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Dear Dr. Meng.</div>
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Thank you so much for suggestion of add and delete H in the command line! This time it works for the structure modification!</div>
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I want to ask you one more question about an error that pop up every time i am trying to modify and I attached the error message above. (this is not a major issue but i just do not understand why it always show up whenever i set modification to the structure.)</div>
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I know the error is related to the Zn atom in the structure, but p53 sequence specific DNA binding domain does contain a Zn atom that binds 4 different amino acids.</div>
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I only know very little python and does not know where the error comes from.</div>
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May you please suggest why is Chimera not happy with the Zn atom in the structure?</div>
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<div id="signature">Thank you!<br>
Zhengzheng<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Wednesday, November 7, 2018 9:29 AM<br>
<b>To:</b> zheng l<br>
<b>Cc:</b> chimera-users<br>
<b>Subject:</b> Re: 1up opt</font>
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<div class="PlainText">Hi Zhengzheng<br>
The format of your PDB file is not standard because all the H atoms are all at the end instead of with their their residues. Also they are all in a different chain (chain A) than the other atoms (chain B). Whatever program wrote this file wrote it incorrectly.
You can easily see all atoms, e.g. commands:<br>
<br>
~ribbon<br>
display<br>
<br>
(or use Actions menu to do the same things) but if you use Chimera features requiring chemical knowledge (findhbond etc.) it will not work correctly if the H and the other atoms are not recognized as being in the same residue. I tried editing so that all atoms
were chain B, but it did not fix the problem, which is apparently instead caused by placing all the H atoms at the end instead of with their individual residues.<br>
<br>
You could fix it be removing and re-adding hydrogens in Chimera, but then the H atom positions wouldn’t be exactly the same. Commands:<br>
<br>
delete H<br>
addh<br>
<br>
It is recommended to send questions to chimera-users@cgl.ucsf.edu (CC’ed here) in case I’m not available to answer.<br>
Best,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Nov 7, 2018, at 8:02 AM, zheng l <zhengsfriend@hotmail.com> wrote:<br>
> <br>
> Dear Dr. Meng<br>
> <br>
> I used Chimera software for analyzing many protein crystal structures and then modified them and it has so faithfully doing job for me. However, this structure that I attached below is very difficult to modify.
<br>
> <br>
> The problem is that the hydrogens in structure are hidden. Usually when I need to, for example, replaces a carbon to a nitrogen in a Phe the nitrogen will attached with a hydrogen if I set to have 3 bond for the nitrogen. But this structure is not showing
hydrogens at all<br>
> <br>
> Would you please help me find a way of show all hydrogens need for modifying the protein structure?<br>
> <br>
> Thank you!<br>
> <br>
> Best regards!<br>
> <br>
>> Zhengzheng<br>
> <br>
> <1tup chain b opt 2.pdb><br>
<br>
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