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Hi Ulrich,<br>
<br>
in your parameter file just add another map scope to the
electron_density_maps scope, like this:<br>
<br>
<font face="Courier New, Courier, monospace"> electron_density_maps {<br>
map {<br>
mtz_label_amplitudes = "2FOFCWT_kick"<br>
mtz_label_phases = "PH2FOFCWT_kick"<br>
likelihood_weighted = True<br>
obs_factor = 2<br>
calc_factor = 1<br>
kicked = True<br>
fill_missing_f_obs_with_weighted_f_model = False<br>
}<br>
map {<br>
mtz_label_amplitudes = "FOFCWT_kick"<br>
mtz_label_phases = "PHFOFCWT_kick"<br>
likelihood_weighted = True<br>
obs_factor = 1<br>
calc_factor = 1<br>
kicked = True<br>
fill_missing_f_obs_with_weighted_f_model = False<br>
}<br>
}<br>
</font><br>
This will create two additional kick maps in addition to the default
maps.<br>
<br>
Pavel.<br>
<br>
<br>
<br>
On 8/28/09 9:53 AM, Ulrich Baumann wrote:
<blockquote cite="mid:B57912AA44EC4229A124FB6203A25A92@unibe.ch"
type="cite">
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<div><font face="Arial" size="2">Pavel, how can I specify the request
for averaged Kick Maps on the command line , please?</font></div>
<div> </div>
<div><font face="Arial" size="2">Cheers,</font></div>
<div><font face="Arial" size="2">Uli</font></div>
<blockquote
style="border-left: 2px solid rgb(0, 0, 0); padding-right: 0px; padding-left: 5px; margin-left: 5px; margin-right: 0px;">
<div
style="font-family: arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">-----
Original Message ----- </div>
<div
style="background: rgb(228, 228, 228) none repeat scroll 0%; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial; font-family: arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"><b>From:</b>
<a moz-do-not-send="true" title="PAfonine@lbl.gov"
href="mailto:PAfonine@lbl.gov">Pavel Afonine</a> </div>
<div
style="font-family: arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"><b>To:</b>
<a moz-do-not-send="true" title="qunwan1@gmail.com"
href="mailto:qunwan1@gmail.com">qunwan1@gmail.com</a> ; <a
moz-do-not-send="true" title="phenixbb@phenix-online.org"
href="mailto:phenixbb@phenix-online.org">PHENIX user mailing list</a> </div>
<div
style="font-family: arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"><b>Sent:</b>
Friday, August 28, 2009 6:31 PM</div>
<div
style="font-family: arial; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"><b>Subject:</b>
Re: [phenixbb] question about composite SA_omit map in phenix</div>
<div><br>
</div>
Hi Qun Wan,<br>
<br>
Alternatively, you can ask phenix.refine to compute Average Kick Map,
which is expected to be less biased or less noisy. For more details
about kick map, see recent publication:<br>
<br>
Acta Cryst. (2009). D65, 921-931.<br>
<br>
Please let me know if you have questions.<br>
<br>
Pavel.<br>
<br>
<br>
On 8/28/09 7:52 AM, crystallogrphy wrote:
<blockquote
cite="mid:33fd30c80908280752q468277deidd9ed31e65f392c0@mail.gmail.com"
type="cite">Hi, <br>
I am using molecular replacement to build a model against a 2.2A
resolution data set. However, the template model only has 23% sequence
identity. First, I use chainsaw in CCP4i to prune all side chain to be
poly-Ala except the identical residues. Then I use AutoMR and rigid
body refinement, I got Rfree=50%. The continuous electron density is
not bad showing second structures. However, the model has some
out-of-registration problem, for example, two proline are in a
alpha-helix. In other words, it has model bias. I want to use composite
SA-omit to get a less model bias map, not a simple composite omit map
or a SA_omit map ommiting a part of the region. <br>
Does someone know who to do this?<br>
<br>
Thanks!<br>
<br>
Qun Wan<br>
postdoc fellow <br>
Case Western Reserve University<br>
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