[chimerax-users] Build Structure - peptide

[Jeffrey D. Hartgerink]

This is brilliant - thank you very much!

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Jeffrey D. Hartgerink, Ph.D.
Prof. of Chemistry and Bioengineering
Rice University
jdh at rice.edu / 713-348-4142
https://hartgerink.rice.edu

> On Mar 6, 2023, at 7:36 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hello Jeff!
> To avoid repeatedly setting several angles in the GUI, either of the following would work:
> 
> (1) You can use the command implementation of Build Structure, where you would have one very long "build start peptide" command that specifies the sequence and all the angles.  Then you can basically reissue the same command over and over except for whatever you need to be different between your different peptides:
> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/build.html__;!!BuQPrrmRaQ!hKfrY2Rkg_4PNENDjuM5EPai8898gZRt23y4be_5vS0VNKDRNUNUwlXBOZvsRhOGWhMqoyTvrIh8xwdgwA8K_i1E$ >
> 
> Also, it might be easier just to make a .cxc file (command file, plain text, just the same commands you would enter into the command line) in your favorite text-editor.  You could just put several copies of the same command in the file, and then easily edit just the parts in each copy of the command that you need to be different.  It might be less error-prone to do this, perhaps after you get one "build start peptide" command that you are happy with after some trial and error of entering it directly.  The link above has an example of a "build start peptide" command.
> 
> (2) You can use an "attribute assignment file" (filename.defattr) to set the angles after an initial structure of the peptide is built, since phi and psi are residue attributes.  These files are in a simple text format (see link below).  If the residue numbers are the same across the structures, you can simply use residue number as the specifier in each row of that file and either use it repeatedly, once for each peptide if you are building and saving them one by one, or if they are all open at the same time, en masse.  Simply opening the .defattr file assigns the attribute values, and in the case of phi and psi (and omega and chiN), will change the conformation of the structure.  One defattr file can have multiple attributes, so it could have a section for the phi angles and a section for the psi angles.
> 
> Attribute assignment file format:
> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html__;!!BuQPrrmRaQ!hKfrY2Rkg_4PNENDjuM5EPai8898gZRt23y4be_5vS0VNKDRNUNUwlXBOZvsRhOGWhMqoyTvrIh8xwdgwPEP4oux$ >
> 
> Residue attributes:
> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html*residue__;Iw!!BuQPrrmRaQ!hKfrY2Rkg_4PNENDjuM5EPai8898gZRt23y4be_5vS0VNKDRNUNUwlXBOZvsRhOGWhMqoyTvrIh8xwdgwCqqnuBO$ >
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Mar 6, 2023, at 5:17 PM, Jeffrey D. Hartgerink via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Hello,
>> 
>> I’m trying to build a series of related peptides with ChimeraX’s Build Structure - peptide tool. The way it currently works is simple and easy to use. However it is cumbersome to input phi/psi angles repeatedly, especially if the peptide sequences is anything more than very short. I am wondering if there is a way for this tool to take in either a text file list containing (Amino Acid, Phi, Psi), to paste in the same data into the input window, or any other related way to more efficiently generate peptide structures for starting points. This would greatly reduce the time needed to compare a variety of related sequences and conformations. Thank you very much for your time and consideration!
>> 
>> -Jeff
> 

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