >> alignment has been done. >> > > this is not possible with super_all. > > But PyMOL can do this even without the super_all script. On the > button-panel to the right, try: "A > align > all to this" > > You'll get an new object called like "aln_all_to_XYZ", this you can save: > > save file.aln, aln_all_to_XYZ > > > > Cheers, > Thomas > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > |
From: zjxu <zj...@ma...> - 2011-12-29 10:51:45
|
Dear Pavan, align 4-5 structures at a time (with low sequence identity). check cealign: http://www.pymolwiki.org/index.php/Cealign In pymol1.4, you could use 'alignto': PyMOL>help alignto DESCRIPTION NOTE: This feature is experimental and unsuspported. "alignto" aligns all other loaded objects to the given selected object using the CEalign algorithm. USAGE alignto target [, quiet ] EXAMPLE # fetch some calmodulins fetch 1cll 1sra 1ggz 1k95, async=0 alignto 1cll Hope this helps, Zhijian Xu PAVAN PAYGHAN wrote: > > Dear, > > > > Thanks a lot for the information. As you mentioned super is only for > aligning two structures while with super_all to align the multiple > structures, but the most important thing is to obtain the alignment > file out of all this excercise, can it be possible with super, super_all? > > If not which option exist in Pymol wherein one can align 4-5 > structures at a time (with low sequence identity). > > > > Pavan Payghan > > > > > > > On Wed, Dec 28, 2011 at 6:11 PM, Thomas Holder > <sp...@us... <mailto:sp...@us...>> > wrote: > > Hi Pavan, > > > Thank you very much for the modified script. > > Its working fine, only thing I am facing is that it can not be > used for aligning more than two structures at a time(I want it > for around 4 -5 structure alignment). The command used to do > so is > > super abc,def,XYZ > > > "super" is for two structures, "super_all" (from the script) is > for many structures. But the syntax is without comma in mobile > selection: > > super_all abc, def ghi jkl > > for the third structure its giving error like ,ValueError: > invalid literal for float (): XYZ. > > Apart form this could you please explain > > 1. Number of alignment residues should match exactly in all the > structures. > > > you can't influence this with super_all. > > 2. How to get alignment file for super, super_all command after > alignment has been done. > > > this is not possible with super_all. > > But PyMOL can do this even without the super_all script. On the > button-panel to the right, try: "A > align > all to this" > > You'll get an new object called like "aln_all_to_XYZ", this you > can save: > > save file.aln, aln_all_to_XYZ > > > > Cheers, > Thomas > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex > infrastructure or vast IT resources to deliver seamless, secure access to > virtual desktops. With this all-in-one solution, easily deploy virtual > desktops for less than the cost of PCs and save 60% on VDI infrastructure > costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox > ------------------------------------------------------------------------ > > _______________________________________________ > 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: PAVAN P. <pav...@gm...> - 2011-12-29 12:23:54
|
Dear , "A > align > all to this" and "alignto" both are the same or different? If different in what context. Pavan Payghan On Thu, Dec 29, 2011 at 4:23 PM, zjxu <zj...@ma...> wrote: > Dear Pavan, > > > align 4-5 structures at a time (with low sequence identity). > > check cealign: http://www.pymolwiki.org/**index.php/Cealign<http://www.pymolwiki.org/index.php/Cealign> > > In pymol1.4, you could use 'alignto': > PyMOL>help alignto > DESCRIPTION > NOTE: This feature is experimental and unsuspported. > "alignto" aligns all other loaded objects to the given selected object > using the CEalign algorithm. > USAGE > alignto target [, quiet ] > EXAMPLE > # fetch some calmodulins > fetch 1cll 1sra 1ggz 1k95, async=0 > alignto 1cll > > Hope this helps, > > Zhijian Xu > > > PAVAN PAYGHAN wrote: > >> >> Dear, >> >> >> Thanks a lot for the information. As you mentioned super is only for >> aligning two structures while with super_all to align the multiple >> structures, but the most important thing is to obtain the alignment file >> out of all this excercise, can it be possible with super, super_all? >> >> If not which option exist in Pymol wherein one can align 4-5 structures >> at a time (with low sequence identity). >> >> >> Pavan Payghan >> >> >> >> On Wed, Dec 28, 2011 at 6:11 PM, Thomas Holder < >> sp...@us... <mailto:speleo3@users.**sourceforge.net<sp...@us...>>> >> wrote: >> >> Hi Pavan, >> >> >> Thank you very much for the modified script. >> >> Its working fine, only thing I am facing is that it can not be >> used for aligning more than two structures at a time(I want it >> for around 4 -5 structure alignment). The command used to do >> so is >> >> super abc,def,XYZ >> >> >> "super" is for two structures, "super_all" (from the script) is >> for many structures. But the syntax is without comma in mobile >> selection: >> >> super_all abc, def ghi jkl >> >> for the third structure its giving error like ,ValueError: >> invalid literal for float (): XYZ. >> >> Apart form this could you please explain >> >> 1. Number of alignment residues should match exactly in all the >> structures. >> >> >> you can't influence this with super_all. >> >> 2. How to get alignment file for super, super_all command after >> alignment has been done. >> >> >> this is not possible with super_all. >> >> But PyMOL can do this even without the super_all script. On the >> button-panel to the right, try: "A > align > all to this" >> >> You'll get an new object called like "aln_all_to_XYZ", this you >> can save: >> >> save file.aln, aln_all_to_XYZ >> >> >> >> Cheers, >> Thomas >> >> -- Thomas Holder >> MPI for Developmental Biology >> Spemannstr. 35 >> D-72076 Tübingen >> >> >> ------------------------------**------------------------------** >> ------------ >> >> ------------------------------**------------------------------** >> ------------------ >> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex >> infrastructure or vast IT resources to deliver seamless, secure access to >> virtual desktops. With this all-in-one solution, easily deploy virtual >> desktops for less than the cost of PCs and save 60% on VDI infrastructure >> costs. Try it free! http://p.sf.net/sfu/Citrix-**VDIinabox<http://p.sf.net/sfu/Citrix-VDIinabox> >> ------------------------------**------------------------------** >> ------------ >> >> >> ______________________________**_________________ >> PyMOL-users mailing list (PyMOL-users@lists.**sourceforge.net<PyM...@li...> >> ) >> Info Page: https://lists.sourceforge.net/**lists/listinfo/pymol-users<https://lists.sourceforge.net/lists/listinfo/pymol-users> >> Archives: http://www.mail-archive.com/**pym...@li...urceforge.** >> net <http://www.mail-archive.com/pym...@li...> >> > > |
From: Thomas H. <sp...@us...> - 2011-12-29 20:45:31
|
PAVAN PAYGHAN wrote, On 12/29/11 13:23: > Dear , > > "A > align > all to this" and "alignto" both are the same or different? > If different in what context. It's different. The first method uses "align" and gives you an alignment object (uses util.mass_align function). The second uses "cealign" and cannot make an alignment object. http://pymolwiki.org/index.php/Align http://pymolwiki.org/index.php/Cealign "align" does sequence based alignment and RMSD minimization, "cealign" is a more sophisticated structure based alignment. Cheers, Thomas > Pavan Payghan > > > On Thu, Dec 29, 2011 at 4:23 PM, zjxu <zj...@ma... > <mailto:zj...@ma...>> wrote: > > Dear Pavan, > > > align 4-5 structures at a time (with low sequence identity). > > check cealign: http://www.pymolwiki.org/index.php/Cealign > <http://www.pymolwiki.org/index.php/Cealign> > > In pymol1.4, you could use 'alignto': > PyMOL>help alignto > DESCRIPTION > NOTE: This feature is experimental and unsuspported. > "alignto" aligns all other loaded objects to the given selected object > using the CEalign algorithm. > USAGE > alignto target [, quiet ] > EXAMPLE > # fetch some calmodulins > fetch 1cll 1sra 1ggz 1k95, async=0 > alignto 1cll > > Hope this helps, > > Zhijian Xu > > > PAVAN PAYGHAN wrote: > > > Dear, > > > Thanks a lot for the information. As you mentioned super is only > for aligning two structures while with super_all to align the > multiple structures, but the most important thing is to obtain > the alignment file out of all this excercise, can it be possible > with super, super_all? > > If not which option exist in Pymol wherein one can align 4-5 > structures at a time (with low sequence identity). > > > Pavan Payghan > > > > On Wed, Dec 28, 2011 at 6:11 PM, Thomas Holder > <sp...@us... > <mailto:sp...@us...> > <mailto:sp...@us... > <mailto:sp...@us...>>> wrote: > > Hi Pavan, > > > Thank you very much for the modified script. > > Its working fine, only thing I am facing is that it can > not be > used for aligning more than two structures at a time(I > want it > for around 4 -5 structure alignment). The command used to do > so is > > super abc,def,XYZ > > > "super" is for two structures, "super_all" (from the script) is > for many structures. But the syntax is without comma in mobile > selection: > > super_all abc, def ghi jkl > > for the third structure its giving error like ,ValueError: > invalid literal for float (): XYZ. > > Apart form this could you please explain > > 1. Number of alignment residues should match exactly in > all the > structures. > > > you can't influence this with super_all. > > 2. How to get alignment file for super, super_all > command after > alignment has been done. > > > this is not possible with super_all. > > But PyMOL can do this even without the super_all script. On the > button-panel to the right, try: "A > align > all to this" > > You'll get an new object called like "aln_all_to_XYZ", this you > can save: > > save file.aln, aln_all_to_XYZ > > > > Cheers, > Thomas > > -- Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: PAVAN P. <pav...@gm...> - 2011-12-30 06:21:15
|
Dear, cealign,super,super_all cannot make an alignment object , as the most important thing is to obtain the alignment file out of all this exercise remains unresolved ,Please suggest me structure based alignment method in PyMol wherein I can use multiple structures at a time (with low sequence identity) . Pavan Payghan On Fri, Dec 30, 2011 at 2:15 AM, Thomas Holder < sp...@us...> wrote: > PAVAN PAYGHAN wrote, On 12/29/11 13:23: > > Dear , >> >> "A > align > all to this" and "alignto" both are the same or different? >> If different in what context. >> > > It's different. > > The first method uses "align" and gives you an alignment object (uses > util.mass_align function). > > The second uses "cealign" and cannot make an alignment object. > > http://pymolwiki.org/index.**php/Align<http://pymolwiki.org/index.php/Align> > http://pymolwiki.org/index.**php/Cealign<http://pymolwiki.org/index.php/Cealign> > > "align" does sequence based alignment and RMSD minimization, "cealign" is > a more sophisticated structure based alignment. > > Cheers, > Thomas > > Pavan Payghan >> >> >> >> On Thu, Dec 29, 2011 at 4:23 PM, zjxu <zj...@ma... <mailto: >> zj...@ma...>**> wrote: >> >> Dear Pavan, >> >> >> align 4-5 structures at a time (with low sequence identity). >> >> check cealign: http://www.pymolwiki.org/**index.php/Cealign<http://www.pymolwiki.org/index.php/Cealign> >> <http://www.pymolwiki.org/**index.php/Cealign<http://www.pymolwiki.org/index.php/Cealign> >> > >> >> In pymol1.4, you could use 'alignto': >> PyMOL>help alignto >> DESCRIPTION >> NOTE: This feature is experimental and unsuspported. >> "alignto" aligns all other loaded objects to the given selected object >> using the CEalign algorithm. >> USAGE >> alignto target [, quiet ] >> EXAMPLE >> # fetch some calmodulins >> fetch 1cll 1sra 1ggz 1k95, async=0 >> alignto 1cll >> >> Hope this helps, >> >> Zhijian Xu >> >> >> PAVAN PAYGHAN wrote: >> >> >> Dear, >> >> Thanks a lot for the information. As you mentioned super >> is only >> for aligning two structures while with super_all to align the >> multiple structures, but the most important thing is to obtain >> the alignment file out of all this excercise, can it be possible >> with super, super_all? >> >> If not which option exist in Pymol wherein one can align 4-5 >> structures at a time (with low sequence identity). >> >> Pavan Payghan >> >> >> On Wed, Dec 28, 2011 at 6:11 PM, Thomas Holder >> <sp...@us... >> <mailto:speleo3@users.**sourceforge.net<sp...@us...> >> > >> <mailto:speleo3@users.**sourceforge.net<sp...@us...> >> >> <mailto:speleo3@users.**sourceforge.net<sp...@us...>>>> >> wrote: >> >> Hi Pavan, >> >> >> Thank you very much for the modified script. >> >> Its working fine, only thing I am facing is that it can >> not be >> used for aligning more than two structures at a time(I >> want it >> for around 4 -5 structure alignment). The command used to >> do >> so is >> >> super abc,def,XYZ >> >> >> "super" is for two structures, "super_all" (from the script) is >> for many structures. But the syntax is without comma in mobile >> selection: >> >> super_all abc, def ghi jkl >> >> for the third structure its giving error like ,ValueError: >> invalid literal for float (): XYZ. >> >> Apart form this could you please explain >> >> 1. Number of alignment residues should match exactly in >> all the >> structures. >> >> >> you can't influence this with super_all. >> >> 2. How to get alignment file for super, super_all >> command after >> alignment has been done. >> >> >> this is not possible with super_all. >> >> But PyMOL can do this even without the super_all script. On the >> button-panel to the right, try: "A > align > all to this" >> >> You'll get an new object called like "aln_all_to_XYZ", this you >> can save: >> >> save file.aln, aln_all_to_XYZ >> >> >> >> Cheers, >> Thomas >> >> -- Thomas Holder >> MPI for Developmental Biology >> Spemannstr. 35 >> D-72076 Tübingen >> > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > |
From: Thomas H. <sp...@us...> - 2011-12-30 09:50:46
|
Dear Pavan, I'm sorry that this appears to be so complicated. The "super" command in PyMOL is structure based (not as good as cealign) and can create alignment objects. The closest solution to your request that I can think of at the moment is the piece of script below. You can copy-paste this into the PyMOL command line (including the "python"/"python end" lines). python # example structures cmd.fetch('1e4y 1ake 4ake 3hpq', async=0) # all to one alignment target = '1ake' # <-- you can change this sele = ' and name CA' models = cmd.get_object_list() for model in models: cmd.super(model + sele, target + sele, object='aln') # save alignment to file cmd.save('all-to-one.aln', 'aln') python end Hope that helps. Cheers, Thomas PAVAN PAYGHAN wrote, On 12/30/11 07:21: > Dear, > > cealign,super,super_all cannot make an alignment object , as the most > important thing is to obtain > the alignment file out of all this exercise remains unresolved ,Please > suggest me structure based > alignment method in PyMol wherein I can use multiple structures at a > time (with low sequence identity) . > > Pavan Payghan > > > > > > > On Fri, Dec 30, 2011 at 2:15 AM, Thomas Holder > <sp...@us... <mailto:sp...@us...>> > wrote: > > PAVAN PAYGHAN wrote, On 12/29/11 13:23: > > Dear , > > "A > align > all to this" and "alignto" both are the same or > different? > If different in what context. > > > It's different. > > The first method uses "align" and gives you an alignment object > (uses util.mass_align function). > > The second uses "cealign" and cannot make an alignment object. > > http://pymolwiki.org/index.php/Align > <http://pymolwiki.org/index.php/Align> > http://pymolwiki.org/index.php/Cealign > <http://pymolwiki.org/index.php/Cealign> > > "align" does sequence based alignment and RMSD minimization, > "cealign" is a more sophisticated structure based alignment. > > Cheers, > Thomas > > Pavan Payghan > > > > On Thu, Dec 29, 2011 at 4:23 PM, zjxu <zj...@ma... > <mailto:zj...@ma...> <mailto:zj...@ma... > <mailto:zj...@ma...>>> wrote: > > Dear Pavan, > > > align 4-5 structures at a time (with low sequence identity). > > check cealign: http://www.pymolwiki.org/index.php/Cealign > <http://www.pymolwiki.org/index.php/Cealign> > <http://www.pymolwiki.org/index.php/Cealign > <http://www.pymolwiki.org/index.php/Cealign>> > > In pymol1.4, you could use 'alignto': > PyMOL>help alignto > DESCRIPTION > NOTE: This feature is experimental and unsuspported. > "alignto" aligns all other loaded objects to the given > selected object > using the CEalign algorithm. > USAGE > alignto target [, quiet ] > EXAMPLE > # fetch some calmodulins > fetch 1cll 1sra 1ggz 1k95, async=0 > alignto 1cll > > Hope this helps, > > Zhijian Xu > > > PAVAN PAYGHAN wrote: > > > Dear, > > Thanks a lot for the information. As you > mentioned super is only > for aligning two structures while with super_all to align the > multiple structures, but the most important thing is to > obtain > the alignment file out of all this excercise, can it be > possible > with super, super_all? > > If not which option exist in Pymol wherein one can align 4-5 > structures at a time (with low sequence identity). > > Pavan Payghan > > > On Wed, Dec 28, 2011 at 6:11 PM, Thomas Holder > <sp...@us... > <mailto:sp...@us...> > <mailto:sp...@us... > <mailto:sp...@us...>> > <mailto:sp...@us... > <mailto:sp...@us...> > > <mailto:sp...@us... > <mailto:sp...@us...>>>> wrote: > > Hi Pavan, > > > Thank you very much for the modified script. > > Its working fine, only thing I am facing is that > it can > not be > used for aligning more than two structures at a time(I > want it > for around 4 -5 structure alignment). The command > used to do > so is > > super abc,def,XYZ > > > "super" is for two structures, "super_all" (from the > script) is > for many structures. But the syntax is without comma > in mobile > selection: > > super_all abc, def ghi jkl > > for the third structure its giving error like > ,ValueError: > invalid literal for float (): XYZ. > > Apart form this could you please explain > > 1. Number of alignment residues should match > exactly in > all the > structures. > > > you can't influence this with super_all. > > 2. How to get alignment file for super, super_all > command after > alignment has been done. > > > this is not possible with super_all. > > But PyMOL can do this even without the super_all > script. On the > button-panel to the right, try: "A > align > all to this" > > You'll get an new object called like "aln_all_to_XYZ", > this you > can save: > > save file.aln, aln_all_to_XYZ > > > > Cheers, > Thomas > > -- Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > > -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: Thomas H. <sp...@us...> - 2011-12-30 11:40:33
|
Hi, I put a new script on the PyMOLWiki that is more flexible than the other all-to-one solutions: http://pymolwiki.org/index.php/Extra_fit Cheers, Thomas Thomas Holder wrote, On 12/30/11 10:50: > Dear Pavan, > > I'm sorry that this appears to be so complicated. The "super" command in > PyMOL is structure based (not as good as cealign) and can create > alignment objects. > > The closest solution to your request that I can think of at the moment > is the piece of script below. You can copy-paste this into the PyMOL > command line (including the "python"/"python end" lines). > > python > > # example structures > cmd.fetch('1e4y 1ake 4ake 3hpq', async=0) > > # all to one alignment > target = '1ake' # <-- you can change this > sele = ' and name CA' > models = cmd.get_object_list() > for model in models: > cmd.super(model + sele, target + sele, object='aln') > > # save alignment to file > cmd.save('all-to-one.aln', 'aln') > > python end > > > Hope that helps. > > Cheers, > Thomas > > PAVAN PAYGHAN wrote, On 12/30/11 07:21: >> Dear, >> >> cealign,super,super_all cannot make an alignment object , as the most >> important thing is to obtain >> the alignment file out of all this exercise remains unresolved >> ,Please suggest me structure based alignment method in PyMol wherein I >> can use multiple structures at a time (with low sequence identity) . >> Pavan Payghan -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |