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Hello,</div>
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I am using molmap to simulate cryo-em density maps from protein pdb file. I follow the two steps outlined in Chimera tutorial (<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html#onGrid">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html#onGrid</a>). </div>
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I first create an empty map with specific size, grid spacing, and origin. </div>
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vop new #1 size 116,96,152 gridspacing 1 origin -99.0,-39.0,-58.0</div>
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Then simulate the pdb file on the empty map using the option the grid spacing </div>
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molmap #0 3 onGrid #1</div>
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<font color="#000000" face="Calibri, Arial, Helvetica, sans-serif">the resulting simulated map has grid spacing changed from 1A to 2A and the origin coordinates are also changed to half the values I provided. This does not happen with all cases. The following
commands work perfectly and generate a simulated map with grid spacing of 1A</font>
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<div><font color="#000000" face="Calibri, Arial, Helvetica, sans-serif">vop new #1 size 78,88,121 gridspacing 1 origin -32.73,-28.64,-63.42</font></div>
<div><font color="#000000" face="Calibri, Arial, Helvetica, sans-serif">molmap #0 3 onGrid #1 </font></div>
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<div><font color="#000000" face="Calibri, Arial, Helvetica, sans-serif">I can re-sample the map to obtain 1A grid spacing, but it adds extra work (I doing this to 100s of examples) and seems to affect the resolution of the simulated map.</font></div>
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<div><font color="#000000" face="Calibri, Arial, Helvetica, sans-serif">Could you please adive me to why is this phenomenon is happening and how to solve it.</font></div>
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<div><font color="#000000" face="Calibri, Arial, Helvetica, sans-serif">best regards <br>
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<p style="margin-top: 0px; margin-bottom: 0px;"><b>Anes Ouadou</b><span><b> </b> </span></p>
<p style="margin-top: 0px; margin-bottom: 0px;"><span>CS PhD Student<span> </span></span></p>
<p style="margin-top: 0px; margin-bottom: 0px;"><span><span>University of Missouri-Columbia</span></span></p>
<p style="margin-top: 0px; margin-bottom: 0px;"><span><span>aomqc@mail.missouri.edu<span> </span></span></span></p>
<p style="margin-top: 0px; margin-bottom: 0px;"><span><span><span>Mobile: (573 )-289-9073</span></span></span></p>
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