Re: [PyMOL] about super_all.py Plugin installation.
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
spel...@users.sourceforge.net mailto:spel...@users.sourceforge.net
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 z...@mail.shcnc.ac.cn
mailto:z...@mail.shcnc.ac.cn mailto:z...@mail.shcnc.ac.cn
mailto:z...@mail.shcnc.ac.cn 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':
PyMOLhelp 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
spel...@users.sourceforge.net
mailto:spel...@users.sourceforge.net
mailto:spel...@users.sourceforge.net
mailto:spel...@users.sourceforge.net
mailto:spel...@users.sourceforge.net
mailto:spel...@users.sourceforge.net
mailto:spel...@users.sourceforge.net
mailto:spel...@users.sourceforge.net 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
Re: [PyMOL] about super_all.py Plugin installation.
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
--
Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
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costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
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Re: [PyMOL] about super_all.py Plugin installation.
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 z...@mail.shcnc.ac.cn wrote: Dear Pavan, align 4-5 structures at a time (with low sequence identity). check cealign: http://www.pymolwiki.org/**index.php/Cealignhttp://www.pymolwiki.org/index.php/Cealign In pymol1.4, you could use 'alignto': PyMOLhelp 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 spel...@users.sourceforge.net mailto:speleo3@users.**sourceforge.netspel...@users.sourceforge.net 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-**VDIinaboxhttp://p.sf.net/sfu/Citrix-VDIinabox --**--** __**_ PyMOL-users mailing list (PyMOL-users@lists.**sourceforge.netPyMOL-users@lists.sourceforge.net ) Info Page: https://lists.sourceforge.net/**lists/listinfo/pymol-usershttps://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/**pymol-users@lists.sourceforge.** net http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- 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 (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] about super_all.py Plugin installation.
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 spel...@users.sourceforge.net 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 (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] about super_all.py Plugin installation.
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 z...@mail.shcnc.ac.cn mailto:z...@mail.shcnc.ac.cn 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': PyMOLhelp 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 spel...@users.sourceforge.net mailto:spel...@users.sourceforge.net mailto:spel...@users.sourceforge.net mailto:spel...@users.sourceforge.net 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 -- 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 (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] about super_all.py Plugin installation.
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 spel...@users.sourceforge.net 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/Alignhttp://pymolwiki.org/index.php/Align http://pymolwiki.org/index.**php/Cealignhttp://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 z...@mail.shcnc.ac.cn mailto: z...@mail.shcnc.ac.cn** wrote: Dear Pavan, align 4-5 structures at a time (with low sequence identity). check cealign: http://www.pymolwiki.org/**index.php/Cealignhttp://www.pymolwiki.org/index.php/Cealign http://www.pymolwiki.org/**index.php/Cealignhttp://www.pymolwiki.org/index.php/Cealign In pymol1.4, you could use 'alignto': PyMOLhelp 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 spel...@users.sourceforge.net mailto:speleo3@users.**sourceforge.netspel...@users.sourceforge.net mailto:speleo3@users.**sourceforge.netspel...@users.sourceforge.net mailto:speleo3@users.**sourceforge.netspel...@users.sourceforge.net 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 -- 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 (PyMOL-users@lists.sourceforge.net) Info Page:
Re: [PyMOL] about super_all.py Plugin installation.
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 spel...@users.sourceforge.net 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-keller2@fsm.northwestern.**edu j-kell...@fsm.northwestern.edumailto: j-keller2@fsm.**northwestern.edu j-kell...@fsm.northwestern.edu 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 pavana...@gmail.com mailto:pavana...@gmail.com 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-kell...@northwestern.edu mailto:j-keller2@**northwestern.eduj-kell...@northwestern.edu * -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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 (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] about super_all.py Plugin installation.
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-kell...@fsm.northwestern.edu 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 pavana...@gmail.com mailto:pavana...@gmail.com mailto:pavana...@gmail.com mailto:pavana...@gmail.com 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-kell...@northwestern.edu *** -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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 (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] about super_all.py Plugin installation.
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-kell...@fsm.northwestern.edu mailto:j-kell...@fsm.northwestern.edu 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 pavana...@gmail.com mailto:pavana...@gmail.com 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-kell...@northwestern.edu mailto:j-kell...@northwestern.edu *** -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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 (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] about super_all.py Plugin installation.
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 spel...@users.sourceforge.net 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-keller2@fsm.northwestern.**edu j-kell...@fsm.northwestern.edu 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 pavana...@gmail.com mailto:pavana...@gmail.com mailto:pavana...@gmail.com mailto:pavana...@gmail.com 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-kell...@northwestern.edu * -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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 (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] about super_all.py Plugin installation.
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 -- 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 (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] about super_all.py Plugin installation.
You can try the alignto command as an alternative, if you want. JPK On Mon, Dec 26, 2011 at 12:45 PM, PAVAN PAYGHAN pavana...@gmail.com 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 (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 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- 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 (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] about super_all.py Plugin installation.
Dear Pavan, On Tue, 27 Dec 2011 00:15:38 +0530, PAVAN PAYGHAN pavana...@gmail.com wrote: Dear PyMol Users, I am using PyMol +v0.97 version on Windows XP .I have downloded super_all.pyhttp://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 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- 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 (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
