[Chimera-users] morph interpolation

Souroprobho Chowdhury souro at ebi.ac.uk
Tue Jul 11 14:04:51 PDT 2017


Hi Elaine, 

Thank you for getting back with your detailed response. The 6574 is part of the PO4 residue because that is how Maestro ‘preserves’ the information that the atom has originally come from a phopsphate? I am using Maestro to do the modelling, essentially breaking a X—H bond and making a Y—H bond with the same hydrogen. 

Essentially we are trying to make ‘movies’ of 3D enzyme mechanisms. This means that morph interpolate should be able to know that atom X from residue N goes to position Y of residue M. Am I missing something obvious? 

Thanks,
Souro 

—

Souro Chowdhury
Researcher, Thornton Group 
European Bioinformatics Institute, EMBL-EBI 
Cambridge, United Kingdom 
http://www.ebi.ac.uk/research/thornton


> On 11 Jul 2017, at 19:09, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Souro,
> Your two input files I2.pdb and I3.pdb have severe errors.  Looking at I2.pdb with a text editor, I see that the hydrogen that is supposedly on the histidine is actually part of the PO4 residue according to that file, and the connectivity of the histidine-1082  sidechain is badly messed up.  For example, hydrogen HD1 with serial number 3865 is bonded to two other atoms (according to the CONECT section at the bottom of the file) .   See image attached with atoms labeled by serial number and “ligand” selected, so that you can see that hydrogen 6574 is part of the ligand residue PO4 even though the CONECT lines have it bonded to the histidine.
> 
> When I tried the morphing, it seemed to me that the movement of O3 was reasonable, however (just goes between starting and ending positions).
> 
> Initially I was going to answer that Chimera's morphing was developed mainly for the biopolymer parts  (protein and nucleic chains) and I wouldn’t necessarily expect good performance on ligand conformations.  However, when I saw how badly messed up the input files are, now I think it might work a lot better if those connectivity issues (and putting the H in the histidine residue instead of the PO4 residue) were fixed.
> 
> I don’t use Pymol, so I didn’t look at that script.  If morphing works in pymol it may be because it is ignoring the connectivity information (CONECT lines at the bottom) in your PDB files.
> 
> I hope this clarifies the situation.  Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> <i2-mess.png>
> 
>> On Jul 11, 2017, at 6:25 AM, Souroprobho Chowdhury <souro at ebi.ac.uk <mailto:souro at ebi.ac.uk>> wrote:
>> 
>> Hello, 
>> 
>> I am trying to use morph interpolate on two (for this post) PDBs (I2.pdb and I3.pdb, attached) but something peculiar is happening. The Hydrogen on the HIS 1082 (N1) does a ‘cork-screw’ like movement. Essentially, instead of interpolating directly from position A to B, it is taking a more round-about angle. A similar movement is observed for the O3 in the T1 O ligand. 
>> 
>> This problem has come up recurrently in my work and I am yet to find a solution. I have used most of the options that apply on morph interpolate that are mentioned on the chimera website without much improvement. 
>> 
>> I am using Maestro by Schrodinger to model my structures. 
>> 
>> Please find attached I2.pdb , I3.pdb and mov_all.pdb. mov_all.pdb is the trajectory file, works on Pymol (I am attaching a pymol script called auto-script.pml as well for selection of the correct residues, and a reasonable representation). The chimera interpolation script is also attached. 
>> 
>> Thanks! 
>> 
>> Souro 
>> 
>> <I2.pdb>
>> <I3.pdb>
>> <interpolate.com <http://interpolate.com/>>
>> <mov_all.pdb>
>> <auto-script.pml>
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