<div dir="ltr"><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:16px;line-height:normal;font-family:"Times New Roman";color:rgb(0,0,0)"><span class="gmail-s1" style="font-kerning:none">Hello All,</span></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:16px;line-height:normal;font-family:"Times New Roman";color:rgb(0,0,0)"><span class="gmail-s1" style="font-kerning:none"><br></span></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:16px;line-height:normal;font-family:"Times New Roman";color:rgb(0,0,0)"><span class="gmail-s1" style="font-kerning:none">I have several questions regarding sugar modeling. These are questions for both Coot (0.9.4-pre/CCPEM) and Phenix (1.18.2-3874) usage (on a Mac) for modeling as correctly as possible several N-linked glycosylation (i.e. not ligand) sugars within a protein, and about the approach as it pertains to higher resolution X-ray maps (better than 2A) or to lower resolution EM maps (~3-4A). I am new to the world of glycoproteins and cryoEM, not new to model building or X-ray crystallography, and would welcome any advice or insight.</span></p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:16px;line-height:normal;font-family:"Times New Roman";color:rgb(0,0,0);min-height:18px"><span class="gmail-s1" style="font-kerning:none"></span><br></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:16px;line-height:normal;font-family:"Times New Roman";color:rgb(0,0,0)"><span class="gmail-s1" style="font-kerning:none">For relatively low resolution maps, where sugar moieties cannot be placed unambiguously, in theory (say Agirre<span class="gmail-Apple-converted-space"> </span>(2017) and Emsley and Crispin (2018)) pyranose placement within the map should be quite highly restrained by ideal geometry for the specific sugar expected from prior knowledge. In practice, however, it’s not entirely clear how to maintain these restraints on pyranose geometry and conformation during manual building in Coot, or how to apply any special restraints in Phenix. The Glyco module of Coot does indeed place fine looking Asn-NAGs after a few iterations of manual placing and refining to account for the poor resolution of the acetyl group, just as discussed by Emsley and Crispin (2018). However, the validation report that is obtained from the OneDep system at the rcsb web server for the resulting structure shows many outliers in bonds and angles within the NAG or between the NAG and protein Asn residue. In Coot I have experimented with various restraints<span class="gmail-Apple-converted-space"> </span>(in the R/RC menu), including decreasing the Refinement weight/weight matrix to zero, or some small non-zero number, thinking this places less weight on the map signal and more on the ideal values within Coot’s libraries. I have tried a variety of refinement restraint combinations in Coot to address individual bonds and angles outliers within the sugar, but the rcsb validation report still finds departures from ideal geometry. Meanwhile, in Phenix I don’t do anything specific for the refinement of glycosylation sugars (should I?) other than apply the appropriate restraints for any low resolution EM map; are there specific restraints files I ought to be using within Phenix real space refine jobs for N-linked sugars?</span></p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:16px;line-height:normal;font-family:"Times New Roman";color:rgb(0,0,0);min-height:18px"><span class="gmail-s1" style="font-kerning:none"></span><br></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:16px;line-height:normal;font-family:"Times New Roman";color:rgb(0,0,0)"><span class="gmail-s1" style="font-kerning:none">Then I noticed that loads of existing PDB entries containing N-linked glycans contain similar outliers in pyranose geometry. So this prompted me to wonder whether we’re not doing things right, that in practice we’re not correctly following what’s advised in theory, or whether this is just the state of model building currently. Could someone more experienced than am I on sugar building please comment here on how exactly to get the sugars better built? e.g. what buttons to press and why, in Phenix and/or in Coot. Or is this a tolerable situation where sugar geometries differ from ideal even at low resolution? Is it perhaps a matter of different targets being used for PDB validation by the rcsb versus by Coot?</span></p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:16px;line-height:normal;font-family:"Times New Roman";color:rgb(0,0,0);min-height:18px"><span class="gmail-s1" style="font-kerning:none"></span><br></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:16px;line-height:normal;font-family:"Times New Roman";color:rgb(0,0,0)"><span class="gmail-s1" style="font-kerning:none">It turns out that regarding higher resolution maps I am also unsure of exactly how to apply restraints within Coot. For example, using PDB ID 5VAA and its map with a reported resolution of 1.55A, I centered on Asn297 and its associated glycosylation sugars. I experimented with refinement strategies (i.e. the settings of R/RC), thinking that the best approach would be little restraint on ideal geometry and higher weight on the map signal. But no matter what combination of restraints I used, I was unable to keep the model locally from distorting; i.e. the deposited model versus map looks great, but within Coot I find a hundred ways to destroy it. I must be doing something wrong.<span class="gmail-Apple-converted-space"> </span></span></p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:16px;line-height:normal;font-family:"Times New Roman";color:rgb(0,0,0);min-height:18px"><span class="gmail-s1" style="font-kerning:none"></span><br></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:16px;line-height:normal;font-family:"Times New Roman";color:rgb(0,0,0)"><span class="gmail-s1" style="font-kerning:none">Any advice or references you’d recommend would be greatly appreciated.</span></p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:16px;line-height:normal;font-family:"Times New Roman";color:rgb(0,0,0);min-height:18px"><span class="gmail-s1" style="font-kerning:none"></span><br></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:16px;line-height:normal;font-family:"Times New Roman";color:rgb(0,0,0)"><span class="gmail-s1" style="font-kerning:none">Thanks.</span></p><div><br></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr">"<span style="font-size:small">Study as if you were going to live forever; live as if you were going to die tomorrow." </span><span style="font-size:small">- Maria Mitchell</span><span style="font-size:small"><br></span></div><div dir="ltr"><div><div><br></div><div>"I'm not afraid of storms for I'm learning to sail my ship." - Louisa May Alcott<br><br></div></div></div></div></div></div></div></div></div></div>