Re: [ccp4bb] Extra electron density

2012-11-05 Thread Herman . Schreuder
Dear Yogesh,

Since your difference density is at the center of a hexamer, you might
be looking at the 6-fold average density of one or two fatty acid
molecules. Just try to fit one and generate to other 5 equivalent
molecules and look if this makes sense.

Otherwise, I agree with Mark that with hardly any 2mFo-dFC density, you
may also be looking at an artifact.

Best regards,
Herman  

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Mark J van Raaij
Sent: Monday, November 05, 2012 9:39 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Extra electron density

It may just be noise. Notice there there appears to be no electron
density, only difference density.

Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij



On 5 Nov 2012, at 01:38, yogesh khandokar wrote:

 Dear All
 
 I am working on an enzyme which involved in fatty acid biosynthesis.
We solved the crystal structure of it. Biological unit of this enzyme is
Hexamer and showing extra electron density in the center of Hexamer.
Wincoot software doesn't recognize this extra electron density as water
molecules/ substrate.  
 
 My question is:Is there any way to find the molecules responsible for
extra electron density?
 
 Picture is attached with email.
 
 Thanks in advance for your comments.
 
 Regards
 --
 Yogesh Khandokar
 PhD Student
 School of Biomedical Sciences
 Charles Sturt University
 Wagga Wagga, NSW,
 Australia
 http://www.csu.edu.au/faculty/science/biomed/
 
 Doc1.doc


Re: [ccp4bb] Extra electron density

2012-11-05 Thread Sangeetha Vedula
You know what? Scratch what I said. As Mark says, there isn't any 2Fo-Fc
density, which is suspicious.

However, I would still model what may fit in it, with appropriate
occupancy, based on the symmetry. To be doubly sure.

I have, in the past, used
ProDRGhttp://davapc1.bioch.dundee.ac.uk/prodrg/submit.htmlfor
obtaining pdf, topology and parameter files for ligands. ARP/wARP can
be used for a first fit of ligand into density.

You may find appropriate fatty acid pdb-top-param files already in the
HIC-UP http://xray.bmc.uu.se/hicup/ database.

I would do a quick search for a fatty acid of an appropriate length.

If it is truly spurious density as I suspect it is, you'll see negative
density lighting up your screen despite using appropriately low occupancy.

Good luck!

Sangeetha.

On Sun, Nov 4, 2012 at 8:17 PM, Sangeetha Vedula sangeetha...@gmail.comwrote:

 Could it be a fatty acid? It looks like it has a (hydrophobic?) tail with
 a (charged?) head. Partially occupied perhaps, as they're so close together.


 On Sun, Nov 4, 2012 at 7:38 PM, yogesh khandokar 
 yogesh.khando...@gmail.com wrote:

 Dear All

 I am working on an enzyme which involved in fatty acid biosynthesis. We
 solved the crystal structure of it. Biological unit of this enzyme is
 Hexamer and showing extra electron density in the center of Hexamer.
 Wincoot software doesn't recognize this extra electron density as water
 molecules/ substrate.

 My question is:Is there any way to find the molecules responsible for
 extra electron density?

 Picture is attached with email.

 Thanks in advance for your comments.

 Regards
 --
 Yogesh Khandokar
 PhD Student
 School of Biomedical Sciences
 Charles Sturt University
 Wagga Wagga, NSW,
 Australia
 http://www.csu.edu.au/faculty/science/biomed/





Re: [ccp4bb] Extra electron density

2012-11-04 Thread Sangeetha Vedula
Could it be a fatty acid? It looks like it has a (hydrophobic?) tail with a
(charged?) head. Partially occupied perhaps, as they're so close together.

On Sun, Nov 4, 2012 at 7:38 PM, yogesh khandokar yogesh.khando...@gmail.com
 wrote:

 Dear All

 I am working on an enzyme which involved in fatty acid biosynthesis. We
 solved the crystal structure of it. Biological unit of this enzyme is
 Hexamer and showing extra electron density in the center of Hexamer.
 Wincoot software doesn't recognize this extra electron density as water
 molecules/ substrate.

 My question is:Is there any way to find the molecules responsible for
 extra electron density?

 Picture is attached with email.

 Thanks in advance for your comments.

 Regards
 --
 Yogesh Khandokar
 PhD Student
 School of Biomedical Sciences
 Charles Sturt University
 Wagga Wagga, NSW,
 Australia
 http://www.csu.edu.au/faculty/science/biomed/