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PostPosted: 2011.01.05 01:53 
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Hello everybody,
using Crysol I tried to change manually in the pdb file of myoglobin (1A6N) the S atom of both methionine with a Se atom, simply changing the name of the atom in the pdb file. Apparently this change has no effect on the scattering curve calculated by Crysol. How is it possible?
Thank you for your help.


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PostPosted: 2011.01.05 10:03 
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Joined: 2007.08.10 11:09
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maxrinnel wrote:
How is it possible?

Don't know. It may be problem in the program or a user error - who knows? It is probably impossible to reply to this question without being a medium.

Without (a) the original and (b) the modified input files and (c) your exact command line parameters or (d) interactive configuration, how shall anyone tell what happens and what is not?


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PostPosted: 2011.01.05 13:37 
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I have attached the pdb file modified: I have changed the symbol S to Se (at the positions 484 and 1131).

The parameters used:
C R Y S O L Version 2.6 -- 26/01/05
-- Program started at 04-Jan-2011 23:00:30--

-------- Real space resolution and grid --------

Maximum order of harmonics ............................ : 15
Order of Fibonacci grid ............................... : 17
Total number of directions ............................ : 2585

------------ Reciprocal space grid -------------

in s = 4*pi*sin(theta)/lambda [1/angstrom]
Maximum scattering angle .............................. : 2.300
Number of angular points .............................. : 231

--- Structural parameters (sizes in angstroms) ---

PDB file name .......................................... : 1A6N_deoxy_Se.pdb
Number of atoms read .................................. : 1389
Number of discarded waters ............................ : 194
Geometric Center: 13.891 20.945 7.982
Center of the excess electron density: 0.629 -0.480 0.395
Electron Rg : 15.16 Envelope Rg : 15.18
Shape Rg : 15.12 Envelope volume : 0.2405E+05
Shell volume : 0.1365E+05 Envelope surface : 3867.
Shell Rg : 20.44 Envelope radius : 25.06
Shell width : 3.000 Envelope diameter : 49.07
Molecular Weight: 0.1970E+05 Dry volume : 0.2387E+05
Displaced volume: 0.2519E+05 Average atomic rad.: 1.630
Number of residuals : 151

-- No data fitting, parameters entered manually --

Solvent density ........................................ : 0.3340
Contrast of the solvation shell ........................ : 3.000e-2
Average atomic radius .................................. : 1.630
Excluded Volume ........................................ : 2.519e+4
Average atomic volume .................................. : 18.14
Radius of gyration from atomic structure
Rg ( Atoms - Excluded volume + Shell ) ................. : 16.33
Rg from the slope of net intensity ..................... : 16.73
Average electron density ............................... : 0.4190


Attachments:
1A6N_deoxy_Se.pdb [284.44 KiB]
Downloaded 212 times
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PostPosted: 2011.01.06 12:23 
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Joined: 2008.10.29 13:50
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Location: University of Copenhagen
Hi,
The element in the pdb file (end of the line with coordinates and displacement parameters) should be right-justified, thus I suggest moving "Se" one column left in your pdb file, otherwise I presume it is still read as "S", which is why you then see no change in the crysol output.
See e.g. http://www.wwpdb.org/documentation/format32/sect9.html for details on the pdb-format.
Hope this can change your output as expected.


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