<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Dear Tom and Elaine<div><br></div><div>The suggestion to use the vop resample command works very well - many thanks</div><div><br></div><div>@Tom: If we could have the script which does the map on the second grid without interpolation that would be very useful. We would like to run FSCs as well between the different ways maps are being derived from models and it would be interesting to see to what extent the interpolation affects things at different spatial frequencies.</div><div><br></div><div>Many thanks and best wishes</div><div><br><div><div>On 26 May 2016, at 19:26, Tom Goddard <<a href="mailto:goddard@sonic.net">goddard@sonic.net</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=utf-8"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Ardan,<div class=""><br class=""></div><div class=""> Sounds like you want the molmap calculated map to have a grid that exactly matches a second map which is a cube centered on the molecule. The way to do that is compute the molmap in the normal way then use “vop resample” to interpolate the molmap map on exactly the grid of the second map. This is more reliable than trying to figure out the molecule center and make a matching cube map without using the second map. I can think of at least 3 reasonable ways to define the center (equal weighted atoms, mass weighted atoms, bounding box center) and it is just too easy to get a grid that doesn’t really match the second map. So if #0 is your molecule and #1 is your second map use</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>molmap #0 5 gridSpacing 1.3 model #2</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>vop resample #2 onGrid #1 model #3</div><div class=""><br class=""></div><div class="">then map #3 will exactly match the grid of map #1. The interpolation is trilinear (using nearest 8 grid points) and will be very close to the exact values you would obtain by using the second map grid to sum the atom Gaussians. If you really want the exact sum of Gaussians on the second map grid with no interpolation step I can give you a Chimera Python script that will do that.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div><blockquote type="cite" class=""><div class="">On May 26, 2016, at 12:43 AM, Ardan Patwardhan wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear all<div class=""><br class=""></div><div class="">We are using Chimera to align PDB models to maps, then creating maps from the models using the following command (as an example):</div><div class="">molmap #0 5 gridSpacing 1.3</div><div class=""><br class=""></div><div class="">This should create a map with the voxel spacing of 1.3A and a gaussian atom spread function with the width related to 5A resolution (<a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html</a>).</div><div class=""><br class=""></div><div class="">Our problem is</div><div class="">a) the map that is created can have an arbitrary size - we need it to be cubic and have the same (known) dimensions as the second map against which it will be compared</div><div class="">b) we have tried padding it in other programs like bsoft but then we sometimes run into problems of centring the model.</div><div class=""><br class=""></div><div class="">I was wondering if there was a way to get a centred map of a certain size from a model directly from Chimera?</div><div class="">Perhaps there are certain parameters that can be used in molmap?</div><div class=""><br class=""></div><div class="">You thoughts and advice on this issue are much appreciated!</div><div class=""><br class=""></div><div class="">Many thanks and best wishes</div><div class=""><br class=""></div><div class=""><div class="">
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Ardan Patwardhan</div><div class="">Coordinator - cellular structure & PDBe production<br class="">Protein Data Bank in Europe (PDBe)</div><div class="">European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory<br class="">Wellcome Trust Genome Campus<br class="">Hinxton, Cambridge CB10 1SD<br class="">Tel: +44 1223 492649</div></div></div>
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