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 > P

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

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

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 "ceal

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 wrote: > Dear Pavan, > > > align 4-5 structures at a time (with low sequence identity). > > check cealign: > http://www.pym

Re: [PyMOL] about super_all.py Plugin installation.

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 t

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 whic

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 ---

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 menti

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 c

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 usi

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 f

Re: [PyMOL] about super_all.py Plugin installation.

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

Re: [PyMOL] about super_all.py Plugin installation.

Dear Pavan, On Tue, 27 Dec 2011 00:15:38 +0530, PAVAN PAYGHAN 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 Plugi

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 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 > me

[PyMOL] about super_all.py Plugin installation.

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-i