Re: [PyMOL] Dss when creating movie from dcd traj

Hi Effie, try to load the trajectory with the option discrete=1: load trajectory.dcd, discrete=1 Best, Norbert Am 09.11.2023 um 19:38 schrieb Effie Artikis: Hello, I’ve uploaded my MD simulation and am trying to create a movie but I’ve noticed that when I play the MD simulation, the second

[PyMOL] Dss when creating movie from dcd traj

Hello, I’ve uploaded my MD simulation and am trying to create a movie but I’ve noticed that when I play the MD simulation, the secondary structure isn’t updated frame by frame. For example, although it is an unfolding simulation the protein maintains the secondary structure of the initial frame th

Re: [PyMOL] dss

Hi Bradley, "help dss" should give you a strong hint and usage info: cmd.dss( selectionName, state ); Cheers, -- Jason On Fri, Sep 10, 2010 at 1:21 PM, Bradley Hintze wrote: > Is there a way i can call dss from a script? e.g. cmd.dss. > > -- > Bradley J. Hintze > Graduate Student > Duke Unive

[PyMOL] dss

Is there a way i can call dss from a script? e.g. cmd.dss. -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 -- Start uncovering the many advantages of virtual appliances and start usi

Re: [PyMOL] DSS

I'm writing a manuscript and just need clarification. Does "cmd.iterate('all and n. ca', 'stored.stored_ss.append([ss])')" use pymol's DSS to assign secondary structure? If not, how is this command assigning secondary structure? Thanks, Bradley On Tue, Jun 22, 2010 at 7:37 PM, Jason Vertrees w

Re: [PyMOL] DSS

Hi Bradley, > Does "cmd.iterate('all and n. ca', 'stored.stored_ss.append([ss])')" 'ss' in this usage just reads from the current model of the molecule in memory. PyMOL can read secondary structure from the PDB files if it's present or determine it by itself using dss. PyMOL defaults to the for

Re: [PyMOL] DSS

Hi Bradley, PyMOL uses its own internal routine for secondary structure classification. The iterator token is "ss". Check out http://pymolwiki.org/index.php/Ss and http://pymolwiki.org/index.php/Iterate_sses and http://pymolwiki.org/index.php/WriteSS. Cheers, -- Jason On Tue, Jun 22, 2010 at

[PyMOL] DSS

Hi all, Is there a way to get an output from PyMol's DSS command (like a dssp output)? -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799 -- ThinkGeek and WIRED's GeekDad team up for t

RE: [PyMOL] dss & ribbon representation

Behalf Of > Igor Pechersky > Sent: Friday, November 14, 2003 3:07 AM > To: andr...@biochem.utah.edu; Andreas Foerster > Cc: pymol > Subject: Re: [PyMOL] dss & ribbon representation > > > Andreas Foerster : > > > - The dss algorithm is great, a very quic

Re: [PyMOL] dss & ribbon representation

Andreas Foerster : > - The dss algorithm is great, a very quick way to assign secondary > structure. Is there a way of conserving the information when saving the > pdb? There are at least 3 ways to store SS assignments from PyMOL. Depends on your needs: 1. Save PyMOL session (*.pse). Atom prop

[PyMOL] dss & ribbon representation

Hi pymol community. Two questions. - The dss algorithm is great, a very quick way to assign secondary structure. Is there a way of conserving the information when saving the pdb? Sometimes it's nice to edit the assignment. - In contrast to versions 0.9 and earlier, version 0.93 connects the CA wi