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<p style="margin-top:0;margin-bottom:0">Dear Sonali,</p>
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<p style="margin-top:0;margin-bottom:0">I guess you mean a spherical mask. I am not familiar with dynamo but if t produces a binary mask, try creating a soft mask (for example using spider): this will emphasize the masked region without leaving out the densities
outside the mask.</p>
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<p style="margin-top:0;margin-bottom:0">Best wishes,</p>
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<p>Montserrat Samso, Ph.D.</p>
<p>Assistant Professor</p>
<p>Director, CryoEM Facility</p>
<p>Dept. Physiology and Biophysics</p>
<p>Virginia Commonwealth University</p>
<p>1101 E. Marshall St., RM 3-009</p>
<p>Richmond, VA 23298</p>
<p></p>
<p style="margin-top:0px; margin-bottom:0px">Tel: (804) 828-8728</p>
<p style="margin-top:0px; margin-bottom:0px">Fax: (804) 828-8492</p>
<p></p>
<p>E-mail: Montserrat.Samso@vcuhealth.org</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of Sonali Dhindwal <sdhindwal@ccny.cuny.edu><br>
<b>Sent:</b> Tuesday, December 26, 2017 9:14:23 AM<br>
<b>To:</b> 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> [EXTERNAL] [3dem] focused refinement</font>
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<span style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">Dear All,</span></p>
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<span style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><br>
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<span style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">I have a query regarding focused refinement. </span></p>
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I have a complex that I am trying to refine using Class3D and Refine3D module in relion.<br>
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<p style="background-color:rgb(255,255,255); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
Due to the possible heterogeneity in positioning of these interacting partner with respect to each other, I have created a circular mask using dynamo and using it in relion to mask one of the interacting partner, so that the refinement focuses on it not the
other interacting partner. But in doing so, it just chops the region outside the mask. </p>
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<br>
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<p style="background-color:rgb(255,255,255); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">
Please guide, how to create mask so that refinement program just put less weight on the structure outside the mask and not removing it and do refinement on the structure focusing in the inside of mask.<br>
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Thanks and Regards<br>
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