No subject

adding water and ions (probably the + sign).
Choose other and enter Mg then click ok.
This will place a Mg2+ in that blob of yours. Save it and refine it.

Do the whole thing while your pointer in your coot is placed in the middle
of the blob where you want to put Mg.

Happy modelling !

Best,
Abhisek


On Mon, Jul 6, 2020 at 4:16 PM Shirin Akbar <shirin.akbar09 at gmail.com>
wrote:

> Dear all,
>
> I am using the phenix.real_space_refine program for refinement of crystal
> structure in cryo-EM map (ribosome map, 3.4 A resolution). Prior to
> real_space_refinement I had removed all the heteroatoms. What is the
> correct way to add the cations (eg. Mg2+ ions) to the structure and how do
> I do it? Can anyone kindly suggest..
>
> Thanks & Regards
> Shirin
>
> --
> *Shirin Akbar*
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org



-- 
*Abhisek Mondal, Ph.D.*











*Cardiovascular Research InstituteUniversity of California San Francisco555
Mission Bay Blvd. South. Rm 482Dan Minor's LabSan Francisco, CA 94158USPS
address:UCSFAbhisek Mondal, Ph.D.Cardiovascular Research Institute, Box
3122555 Mission Bay Blvd., Floor 4San Francisco, CA 94143*

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<div dir=3D"ltr">Hi Shirin,<div><br></div><div>You=C2=A0can not add hetam i=
n phenix. You have to do it while building your model in coot.</div><div>Fr=
om the right toolbar in the coot, you&#39;ll find an option to be used for =
adding water and ions (probably the + sign).</div><div>Choose other and ent=
er Mg then click ok.=C2=A0</div><div>This will place a Mg2+ in that blob of=
 yours. Save it and refine it.</div><div><br></div><div>Do the whole thing =
while your pointer in your coot is placed in the middle of the blob where y=
ou want to put Mg.</div><div><br></div><div>Happy modelling !</div><div><br=
></div><div>Best,</div><div>Abhisek</div><div><br></div></div><br><div clas=
s=3D"gmail_quote"><div dir=3D"ltr" class=3D"gmail_attr">On Mon, Jul 6, 2020=
 at 4:16 PM Shirin Akbar &lt;<a href=3D"mailto:shirin.akbar09 at gmail.com">sh=
irin.akbar09 at gmail.com</a>&gt; wrote:<br></div><blockquote class=3D"gmail_q=
uote" style=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,2=
04);padding-left:1ex"><div dir=3D"ltr">Dear all,<div><br></div><div>I am us=
ing the phenix.real_space_refine program for refinement of crystal structur=
e in cryo-EM map=C2=A0(ribosome map, 3.4 A resolution). Prior to real_space=
_refinement I had removed all the heteroatoms. What is the correct way to a=
dd the cations (eg. Mg2+ ions) to the structure=C2=A0and how do I do it? Ca=
n anyone kindly suggest..</div><div>=C2=A0</div><div>Thanks &amp; Regards</=
div><div>Shirin</div><div><div><br></div>-- <br><div dir=3D"ltr"><div dir=
=3D"ltr"><div><div dir=3D"ltr"><b><font size=3D"2">Shirin Akbar</font></b><=
div><br></div></div></div></div></div></div></div>
_______________________________________________<br>
phenixbb mailing list<br>
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enix-online.org</a><br>
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errer" target=3D"_blank">http://phenix-online.org/mailman/listinfo/phenixbb=
</a><br>
Unsubscribe: <a href=3D"mailto:phenixbb-leave at phenix-online.org" target=3D"=
_blank">phenixbb-leave at phenix-online.org</a></blockquote></div><br clear=3D=
"all"><div><br></div>-- <br><div dir=3D"ltr" class=3D"gmail_signature"><div=
 dir=3D"ltr"><div><div dir=3D"ltr"><div dir=3D"ltr"><div dir=3D"ltr"><div d=
ir=3D"ltr"><div dir=3D"ltr"><div dir=3D"ltr"><div dir=3D"ltr"><div style=3D=
"margin:0px;padding:0px;border:0px;font-stretch:inherit;line-height:inherit=
;vertical-align:baseline;color:rgb(0,0,0)"><i><font face=3D"arial, helvetic=
a, sans-serif">Abhisek Mondal, Ph.D.</font></i></div><div style=3D"margin:0=
px;padding:0px;border:0px;font-stretch:inherit;line-height:inherit;vertical=
-align:baseline;color:rgb(0,0,0)"><i><span style=3D"font-family:Helvetica">=
Cardiovascular Research=C2=A0Institute</span><br style=3D"font-family:Helve=
tica"><span style=3D"font-family:Helvetica">University of California San=C2=
=A0Francisco</span><br style=3D"font-family:Helvetica"><span style=3D"font-=
family:Helvetica">555 Mission Bay Blvd. South.=C2=A0Rm 482</span><br style=
=3D"font-family:Helvetica"><span style=3D"font-family:Helvetica">Dan Minor&=
#39;s Lab</span><br style=3D"font-family:Helvetica"><span style=3D"font-fam=
ily:Helvetica">San Francisco, CA 94158</span><br style=3D"font-family:Helve=
tica"><br style=3D"font-family:Helvetica"><span style=3D"font-family:Helvet=
ica">USPS address:</span><br style=3D"font-family:Helvetica"><span style=3D=
"font-family:Helvetica">UCSF</span><br style=3D"font-family:Helvetica"><spa=
n style=3D"font-family:Helvetica">Abhisek Mondal, Ph.D.</span><br style=3D"=
font-family:Helvetica"><span style=3D"font-family:Helvetica">Cardiovascular=
 Research=C2=A0Institute, Box 3122</span><br style=3D"font-family:Helvetica=
"><span style=3D"font-family:Helvetica">555 Mission Bay Blvd., Floor 4</spa=
n><br style=3D"font-family:Helvetica"><span style=3D"font-family:Helvetica"=
>San Francisco, CA 94143</span></i><br></div></div></div></div></div></div>=
</div></div></div></div></div>

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