[Chimera-users] importing xyz file

[Eric Pettersen]

Okay, you can do that by “fixing up” your original file (tmp.pdb) after opening it.  So open your original file and then get rid of the “missing structure” pseudobonds by going to “Tools->General Controls->Pseudobond Panel” and choosing the “missing structure” group in the table and clicking the “close” button on the right (not the bottom! Afterward you can dismiss the panel with the bottom Close button).  Then you can force chimera to show the suppressed “long” covalent bonds with this command: “setattr b display 2”.  That will result in Chimera treating those bonds normally (i.e. shown if both endpoint atoms are shown) instead of as chain breaks.

—Eric

> On Mar 10, 2016, at 12:11 AM, Michał Kadlof <m.kadlof at cent.uw.edu.pl> wrote:
> 
> Thank you for your fast and detailed answer. Is it the only solution? I would like not to loose the possibility of rendering it in rainbow or ribbon style.
> 
> ----- Oryginalna wiadomość -----
> Od: "Eric Pettersen" <pett at cgl.ucsf.edu>
> Do: "Michał Kadlof" <m.kadlof at cent.uw.edu.pl>
> DW: "chimera List" <chimera-users at cgl.ucsf.edu>
> Wysłane: czwartek, 10 marzec 2016 0:31:58
> Temat: Re: [Chimera-users] importing xyz file
> 
> 
> Hi Michał, 
> When Chimera reads a PDB file, it adheres to the implied conventions of the PDB — which is what is tripping you up here. The two conventions that are getting you are: (1) consecutive residues in ATOM records with no intervening TER card are connected, and (2) jumps in the residue numbering of consecutive residues along with separation in 3D space imply missing intervening structure. (1) will add extra bonds you didn’t explicitly put in your CONECT records. (2) will change some inter-residue bonds into “missing structure” pseudobonds. 
> So if we fix your PDB file, Chimera will like it better. :-) The changes are: 
> 
> 
> — Change ATOM records to HETATM records 
> — Put all the atoms into a single residue 
> — Change the residue name from GLY to UNK 
> — Give the atoms unique names (I used C0 through C69) 
> 
> 
> I have attached the edited version of your file. 
> 
> 
> —Eric 
> 
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> Eric Pettersen 
> UCSF Computer Graphics Lab 
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> On Mar 9, 2016, at 1:48 PM, Michał Kadlof < m.kadlof at cent.uw.edu.pl > wrote: 
> 
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> 
> Thank you for your advice. I decided to translate my XYZ structure into PDB file with CONNECT records but I observe strange behaviour. Chimera seems not rendering all of bonds. Some of them in dense place, are render as pseudobonds. Is it how it supposed to work? bond command tells me: Attempt to form duplicate covalent bond. 
> 
> I'm including screenshot, and my structure. It's obviously not a protein, but I would like to use some tools from chimera to work with it. 
> 
> Can you help me? 
> 
> -- 
> Michał Kadlof 
> 
> 
> ----- Oryginalna wiadomość ----- 
> Od: "Eric Pettersen" < pett at cgl.ucsf.edu > 
> Do: " chimera-users at cgl.ucsf.edu BB" < chimera-users at cgl.ucsf.edu > 
> DW: "Michał Kadlof" < m.kadlof at cent.uw.edu.pl > 
> Wysłane: środa, 13 styczeń 2016 19:03:32 
> Temat: Re: [Chimera-users] importing xyz file 
> 
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> On Jan 13, 2016, at 9:58 AM, Elaine Meng < meng at cgl.ucsf.edu > wrote: 
> 
> (1) after reading in the XYZ file, add bonds manually yourself, for example, select two “atoms” (Ctrl-click, Shift-Ctrl-click) and then use command “bond sel”. Repeat. This could be tedious if you have a lot of bonds to add. You could also use atom names instead of selecting, for example “bond @c1,c2”. Although the XYZ file doesn’t contain atom names, “atoms” of the same “element” will be named in Chimera according to element with a sequential number appended (the first C is named C1, the second C is named C2, etc.). 
> < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/xyz.html > 
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> And the above could be combined into a script, e.g.: 
> 
> 
> open myfile.xyz 
> bond @c1,c2 
> bond @c1,c7 
> … 
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> That script file could then be opening with a single command in Chimera: “open myscript.cmd”. 
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> —Eric 
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> Eric Pettersen 
> UCSF Computer Graphics Lab 
> 
> 
> 
> <Screenshot_2016-03-09_22-47-44.png> <tmp.pdb> _______________________________________________ 
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