Re: [ccp4bb] Solvent accessible regions of the channel (Pore)

- Protein crystallography

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: crystals of 1D
From: Christian Roth christian {- dot -} roth {- at -} BBZ {- dot -} UNI-LEIPZIG {- dot -} DE
Date: 2010-04-07

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Subject: PDBe to retire the OCA search system in October 2010
From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2010-04-07

Subject: Re: Solvent accessible regions of the channel (Pore)
From: Manish Chandra Pathak pmxtal {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2010-04-07

Hi Bashir,

In Pymol:
1. Show-------Surface (will generate surface around the protein)
2. Setting-----Surface-------Cavities & Pockets Only. (will show only Cavities inside)
3. Use cavity_cull command to set the filter for cavities.
(eg. set cavity_cull, 40)

Manish

--
Manish Chandra Pathak, Ph.D.
Department of Biochemistry
Emory University School of Medicine
1510 Clifton Road, NE, Room G235
Atlanta, GA 30322 USA
Tel: +1-404-727-2563 Fax: +1-404-727-2738

----- Original Message ----
> From: Muhammed bashir Khan
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Wed, April 7, 2010 9:58:20 AM
> Subject: [ccp4bb] Solvent accessible regions of the channel (Pore)
>
> Dear all;

Can anybody help me how I can make the solvent accessible
> surface(inside)
of the channel(pore)by pymol, or by any other
> programme.

Thanks in Advance

--
Muhammad Bashir
> Khan
Department for Biomolecular Structural Chemistry
Max F. Perutz
> Laboratories
University of Vienna
Campus Vienna Biocenter 5
A-1030
> Vienna
Austria

Phone: +43(1)427752224
Fax: +43(1)42779522

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: crystals of 1D
From: Christian Roth christian {- dot -} roth {- at -} BBZ {- dot -} UNI-LEIPZIG {- dot -} DE
Date: 2010-04-07

Next message:
Subject: PDBe to retire the OCA search system in October 2010
From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2010-04-07