Re: [PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol

[Thomas H. <tho...@sc...>]

Since version 1.8.2, PyMOL auto-detects CA-only models, so no ribbon_trace_atoms or cartoon_trace_atoms needed anymore.

A nice tool that can assign secondary structure with CA trace only is SST:
http://lcb.infotech.monash.edu.au/sstweb2/

PSICO has an SST wrapper, so you can run it directly in PyMOL:

run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/editing.py
fetch 3b5d, async=0
sst
show cartoon

Hope that helps.

Cheers,
  Thomas

On 02 Dec 2016, at 08:24, Spencer Bliven <spe...@gm...> wrote:

> There is a cartoon variant too, although everything will look like a loop
> 
> set cartoon_trace_atoms, on
> show cartoon, polymer
> 
> On Wed, Oct 26, 2016 at 12:27 AM, Yuxing Liao <Yux...@ut...> wrote:
> Hi Mohsen,
> 
> The PDB file of 3B5D only contains CA atoms, so most rendering like cartoon fails. You could try to visualize it by "set ribbon_trace_atoms, 1" and then show it as ribbon.
> 
> Yuxing
> 
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> ------------------------------
> 
> Message: 4
> Date: Tue, 25 Oct 2016 21:34:01 +0000
> From: Mohsen Chitsaz <moh...@fl...>
> Subject: [PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol
> To: "pym...@li..."
>         <pym...@li...>
> Message-ID:
>         <SG2...@SG...>
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> Content-Type: text/plain; charset="us-ascii"
> 
> Hi everyone,
> 
> Can someone please assist me opening this pdb file? I am trying to open EmrE protein (pdb: 3B5D) in Pymol a and show it as cartoon representation, but it opens up as many little cross signs seem to be corresponding to CA atoms. When I try to preset it pretty or any other preset options, it disappears. The command "show cartoon" is not doing anything on it.
> 
> Cheers
> Mohsen
> 
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-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.