<html><head></head><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div dir="ltr" id="yui_3_16_0_1_1455556180156_6356"><span id="yui_3_16_0_1_1455556180156_6650">Thank you for valuable advice of the BB. Negative density is observed between sulfur atoms of the disulfide pair, and positive density at the opposite side of the SG atom. I guess it is partial reduction due to radiation damage. Now, I refined using a altlocs and disulfide_bond_exclusions_selection_string to avoid forming a disulfide by altlocs of SG (because the rotamer is the same that the disulfide pair). Around 70 % occupancy is obtained for reduced Cys, and distances between SG increased near to 3 A. Difference density mostly dissapeared. I suppose is better to model only as disulfide for deposition, because reduction is "artifactual" from biological point of view, but it is other discussion... Thank you!</span></div><div id="yui_3_16_0_1_1455556180156_7079" dir="ltr"><span id="yui_3_16_0_1_1455556180156_6650">Ezequiel</span></div> <div class="qtdSeparateBR"><br><br></div><div style="display: block;" class="yahoo_quoted"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"><font face="Arial" size="2"> El Lunes, 15 de febrero, 2016 8:41:49, Pavel Afonine <pafonine@lbl.gov> escribió:<br></font></div> <br><br> <div class="y_msg_container"><div id="yiv2037798344"><div>
Hi Ezequiel,<div class="yiv2037798344yqt0279328783" id="yiv2037798344yqtfd56217"><br clear="none">
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</div><div style="color:#000;background-color:#fff;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"><div class="yiv2037798344yqt0279328783" id="yiv2037798344yqtfd44803">
</div><div dir="ltr" id="yiv2037798344yui_3_16_0_1_1455483927872_4897"><div class="yiv2037798344yqt0279328783" id="yiv2037798344yqtfd83882">Sorry, my
previous email was incomplete. My structure has negative
density in the center of some disulfides (the magnitude of
this effect vary between different monomers in the ASU). I'd
like to refine the structure in an "artificial reduced form",
where cysteines involved in disulfides are treated in reduced
form, but repulsions originating from neighboring sulfur atoms
are turned-off, to monitor distances (I expect that SG atoms
remain close to 2 A), guided only by data.</div><br clear="none">
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there is no option like "disable non-bonded repulsions in a sphere
R=??? Angstroms around given atom". However, there are couple of
tricks to do what you want, such as defining bonds between atoms in
question with large sigma which will make them invisible to
restraints and also disable repulsions. Or playing with altlocs. <br clear="none">
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You can check .geo file to see exactly what restraints atom in
question participates in.<br clear="none">
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Pavel<div class="yiv2037798344yqt0279328783" id="yiv2037798344yqtfd23446"><br clear="none">
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