Dear Gabor,<div><br></div><div>Thanks a lot for your detailed explanation and kind help. I tried your comment. The two ways of defining search procedure gave me the same solution. </div><div><br></div><div>For </div><div><br>
</div><div><meta http-equiv="content-type" content="text/html; charset=utf-8"><span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; ">search {<br> ensembles = a1<br>
copies = 1<br>}<br>search {<br> ensembles = a2<br> copies = 1<br>}<br><br></span></div><div><span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; ">I got also only one result contains one best molecule pdb. Would you have some idea for this? How could I really get several output for each of the input model?</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; "><br></span></div><div><span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; ">Thanks and regards,</span></div>
<div><span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; ">G</span></div><div><span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; "><br>
</span></div><div> <br><br><div class="gmail_quote">On Mon, Aug 8, 2011 at 3:13 PM, Dr G. Bunkoczi <span dir="ltr"><<a href="mailto:gb360@cam.ac.uk">gb360@cam.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Dear G,<br>
<br>
after carefully re-reading your email, I think I have only given half of the answer. By repeating the 'coordinates' scope, you are defining one ensemble using multiple PDB files. If you want to define multiple ensembles, you need to repeat the whole ensemble scope, i.e.<div class="im">
<br>
<br>
ensemble {<br>
model_id = a1<br>
coordinates {<br>
pdb = model1.pdb<br>
identity = 0.9<br>
}<br>
}<br></div>
ensemble {<br>
model_id = a2 <= note the change in model_id<div class="im"><br>
coordinates {<br>
pdb = model2.pdb<br>
identity = 0.9<br>
}<br>
}<br>
<br></div>
If you want Phaser to actually search for all these ensembles, you need to add a search keyword as well:<br>
<br>
1. Conduct a separate search for each ensemble listed. The search order is decided automatically. The solution contains one molecule of a1 + one molecule of a2.<br>
<br>
search {<br>
ensembles = a1<br>
copies = 1<br>
}<br>
search {<br>
ensembles = a2<br>
copies = 1<br>
}<br>
<br>
<br>
2. Phaser will search for each alternative ensembles in turn and pick the best one (the solution will contain one molecule of a1 or one molecule of a2, but not both):<br>
<br>
search {<br>
ensembles = a1,a2<br>
copies = 1<br>
}<br>
<br>
HTH, Gabor<div><div></div><div class="h5"><br>
<br>
<br>
On Aug 8 2011, Dr G. Bunkoczi wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear G,<br>
<br>
I think 'coordinates' is a multiple scope, so you have to define your ensemble as follows:<br>
<br>
ensemble {<br>
model_id = a1<br>
coordinates {<br>
pdb = model1.pdb<br>
identity = 0.9<br>
}<br>
coordinates {<br>
pdb = model2.pdb<br>
identity = 0.9<br>
}<br>
coordinates {<br>
pdb = model3.pdb<br>
identity = 0.9<br>
}<br>
coordinates {<br>
pdb = model4.pdb<br>
identity = 0.9<br>
}<br>
}<br>
<br>
BW, Gabor<br>
<br>
On Aug 8 2011, G Y wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear all,<br>
<br>
I am writing a bash script for running phenix.phaser automatically on an ensemble of multiple pdbs. These pdbs have been superimposed by other tools before running phaser.<br>
<br>
The following is what I wrote for the ensemble part in params.eff file:<br>
<br>
ensemble {<br>
model_id = a1<br>
coordinates {<br>
pdb = model1.pdb<br>
pdb = model2.pdb<br>
pdb = model3.pdb<br>
pdb = model4.pdb<br>
rmsd = None<br>
identity = 0.9<br>
}<br>
<br>
It runs well. When it finished, I want to confirm that it really run MR on<br>
all four models or on a ensemble of these models. However in .log file, I<br>
found at the refinement part it shown me:<br>
<br>
----------<br>
REFINEMENT<br>
----------<br>
<br>
There is 1 solution to refine<br>
Refining solutions<br>
0% 100%<br>
|==| DONE<br>
<br>
<br>
Configuring ensembles<br>
---------------------<br>
PDB file # 1: model1.pdb<br>
This pdb file contains 1 models<br>
The (input) RmsD of this model with respect to the real structure is<br>
0.8<br>
<br>
**************************** Does this mean that phenix.phaser only run MR with the first model? Does it due to the way I wrote in my params.eff file? What would be the correct way?<br>
<br>
Many thanks!<br>
<br>
best,<br>
G<br>
<br>
</blockquote>
<br>
<br>
</blockquote>
<br>
-- <br>
##############################<u></u>####################<br>
<br>
Dr Gabor Bunkoczi<br>
<br>
Cambridge Institute for Medical Research<br>
Wellcome Trust/MRC Building<br>
Addenbrooke's Hospital<br>
Hills Road<br>
Cambridge CB2 0XY<br>
##############################<u></u>####################<br>
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