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<DIV><SPAN class=578200300-20032009><FONT face=Cambria color=#0000ff>As far as I
recall the write-hydrogens options is an expert option, depending on the version
of elbow. Check out the elbow documentation on how to become an expert.
</FONT></SPAN></DIV>
<DIV><SPAN class=578200300-20032009><FONT face=Cambria
color=#0000ff></FONT></SPAN> </DIV>
<DIV><SPAN class=578200300-20032009><FONT face=Cambria color=#0000ff>As far as
hydrogens are concerned, I would second Nigel's concern. Adding hydrogens in
riding mode has the very real potential of improving the geometry of your
structure due to the imposed anti-bumping restraints. You could try refinement
with and without and see where it takes you. </FONT></SPAN></DIV>
<DIV><SPAN class=578200300-20032009><FONT face=Cambria color=#0000ff>As a note
of caution, elbow writes (Nigel correct me if I am wrong) PDB V3 compatible
hydrogen names, which may cause some graphics programs to choke. Newer versions
of coot (0.5.2 or later) seem to work fine. </FONT></SPAN></DIV>
<DIV><SPAN class=578200300-20032009><FONT face=Cambria
color=#0000ff></FONT></SPAN> </DIV>
<DIV><SPAN class=578200300-20032009><FONT face=Cambria
color=#0000ff>HTH</FONT></SPAN></DIV>
<DIV><SPAN class=578200300-20032009><FONT face=Cambria
color=#0000ff></FONT></SPAN> </DIV>
<DIV><SPAN class=578200300-20032009> <FONT face=Cambria
color=#0000ff>Carsten</FONT></SPAN></DIV>
<BLOCKQUOTE>
<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Original Message-----<BR><B>From:</B>
phenixbb-bounces@phenix-online.org
[mailto:phenixbb-bounces@phenix-online.org]<B>On Behalf Of
</B>crystallogrphy<BR><B>Sent:</B> Thursday, March 19, 2009 7:22
PM<BR><B>To:</B> phenixbb@phenix-online.org<BR><B>Subject:</B> [phenixbb]
question about generating cif and pdb file using elbow<BR><BR></FONT></DIV><BR
clear=all>Hi, <BR>I am using phenix.elbow to generate pdb and cif files with
the tripos format file:<BR>
<META content="OpenOffice.org 2.0 (Unix)" name=GENERATOR>
<META content=qun_wan name=AUTHOR>
<META content=20090318;14212000 name=CREATED>
<META content=qun_wan name=CHANGEDBY>
<META content=20090319;20070300 name=CHANGED>
<STYLE>UNKNOWN {
MARGIN: 0.79in; size: 8.5in 11in
}
P {
MARGIN-BOTTOM: 0.08in
}
</STYLE>
<OL start=5>
<P style="MARGIN-BOTTOM: 0in">phenix.elbow --initial_geometry egcg.mol2
--opt --output="LIG" --pdb-ligand</P></OL>The input pdb file contains hydrogen
atoms and the output pdb file also contains hydrogen atom. My crystal data
only difftracted to 2.4A, so hydrogen atoms cannot be seen. In the refinement,
my ligand should not contain hydrogen atoms. So I add one more option not to
add hydrogen following the online phenix documentation:<BR>
<META content="OpenOffice.org 2.0 (Unix)" name=GENERATOR>
<META content=qun_wan name=AUTHOR>
<META content=20090318;14212000 name=CREATED>
<META content=qun_wan name=CHANGEDBY>
<META content=20090319;20070300 name=CHANGED>
<STYLE>UNKNOWN {
MARGIN: 0.79in; size: 8.5in 11in
}
P {
MARGIN-BOTTOM: 0.08in
}
</STYLE>
<OL start=5>
<P style="MARGIN-BOTTOM: 0in">phenix.elbow --initial_geometry
--write-hydrogens=False egcg.mol2 --opt --output="LIG"
--pdb-ligand</P></OL><B>However, the program failed. Does anyone know
why?</B><BR>Usage: phenix.elbow [options]<BR><B>phenix.elbow: error: no such
option: --write-hydrogens</B><BR><BR>-- <BR>Qun Wan<BR>Department of
Pharmacology, Case Western Reserve University<BR>10900 Euclid Avenue,
Cleveland, OH 44106<BR>email: <A
href="mailto:qunwan1@gmail.com">qunwan1@gmail.com</A><BR>lab phone:
216-368-3337<BR></BLOCKQUOTE></BODY></HTML>