[ccp4bb] Fill map/mask with dummy atoms?

2010-10-13 Thread Alex Shkumatov 

Dear Dirk

You might find one of the programs mentioned by Andreas below useful  
for your purpose.


Cheers
Alex

Am 28.07.2010 um 18:26 schrieb Andreas Förster docandr...@gmail.com:

Here's a preliminary summary of the suggestions I got from the ccp4  
community regarding the problem stated below (calculate theoretical  
SAXS data from EM reconstruction):


The program em2dam, currently developed at EMBL-Hamburg (where the  
magicians of SAXS live), converts a Spider map into a pdb file,  
which can then be used as input for another EMBL-Hamburg program,  
crysol. This approach does what I want.  Nice.  Em2dam hasn't been  
released yet, but is available for testing upon request (ashku...@embl-hamburg.de 
).

http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html


HYDRO can also calculate scattering form factors from dummy-bead  
models, but I didn't try that out.  From the group that wrote HYDRO  
comes hydromic, a program that calculates, from an EM map, a  
distance distribution and a P vs. h list whose usefulness didn't  
immediately reveal itself to me.  Those more familiar with SAXS  
might find that this program is just what they want.

http://leonardo.fcu.um.es/macromol/programs/programs.htm


The program vol2pdb, which is part of the situs package, converts  
spider format em maps to dummy-bead models.  I couldn't suppress the  
feeling that the pdbs obtained with em2dam were closer to the  
truth.  Situs also has a SAXS tutorial that might be useful.

http://situs.biomachina.org/tutorial_saxs.html

The EMAN program proc3d with the calcsf option can calculate  
scattering curves.  The output file contains the F**2/s distribution  
for the map with max=0.0.  Some scaling might be required.  I didn't  
try this.

http://blake.bcm.tmc.edu/eman/

Chimera might have a SAXS function.  I didn't check.
http://www.cgl.ucsf.edu/chimera/

Thanks to all who contributed ideas and suggested approaches, and  
special thanks to Alex for sharing em2dam.



Andreas



On 23/07/2010 11:54, Andreas Förster wrote:

Dear all,

the other day I obtained SAXS data from which a low-resolution
structural model was calculated. The model is simpler/less complex  
than

one of the same protein that we obtained with cryo-EM.

Is there a way to estimate theoretical SAXS data from a cryo-EM
reconstruction to compare with the obtained raw data? Is there a  
program
that does for a reconstruction what CRYSOL does for pdbs? I  
understand
that there would be a huge amount of handwaving involved, but it  
might

help us reconcile our models.

Thanks.


Andreas




--
  Andreas Förster, Research Associate
  Paul Freemont  Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
  http://www.msf.bio.ic.ac.uk

Re: [ccp4bb] pH dependent conformational change

2010-12-06 Thread Alex Shkumatov 

Hi

SAXS can be a right tool. However, how big is short peptide linker?

Check Nature paper by Askarieh G. and Hedhammar M. for non-His pH  
sensor.


cheers
Alex





Am 06.12.2010 um 17:59 schrieb Daniel Jin jin_xiec...@yahoo.com:


Dear CCP4 colleagues,

We have a protein that is composed of two domains connected by a  
short peptide linker. We have some indirect evidence showing that  
the two domains may somehow move against each other when exposed to  
different pH. It is unlikely to have any obvious secondary  
structure change since each domain behaves like a rigid body. I am  
wondering whether there is any “easy” way, biochemically or biophy 
sically, to monitor the conformational changes in solution. Many t 
hanks.


As far as I know most of the pH sensing stories are linked to  
histidine residue. Can you point me to any references that show a  
different pH sensing mechanism (other than His)? Thanks.


Best,
Daniel

Re: [ccp4bb] Saxs reviews or books

2011-01-11 Thread Alex Shkumatov 
Hi Rojan

You may as well check SAXS forum at:
www.saxier.org/forum

Cheers
Alex

On Tuesday 11 January 2011 01:33:50 you wrote:
 Hello:
 
  
 
 I am very novice about Small Angle X-ray Scattering. I am looking for
 introductory books or review papers. Could you recommend this type of
 document?
 
  
 
 Regards,
 
  
 
 Rojan 

-- 
Alexander Shkumatov, predoc -- Biological Small Angle Scattering Group
EMBL Hamburg Outstation c/o DESY -- Building 25A
Notkestraße 85 -- 22603 Hamburg -- Germany

tel:+49 40 89902 178fax:+49 40 89902 149
Email: ashku...@embl-hamburg.de

Re: [ccp4bb] Cavity is waiting unknown ligand

2011-08-10 Thread Alex Shkumatov 

Hi Heidi

You can try hunting for similar structural motifs which are likely
to be involved in ligand binding or function:
http://www.russelllab.org/cgi-bin/tools/pints.pl

You can then try fitting suggested ligands to the cavity.

good luck
Alex

On 10.08.2011 13:46, Heidi Tuominen wrote:

Dear All,

I have inside cavity in my protein structure with some conserved 
residues. We do not know function or ligand for that domain.


How I could find ligand candidates which fit to this cavity? Maybe 
somehow with pdbe?


Thank you,
Heidi


--
--
Alexander V. Shkumatov, Ph.D.
Biological Small Angle Scattering Group
EMBL Hamburg Outstation c/o DESY tel: +49 40 89902 178
Building 25A Notkestraße 85  fax: +49 40 89902 149
22603 Hamburg, Germany email: ashku...@embl-hamburg.de
--