[Chimera-users] MD trajectory analysis

[George Tzotzos]

Thank you very much Elaine for the clarification

Have a good day 

George

> On 13 Oct 2016, at 18:39, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi George,
> No, it would find all “contacts” as in the definition:
> "all kinds of direct interactions: polar and nonpolar, favorable and unfavorable (including clashes)”
> 
> Basically, it’s analogous to using a simple zone cutoff.  If you looked for everything within a 4 angstroms, for example, it would find some atoms that were within 4 angstroms but at a good interaction distance, but it would also find any atoms that are too close (clashes), like only 1.5 angstroms away.  It would find some atoms that are the appropriate type for a good interaction (for example, opposite charge), but it would also find any atoms in the zone that were not the right type for a favorable interaction (for example, same charge).
> 
> The “findclash” command is similar to using a simple zone, except that it accounts for different atom types having different sizes.
> 
> I hope this clarifies,
> Elaine
> 
> 
>> On Oct 13, 2016, at 8:02 AM, George Tzotzos <gtzotzos at me.com> wrote:
>> 
>> Hi Elaine,
>> 
>> With reference to your message (below), I’d be grateful for a clarification.
>> 
>> According to the Find Clashes/Contacts instructions contacts are defined as:
>> 	• contacts - all kinds of direct interactions: polar and nonpolar, favorable and unfavorable (including clashes)
>> Furthermore, 
>> 
>> For detecting contacts, negative cutoff values of 0.0-(–1.0) Å with an allowance of 0.0 Å are generally reasonable (default contact 
>> criteria –0.4 and 0.0 Å, respectively).
>> 
>> Therefore, am I right to assume that the command below
>> 
>>> findclash ligand overlap -1 hb 0 make false log true naming simple
>> 
>> produces an output of FAVOURABLE interactions only (i.e no clashes)?
>> 
>> Thank you in advance for your kind help
>> 
>> George
>> 
>>> On 11 Oct 2016, at 00:19, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> 
>>> Hi George, 
>>> Any command you can execute at the command line, you can execute in MD Movie at each frame by defining a per-frame script (MD Movie menu: Per-Frame… Define script).
>>> 
>>> For example, at each frame you could report the frame number, select residues near ligand, and write list of the residues to the Reply Log with a per-frame command script:
>>> 
>>> echo
>>> echo <FRAME>
>>> sel ligand z<3.5
>>> ~sel ligand
>>> writesel - naming simple
>>> 
>>> …. or you could use “findclash” (find clashes or contacts command) instead of zone selection, e.g.
>>> 
>>> echo
>>> echo <FRAME>
>>> findclash ligand overlap -1 hb 0 make false log true naming simple
>>> 
>>> … which would give atoms instead of residues like the first example.  If you wanted residues instead, 
>>> 
>>> echo
>>> echo <FRAME>
>>> findclash ligand overlap -1 hb 0 make false select true
>>> ~sel ligand
>>> writesel - naming simple
>>> 
>>> Of course, these will give you a lot of results: a list of residues (or even the atoms) for each frame of your trajectory.  See the command manual pages for the options of all these commands.
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
>>> 
>>> Guess I don’t understand why you were calculating occupancy.  Each time you do that, it will calculate a separate “density” (occupancy) map.  Looks like you did it at least 3 times, which is why you have 3 histograms in volume viewer.  Then when you chose mesh, it  only changes the “current” map (name highlighted in blue) map to mesh.  The other two are still shown as solid surfaces.  You can delete any of those 3 occupancy maps by clicking the “minus sign” button near the upper right corner of its histogram.
>>> 
>>> I hope this helps,
>>> Elaine
>>> ----------
>>> Elaine C. Meng, Ph.D. 
>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> 
>>>> On Oct 10, 2016, at 1:54 PM, George Tzotzos <gtzotzos at me.com> wrote:
>>>> 
>>>> My task is to identify ligand interactions with protein residues throughout an MD trajectory. I thought of something along the lines 
>>>> sel ligand z<3.5 #for vdW interactions, etc. 
>>>> 
>>>> I don’t think this can be done using the MD movie interface but I may be wrong.
>>>> 
>>>> I then tried the following:
>>>> 1. sel protein/hold selection steady
>>>> 2. sel ligand
>>>> 3. calculate occupancy (MD Movie/Analysis)
>>>> 4. Chimera/select/clear selection
>>>> 5. turned the Volume Viewer to mesh/level2.
>>>> 
>>>> What I obtained is a mesh grid enclosing solid surfaces (see attached snapshot). I’m not able to get rid of these surfaces? 
>>>> 
>>>> I think that the problem ma be in step 2 above (sel :ligand). My ligand is N,N-Diethyl-meta-toluamide. Should I select the aromatic ring part separately of the amide part, run the above process and then repeat selecting the amide part? 
>>>> 
>>>> I also tried MD movie/Analysis/Residue interaction network, first selecting the ligand. 
>>>> 
>>>> The results I obtained are not satisfactory. 
>>>> 
>>>> Is there a better way of dealing with my problem?
>>>> 
>>>> Thanks in advance for your kind help
>>>> 
>>>> George
>>>> 
>>>> 
>>>> <PastedGraphic-1.tiff>  <PastedGraphic-2.tiff>
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>> 
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