<div dir="ltr"><div>Dear Randy,</div><div><br></div><div>Thank you for your suggestion. I should mention that I have tried with single copy, best fitted dimer as well with the whole structure (on different set of runs) but in al the cases PhaserMR is unable to produce identical number of copies comparable with the solved structure although the cell dimension and space group is same with the solved one. What can be the possible reason and how to get rid of that?</div><div><br></div><div>Thanks again for your reply.<br></div><div><br></div><div> <br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Apr 9, 2020 at 4:30 AM Randy Read <<a href="mailto:rjr27@cam.ac.uk">rjr27@cam.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear Shramana,<br>
<br>
I may be reading this incorrectly, but it sounds like you’re providing the entire PDB file from the solved model to Phaser to solve the other structure by MR. You need to edit the PDB file before using it as a model so that what you have is a sensible model for what is in the other crystal form, because Phaser will just take the whole thing as a single rigid body. Given the 100% sequence identity, I would use a single copy as a model and search for the appropriate number of copies (perhaps 4, from what you say). If the model was more distant, then it might be worth looking at it to see if it could plausibly be a dimer or tetramer in solution, and then you could use a higher-order structure. But MR with identical models can usually place a reasonable number of copies independently, and then you don’t have to make any assumptions about quaternary structure.<br>
<br>
Best wishes,<br>
<br>
Randy Read<br>
<br>
-----<br>
Randy J. Read<br>
Department of Haematology, University of Cambridge<br>
Cambridge Institute for Medical Research Tel: +44 1223 336500<br>
The Keith Peters Building Fax: +44 1223 336827<br>
Hills Road E-mail: <a href="mailto:rjr27@cam.ac.uk" target="_blank">rjr27@cam.ac.uk</a><br>
Cambridge CB2 0XY, U.K. <a href="http://www-structmed.cimr.cam.ac.uk" rel="noreferrer" target="_blank">www-structmed.cimr.cam.ac.uk</a><br>
<br>
> On 9 Apr 2020, at 04:43, Shramana Chatterjee <<a href="mailto:schatter90@gmail.com" target="_blank">schatter90@gmail.com</a>> wrote:<br>
> <br>
> Hi,<br>
> <br>
> I am trying to solve a structure using a data solved by SAD as an reference (ensemble in phaser). The structure I am trying to solve has 100% sequence identity with the solved one. The problem that I am facing during Phaser MR is that, in the solved structure there are 6 molecules in the ASU although I am getting maximum 4 molecules in the ASU and also Rfree is around 0.49 just after the phaser. Phaser is showing a good values of LLG (>500) and TFZ (>8).<br>
> <br>
> It would be very helpful if I get any suggestion about the above-mentioned problem.<br>
> <br>
> Thank you in advance.<br>
> <br>
> <br>
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</blockquote></div>