[PyMOL] L->D amino acid conversion using pymol
Gents, I want to try to visualize a retro-enantio Conotoxin peptide (reverse sequence, all D-amino acids, sculpting) and visually compare surface charge to its normal L-amino acid counterpart using Pymol. I use Pymol 0.93 (fink compiled) on a Powerbook G4/667 with three-button mouse. Mutating residues using the mutation wizard works fine, but I get an error upon L->D conversion. Using the mouse, I understand from the reference manual the following procedure: Invert NOTE The invert function is usually bound to CTRL−E in editing mode. The default selections are (lb) and (rb), meaning that you can pick the atom to invert with CTRL−middle click and then pick the stationary atoms with CTRL−SHIFT/left−click and CTRL−SHIFT/right− click, then hit CTRL−E to invert the atom. After correctly following this mouse-procedure selecting c-alpha and nitrogen, an error-message says: invert error: couldn't find basis for inversion. The same applies when trying via command line (example for residue one): PyMOL> edit 1/ca PyMOL> invert 1/n, 1/ca invert error: couldn't find basis for inversion What am I doing wrong ? Kind regards Uwe Hobohm Heinz-Uwe Hobohm
[PyMOL] L->D amino acid conversion using pymol
Gents, I want to try to visualize a retro-enantio Conotoxin peptide (reverse sequence, all D-amino acids, sculpting) and visually compare surface charge to its normal L-amino acid counterpart using Pymol. I use Pymol 0.93 (fink compiled) on a Powerbook G4/667 with three-button mouse. Mutating residues using the mutation wizard works fine, but I get an error upon L->D conversion. Using the mouse, I understand from the reference manual the following procedure: Invert NOTE The invert function is usually bound to CTRL−E in editing mode. The default selections are (lb) and (rb), meaning that you can pick the atom to invert with CTRL−middle click and then pick the stationary atoms with CTRL−SHIFT/left−click and CTRL−SHIFT/right− click, then hit CTRL−E to invert the atom. After correctly following this mouse-procedure selecting c-alpha and nitrogen, an error-message says: invert error: couldn't find basis for inversion. The same applies when trying via command line (example for residue one): PyMOL> edit 1/ca PyMOL> invert 1/n, 1/ca invert error: couldn't find basis for inversion What am I doing wrong ? Kind regards Uwe Hobohm Heinz-Uwe Hobohm
[PyMOL] sorry for posting multiple times...
...Mac-mail did not propagate the message from out-folder to sent-folder for unknown reasons. Uwe
[PyMOL] Homologous modelling
Hi, assume you have a protein structure (P1) and a second protein sequence (S1) without structure. Both sequences align with about 50% sequence identity over a large portion of both sequences without gaps (Smith+Waterman). Is there a way to automatically exchange residues from P1 against the respective residues in S1 (maybe using a script that exploits the mutate wizzard residue by residue ?) and do a final bond relaxation / sidechain orientation / H-bond-length correction ? Yes, I know, this is more than visualizing ... Best regards Uwe Hobohm
Re: [PyMOL] Homologous modelling
Thanks for the replies on my "How to spoil PyMol for modelling"
request. Despite Peitzsch's SwissModel (very convenient) and Sali's
Modeller (less convenient but perhaps more precise ?) I would like to
know, for educational purposes, whether PyMol could do reasonably well
also.
To be more precise; assume you apply a script like
cmd.edit("(1NOT`3)",pkresi=1)
wizard mutagenesis
refresh_wizard
cmd.get_wizard().set_mode("ALA")
cmd.get_wizard().apply()
cmd.set_wizard()
residue by residue according to the alignment, which further
(scriptable !) refinement steps are available in PyMol ?
