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

2016-12-02 Thread Thomas Holder 
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  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 
>  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
> 
> -Original Message-
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> Message: 4
> Date: Tue, 25 Oct 2016 21:34:01 +
> From: Mohsen Chitsaz 
> Subject: [PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol
> To: "pymol-users@lists.sourceforge.net"
> 
> Message-ID:
> 
> 
> 
> 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
> 
> 
> 
> UT Southwestern
> 
> Medical Center
> 
> The future of medicine, today.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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

2016-12-02 Thread Spencer Bliven 
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 <
yuxing.l...@utsouthwestern.edu> 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
>
> -Original Message-
> From: pymol-users-requ...@lists.sourceforge.net [mailto:
> pymol-users-requ...@lists.sourceforge.net]
> Sent: Tuesday, October 25, 2016 4:50 PM
> To: pymol-users@lists.sourceforge.net
> Subject: PyMOL-users Digest, Vol 125, Issue 14
>
> Send PyMOL-users mailing list submissions to
> pymol-users@lists.sourceforge.net
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
> pymol-users-requ...@lists.sourceforge.net
>
> You can reach the person managing the list at
> pymol-users-ow...@lists.sourceforge.net
>
> When replying, please edit your Subject line so it is more specific than
> "Re: Contents of PyMOL-users digest..."
>
> --
>
> Message: 4
> Date: Tue, 25 Oct 2016 21:34:01 +
> From: Mohsen Chitsaz 
> Subject: [PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol
> To: "pymol-users@lists.sourceforge.net"
> 
> Message-ID:
>  apcprd03.prod.outlook.com>
>
> 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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> 
>
> UT Southwestern
>
>
> Medical Center
>
>
>
> The future of medicine, today.
>
>
>
> 
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