[Chimera-users] Placing Autodock Vina Pocket around AA residues from RaptorX

[Elaine Meng]

P.S. Looks like Swiss-Prot server uses Blast to find templates if you used the automated mode.
<https://swissmodel.expasy.org/docs/help#automated_mode>
Elaine

> On Sep 20, 2018, at 4:19 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Leif,
> 
> (1) command: select :252,256,260
> 
> will make a selection ...or if you just want to find out the center coordinates of that set of atoms:
> 
> measure center  :252,256,260
> - or -
> define centroid :252,256,260
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#centroid>
> 
> See command-line specification, which can include chain IDs, model numbers, etc. in addition to residue numbers, in the case that multiple chains/models have the same residue numbers:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
> 
> Command list and links to manual pages:
> 
> (2) it’s far beyond the scope of this mailing list to discuss the relative merits of different comparative modeling methods. You can certainly use whatever works for you.  You have to balance the quality of results with the degree of difficulty for you, control over the parameters you wish to tune, and various other factors that depend on the specific case, like what template structures are available, etc.  Without reviewing in depth how Swiss-Prot works, I believe both methods use  template 3D structure(s) and a sequence alignment of the target to the template(s). Maybe the Swiss-Prot server is easier if it will automatically find template(s) and create the alignment for you under the hood, whereas Chimera requires you to get the alignment yourself, such as by running Blast.  In Chimera, you can still choose which of the structures to use as template(s), assuming it finds more than one.  Also, running Blast isn’t the only way to get the needed sequence alignment and template structure, see list of approaches here:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Sep 20, 2018, at 3:42 PM, <leifepeterson at sbcglobal.net> <leifepeterson at sbcglobal.net> wrote:
>> 
>> Couple newbie questions:
>> 
>> 	• I don’t know if any users have run RaptorX (U-Chicago) for ligand-residue pocket prediction, but the results simply tell you the specific AA residues are which are close to the pocket  For example the locations could simply be e.g. the residues K252, Q256, and K260 in the input PDB file.   So my question in terms of AA annotation in Chimera is, how could I center Autodock Vina’s pocket box around residues something like K252, Q256, and K260? I looked through the select options and didn’t see where numbered residues could be selected.
>> 	• For 3D modeling when x-ray crystallography results are not available in PDB, I commonly will submit a protein’s FASTA sequence to SWISS-MODEL, and then download the PDB and go through dock prep for the receptor and minimization of the ligand(and adding e.e. hydrogens, etc.)   Isn’t the SWISS-MODEL approach an alternative for using the MODELLER add-on for homology modeling.    The MODELLER run I just went through was really using a lot of core resources, and the BLAST template results were complexes between receptors and ligands, and sometimes DNA.  So isn’t there an advantage to  inputting a FASTA from Uniprot into SWISS-MODEL to obtain the predicted 3D structure, when compared with the BLAST results required during MODELLER runs? 
> 
> 
> 
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