[Chimera-users] depict hydrophobicity surface in super large molecules in chimera

Tue Oct 15 02:57:47 PDT 2019

Sure, chimeraX sounded to me super smooth and really nice, specially 
because now I can work so easy with our huge surface structures. An the 
hydrophobicity profile which is super.

It is just that for dummies in structure as I am, with really not any 
idea at all of programming and computing stuff or even scripts, that new 
thinks really take a while to us.

Just as an example, I downloaded Chimera X and tried it, for the 
hydrophobic surfaces is great, but the rest of the things that I 
regularly do such as match maker and now, performing contacts and 
clashes, I could not find straight forward a menu for those. Of course 
if I google it a bit I could finally get my way to manage, and probably 
having a command for the matchmaker or contact clashes would be quicker 
at end. But for sure will involve quite a few trial and errors and 
sometimes not being sure that all the parameters that are being used are 
the right ones or are even specified.

I am always super open to new stuff, but really when one lacks the basis 
new things take really a long time and specially if people around is not 
using ChimeraX, so cannot really share doubts with them. I will really 
try to use Chimera X but I am afraid that most of the things I will have 
to do through regular Chimera, that I have more control, simply because 
I will not manage to do them in Chimera X, but not because it will be no 
possible. And I guess this is what most of the people in my 
circumstances will do, unfortunately.

But anyways  thanks again for all the replies on the list, they are 
always really helpful and I really appreciate your work on Chimera.

Regards

Marta

On 14.10.19 18:48, Elaine Meng wrote:
> We are adding more dialogs to the ChimeraX gradually, and putting more things in its Select and Action menus.  Many things are easier than in Chimera: for example, there are many Toolbar icons across the top for performing actions with a single click.
>
> There’s an icon to show protein surface with default hydrophobicity coloring in the Molecule Display tab of the Toolbar.
> <http://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html>
> <http://rbvi.ucsf.edu/chimerax/docs/user/tools/moldisplay.html>
>
> ChimeraX also has several presets, and the script (cxc file) I sent the link to earlier can be specified as a custom preset in your Startup Preferences (then you can just use it anytime from the ChimeraX Presets menu).
> <http://rbvi.ucsf.edu/chimerax/docs/user/menu.html#presets>
> <http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup>
>
> Regards,
> Elaine
>
>
>> On Oct 14, 2019, at 1:31 AM, MARTA PEREZ ILLANA <marta.perez at cnb.csic.es> wrote:
>>
>> Thanks a lot Elaine. I just downloaded and was playing around yesterday with ChimeraX and it really made my needs!
>>
>> I hope I will get used to use the commands within rather than user interface soon...
>> Regards
>> Marta
>>
>> Elaine Meng <meng at cgl.ucsf.edu> escribió:
>>
>>> Hi Marta,
>>> Two general choices:  use Chimera molmap surface or use ChimeraX, which does not have the molecular surface calculation problems.  Also ChimeraX calculates a molecular lipophilicity potential (MLP) that varies through space analogous to ESP instead of just using amino acid lookup values like Chimera.
>>>
>>> The Chimera amino acid lookup values are shown in this table, kdHydrophobicity column.
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>
>>>
>>> (1) in Chimera just color the “molmap” surface by hydrophobicity.  In this case it is two steps, though: first you have to color the atoms by amino acid hydrophobicity, and then use color zone to make the surface coloring match the nearby atom coloring.  Also be careful when you make the molmap surface that it is calculated only from protein atoms (not solvent, ligands, …).  Details of the two steps:
>>>
>>>      (A) color atoms by hydrophobicity with Render by Attribute (menu: Tools… Depiction… Render by Attribute, and in that dialog choose to color atoms by residue attribute kdHydrophobicity) or “rangecolor” command, e.g.
>>>
>>> rangecolor kdHydrophobicity min dodger blue 0 white max orange red #3
>>>
>>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render>
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
>>>
>>>      (B) use Color Zone (menu: Tools… Volume Data… Color Zone) to make the molmap surface coloring match the atom coloring, or command “scolor zone” e.g. if molmap is #3.1 and atoms are #3:
>>>
>>> scolor #3.1 zone #3&protein range 5
>>>
>>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html#zone>
>>>
>>> (2) get ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>, open your structure, show surface (e.g. command “surface”), and color by MLP (e.g. command “mlp”).
>>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html>
>>>
>>> Alternatively in ChimeraX you can just color by the amino acid kdHydrophobicity values like in Chimera using this script provided in the ChimeraX User Guide as an example of a custom preset (just save the file *.cxc and then open it in ChimeraX to run it):
>>> <http://rbvi.ucsf.edu/chimerax/docs/user/kyte-doolittle_hydrophobicity.cxc>
>>>
>>> I hope this helps,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.
>>> UCSF Chimera(X) team
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>>
>>>> On Oct 13, 2019, at 7:09 AM, Marta Perez Illana <marta.perez at cnb.csic.es> wrote:
>>>>
>>>> Hi all
>>>> I was trying to analyze the hydrophobic surface of two very large structures ( 3 chainsx 900 aa each so 2.700aa). As expected the default surface calculation has failed. Normally for electrostatic potential what works for me is making a mol map (molmap  #3  4 gridSpacing  0.5) and then calling the pdb2pqr and apbs servers directly from chimera, which is very convenient.
>>>>
>>>> However I cannot find an analogous way to make it with hydrophobicity... Since the surface fails for such big molecules, the straight forward way (present-3interactive surface hydrophobicity) does fail as well...
>>>>
>>>> Then... is there any server than can be called from chimera, to get hydrophobicity as an attribute to be depicted? Or alternatively could you suggest any server that gives output hydrophobic column, compatible  to get it after to chimera attributes? Reading a bit I found that, not as electric fields, that can be computed for structures, hydrophobicity comes just for the sequence, without taking into account the neighbours and context...
>>>>
>>>> P.D: I have managed to represent in other programs the hydrophobic surface, but I really want to make it in chimera, to make it more consistent and easy to organize myself...
>>>>
>>>> Thanks a lot! and sorry if the question goes beyond Chimera...
>>>> Marta
>>
>> -- 
>> Marta Pérez Illana, Ph. D. student
>> Dept. of Macromolecular Structures Lab 15
>> Centro Nacional de Biotecnología (CNB-CSIC)
>> Darwin, 3
>> 28049-Madrid (SPAIN)
>> Email:  marta.perez at cnb.csic.es
>> Phone:  (0034) 91 585 4508
>> http://wwwuser.cnb.csic.es/~sanmartinlab
>>
>>
>>
>> _______________________________________________
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-- 
Marta Pérez Illana, Ph. D. student
Dept. of Macromolecular Structures Lab 15
Centro Nacional de Biotecnología (CNB-CSIC)
Darwin, 3
28049-Madrid (SPAIN)
Email:  marta.perez at cnb.csic.es
Phone:  (0034) 91 585 4508
http://wwwuser.cnb.csic.es/~sanmartinlab