Re: [PyMOL] MD analysis (distance, dihedral etc)

) phiL = [] psiL = [] u = MDA.Universe(GRO, TRJ) phi = sum([u.select_atoms(atom) for atom in [C0, N1, CA, C1]]).dihedral psi = sum([u.select_atoms(atom) for atom in [N1, CA, C1, N2]]).dihedral for f in u.trajectory:     phiL.append(phi.value())     psiL.append(psi.value()) On 9/4/20 9:02 AM, Baptiste

[PyMOL] MD analysis (distance, dihedral etc)

Hi all, Is it possible to monitor distances, dihedrals etc. in a protein trajectory? to finally plot distances or something else versus time. (as VMD or others) Thanks. Best, Baptiste ___ PyMOL-users mailing list Archives: http://www.mail-archiv

Re: [PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking

rget_state": PyMOL>rms Crystal_Rfp, Vina_Rfp, mobile_state=1, target_state=1 Executive: RMSD =0.032 (51 to 51 atoms) See also "Notes" section here:https://pymolwiki.org/index.php/Align#Notes Cheers, Thomas On Jul 26, 2018, at 9:42 AM, Baptiste Legrand wrote: Thanks for you

Re: [PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking

molecule looks like, could it be automorphism? -Original Message- From: Baptiste Legrand Sent: Wednesday, July 25, 2018 9:17 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking Dear all, I tried to calculate a

[PyMOL] Calculate RMSD between ligands from a crystal structure and from a docking

Dear all, I tried to calculate a rmsd value between ligands from a crystal structure and after docking. The two molecules share similar nomenclatures and are really well superimposed. I think that the RMSD should be < 1 A. I used the following lines: alter all,segi="" alter all,chain ="" rms

[PyMOL] Chi torsion angles measurements on multiple structures

Dear all, I wounder to know about possible ways to measure chi1, chi2 dihedral angles on a set of structures. For example, I opened 10 pdb files and the phi_psi command allows us to easily obtain the phi and psi values: Ex: To obtain the phi and psi values of the residue 288 of the chain A in

Re: [PyMOL] How to draw a cartoon representation on secondary structures containing beta-amino acids?

Hi, The Tsjerk's solution works without modify the exotic *pdb file. :) set cartoon_trace_atoms select cacb, name c5+c6+c10+c12+c16+c19+c23+c25+c29+c32+c36+c38 alter cacb, ss='H' show cartoon, cacb Thanks all, Baptiste Le 17/08/2011 05:48, Tsjerk Wassenaar a écrit : > Hey, > > I noticed with

Re: [PyMOL] How to draw a cartoon representation on secondary structures containing beta-amino acids?

Thanks Joseph and Thomas for your replies. When I use the "as cartoon" commands, all my molecule disappear. My *pdb file could be the problem as it is a *cif crystal structure file (converted with mercury) from the cambridge crystal data. Cheers, Baptiste 2011/8/16 Thomas Holder > Hi Baptiste,

[PyMOL] How to draw a cartoon representation on secondary structures containing beta-amino acids?

Dear all, I have a small helical pseudopeptide with mixed alpha and beta amino-acids. How can I make a cartoon representation of this helix with Pymol? For the moment, I have selected the peptide backbone atoms and tried the "alter" command to force pymol to recognize the helix but it do not w