B-anisotropic and bulk solvent correction

Simon Terzyan terzyans at OMEGA.OMRF.OUHSC.EDU
Fri Nov 12 17:06:43 EST 1999


This is a multi-part message in MIME format.
--------------92CCADDA327BE086090879DE
Content-Type: multipart/alternative;
 boundary="------------38D5B42720EF74F9A121A962"


--------------38D5B42720EF74F9A121A962
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit


Dear X-PLOR users,

       I am in the late stages of refinement of a 2.3 angstrom Fab
structure
in P212121 with 2 molecules in the assymetric part. The R factors after
positional and B individual refinements in the resolution range 8.-2.3 A
are R=0.237 and Rfree= 0.314.
When I am using bulk solvent correction they become ( 25-2.3A) 0.231 and
0.303, correspondingly. But after it  the electron density  for the
residues on the surface of the molecules  is worse than before.
Refinement of anisotropic B_overall ( without bulk solvent correction,
8-2.3A ) gives R factors 0.214 and 0.289.  Further bulk solvent
correction and positional and B individual refinemt drops the R factors
to 0.199 and 0.266. As it was already mentioned in one of previos
letters from Christelle Sabatier (Message-ID:
<v03007800b02211264fa6@[128.206.29.205]>) this refinement increases the
mean value of B factors. And furthermore, if I go for a second cycle
then the B factors increase more.
I have used also suggestion of Ethan A Merritt and it seems that by this
way it is possible to overcome the problem. Although, the final
R-factors are about the same as without B anisotropic refinement.
So my question is, why B individual factors are growing when one tries
to use  both B-anisotropic refinement and bulk solvent correction. Is
there a bug in X-plor 3.851?
If anyone has any thoughts on this I would appreciate it.


--
Dr. Simon Terzyan
Crystallography Department of OMRF
tel: (405) 2717543 fax: (405) 2713980
email:terzyans at omega.omrf.ouhsc.edu



--------------38D5B42720EF74F9A121A962
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
&nbsp;
<br>Dear X-PLOR users,
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; I am in the late stages of refinement
of a 2.3 angstrom Fab structure
<br>in P212121 with 2 molecules in the assymetric part. The R factors after
positional and B individual refinements in the resolution range 8.-2.3
A are R=0.237 and Rfree= 0.314.
<br>When I am using bulk solvent correction they become ( 25-2.3A) 0.231
and 0.303, correspondingly. But after it&nbsp; the electron density&nbsp;
for the residues on the surface of the molecules&nbsp; is worse than before.
<br>Refinement of anisotropic B_overall ( without bulk solvent correction,
8-2.3A ) gives R factors 0.214 and 0.289.&nbsp; Further bulk solvent correction
and positional and B individual refinemt drops the R factors to 0.199 and
0.266. As it was already mentioned in one of previos letters from Christelle
Sabatier (Message-ID: &lt;v03007800b02211264fa6@[128.206.29.205]>) this
refinement increases the mean value of B factors. And furthermore, if I
go for a second cycle then the B factors increase more.
<br>I have used also suggestion of Ethan A Merritt and it seems that by
this way it is possible to overcome the problem. Although, the final R-factors
are about the same as without B anisotropic refinement.
<br>So my question is, why B individual factors are growing when one tries
to use&nbsp; both B-anisotropic refinement and bulk solvent correction.
Is there a bug in X-plor 3.851?
<br>If anyone has any thoughts on this I would appreciate it.
<br>&nbsp;
<pre>--&nbsp;
Dr. Simon Terzyan
Crystallography Department of OMRF
tel: (405) 2717543 fax: (405) 2713980
email:terzyans at omega.omrf.ouhsc.edu</pre>
&nbsp;</html>

--------------38D5B42720EF74F9A121A962--

--------------92CCADDA327BE086090879DE
Content-Type: text/x-vcard; charset=us-ascii;
 name="terzyans.vcf"
Content-Transfer-Encoding: 7bit
Content-Description: Card for Simon Terzyan
Content-Disposition: attachment;
 filename="terzyans.vcf"

begin:vcard 
n:Terzyan;Simon 
x-mozilla-html:FALSE
org:OMRF
version:2.1
email;internet:terzyans at omega.omrf.ouhsc.edu
title:Research Scientist, Ph.D.
x-mozilla-cpt:;0
fn:Simon  Terzyan
end:vcard

--------------92CCADDA327BE086090879DE--





More information about the X-plor mailing list