Re: [ccp4bb] secondary structure assignment to PDB file

[Pavel Afonine]

Tools like DSSP and such rely on model geometry to annotate SS elements, so
GIGO applies. For example, something that by eye looks like an obvious
helix but has enough distortions is unlikely to be annotated correctly.
Pavel

On Sun, Jan 29, 2017 at 3:50 AM, Antonio Ariza 
wrote:

> I always use DSSP, which I believe has been the gold standard for
> secondary structure assignment from pdb files for many years. PYMOL also
> has a DSSP plugin that can be used to override its own secondary structure
> assignment, which is nowhere near as good as DSSP.
>
>
>
> Best
>
>
>
> Tony
>
>
> --
>
>
>
>
>
>
> * Dr. Antonio Ariza University of Oxford Sir William Dunn School of
> Pathology South Parks Road Oxford OX1 3RE*
>
> *Links to my public profiles:*
> ResearchGate 
> LinkedIn 
> GoogleScholar
> 
> ORCID 
> --
> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of chemocev
> marker [jirivit...@gmail.com]
> *Sent:* 29 January 2017 10:41
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] secondary structure assignment to PDB file
>
> Hi
> Is there any tool that can assign secondary structure to the PDB file. The
> problem is if I used different modelling tools, there are regions in the
> protein which does not remain consistent and looks different in different
> application.
>
> best
>
> J. Vitali
>

Re: [ccp4bb] rigid flexible analysis

[van den Bedem, Henry]

KGS software can do this, as well as sampling based on rigidity 
(10.1016/j.jmps.2015.06.006 or 
10.1021/acs.jctc.5b00995). The software is available from github: 
https://github.com/ExcitedStates/KGS.

Henry

From: CCP4 bulletin board  on behalf of Gauri Misra 

Reply-To: Gauri Misra 
Date: Tuesday, January 24, 2017 at 3:46 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] rigid flexible analysis

Hi everyone!

I would like to know the current online servers available for analyzing the 
rigid and flexible regions of proteins.Looking forward for precious inputs from 
the community.

Sincerely,
Dr. Gauri Misra

Assistant Professor
Amity Institute of Biotechnology
Amity University
Noida (U.P.) India

[ccp4bb] Abraham Szöke

[William G. Scott]

Dear Colleagues:

Is is with great sadness that I report the recent passing of Abraham Szöke, a 
friend, colleague, informal mentor, and an exceptionally intelligent and 
energetic source of boundless intellectual enthusiasm.

Abraham was a physicist at Livermore who helped to design nuclear weapons for a 
living, but he had many other interests. One of these was X-ray 
crystallography, and with his wife and collaborator Hanna Szöke, as well as 
John Somoza, he developed an approach to crystallographic real-space 
electron-density refinement and optimization, implemented in a program called 
EDEN, that produces electron density maps with minimal model bias in a robust 
manner. The source code, along with a brief explanation and extensive user's 
manual, is freely available:

https://code.google.com/archive/p/edencrystallography/

https://github.com/wgscott/edencrystallography

EDEN is written in C and is easy to compile on any unix platform. A fink 
package for OS X is also available, as are packages for various linux 
distributions. 

John and I first met Abraham and Hanna Szöke when we were graduate students at 
Berkeley. A few years later, I had the opportunity to collaborate with them and 
to put EDEN to the test. A single-particle version of EDEN was also under 
development, for use with electron microscopy. Abraham had a wide variety of 
interests in addition to electron density reconstruction, including many novel 
ideas about the origin of life. He enjoyed a multitude of fruitful and 
productive collaborations throughout a period most normal people would consider 
retirement. He passed away on Thursday at age 87 from an opportunistic 
infection while combatting lymphoma.


William G. Scott
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064  
USA

http://scottlab.ucsc.edu

Re: [ccp4bb] secondary structure assignment to PDB file

[Antonio Ariza]

I always use DSSP, which I believe has been the gold standard for secondary 
structure assignment from pdb files for many years. PYMOL also has a DSSP 
plugin that can be used to override its own secondary structure assignment, 
which is nowhere near as good as DSSP.



Best



Tony



--

Dr. Antonio Ariza
University of Oxford
Sir William Dunn School of Pathology
South Parks Road
Oxford
OX1 3RE

Links to my public profiles:
ResearchGate
LinkedIn
GoogleScholar
ORCID

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of chemocev marker 
[jirivit...@gmail.com]
Sent: 29 January 2017 10:41
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] secondary structure assignment to PDB file

Hi
Is there any tool that can assign secondary structure to the PDB file. The 
problem is if I used different modelling tools, there are regions in the 
protein which does not remain consistent and looks different in different 
application.

best

J. Vitali

[ccp4bb] secondary structure assignment to PDB file

[chemocev marker]

Hi
Is there any tool that can assign secondary structure to the PDB file. The
problem is if I used different modelling tools, there are regions in the
protein which does not remain consistent and looks different in different
application.

best

J. Vitali