Re: [PyMOL] Is cyclododecene in the database of PyMol?

Dear Prof. Wassenaar and Prof. Martin, We thank you very much for taking time to send us the information we needed. Regards, Rajib & Yuktimmana -- One dashboard for servers and applications across Physical-Virtual-Cloud W

[PyMOL] regarding theseus wrapper

Dear pymol-users There is some trouble I end up with while using theseus from psico in pymol. I am not sure what is causing this. Can anyone help me fix this one. The log I get when executing theseus is given below. thank you in advance, Best Regards Priyan BEGIN THESEUS 3.0.0 > I===-===-===-

Re: [PyMOL] Is cyclododecene in the database of PyMol?

Hi Rajib & Yuktimmana, I found this paper that describes the conformational preferences of trans-cyclododecene. http://pubs.acs.org/doi/abs/10.1021/jo990628w I hope it helps. Cheers, Osvaldo. On Thu, May 7, 2015 at 5:51 PM, Tsjerk Wassenaar wrote: > Hi Rajib & Yuktimmana, > > Cyclododecene

Re: [PyMOL] Is cyclododecene in the database of PyMol?

Hi Rajib & Yuktimmana, Cyclododecene has twelve carbon atoms in a ring, and one of the bonds is a double bond. This means that there are two forms, cis and trans. Neither is wrong, if not specified explicitly. For the rest, the structure is very flexible, so there is not a single structure, but it

Re: [PyMOL] Is cyclododecene in the database of PyMol?

Dear Rajib & Yuktimmana, The most reliable computational tool to determine the lowest energy conformation of a molecule is to use quantum chemical computations (using software like Gaussian or GAMESS). Within PyMOL you can try with the optimize plugin

Re: [PyMOL] Is cyclododecene in the database of PyMol?

We have searched for cyclododecene and different website has different structure. Which of these is true? Is it possible for it to be analysed by PyMol? Regards, Rajib & Yuktimmana -- One dashboard for servers and applica

Re: [PyMOL] RMS or RMSD for two structures

Hi Dmitry, You have to load both molecules and then you could use the command fit x-mol, dft-mol You can find more examples and options on the PyMOL wiki, http://www.pymolwiki.org/index.php/Fit Cheers, Osvaldo. El may 7, 2015 6:00 a.m., "Dmitry B. Eremin" escribió: > Hello everyone, > > I ha

[PyMOL] RMS or RMSD for two structures

Hello everyone, I have a problem: I want to calculate RMS or RMSD for to structures one i’ve got from x-ray structure analysis and another from DFT calculations, but still can not understand how to perform it. hope You can help me. Sincerely, Eremin D., Section of structural studies, Laborator