[Chimera-users] Label secondary structure elements

Repic Matej matej.repic at epfl.ch
Thu May 7 04:33:11 PDT 2015

2dlabels seem appropriate for the job.


Matej Repic
Ecole Polytechnique Fédérale de Lausanne
BCH 4108
CH - 1015 Lausanne


On 5/7/15, 12:04, "MarcoSette" <sette at uniroma2.it> wrote:

>Dear all,
>do you know if it is possible to label the different strands and helices
>on a protein with something like B1, B2, H1, H2, etc. ?
>The label option does not contain this possibility.
>Dr.Marco Sette, Ph.D.
>Assistant professor of Biochemistry
>Department of Chemical Sciences and Technology
>University of Rome, "Tor Vergata"
>via della Ricerca Scientifica, 00133, Rome, Italy
>e-mail: sette at uniroma2.it
>e-mail: m77it at yahoo.it
>Tel.: +39-0672594424
>Fax: +39-0672594328
>Il 01/05/2015 18.23, Elaine Meng ha scritto:
>> Dear Mathias,
>> Chimera automatically excludes water from the molecular surface
>>calculation, so in general (unless something is weird about your input
>>file) you wouldn¹t have to worry about that.
>> One approach is to only show the surface of the protein for the atoms
>>lining the pocket.  In most cases, the pocket is not completely
>>enclosed, however, so there will be an opening and somewhat rough edges.
>> For example, see this figure in the ³structure analysis and comparison²
>> Another difficulty is that of figuring out which atoms line the pocket
>>and thus which surface patches to show.  If you use the CASTp interface,
>>that is taken care of; CASTp calculates pocket areas/volumes and figures
>>out which sets of atoms define each pocket and tunnel.  You can fetch
>>directly from the CASTp database (if your structure of interest is in
>>the PDB, its results may already be there) or upload a structure to the
>>CASTp server and have the results emailed to you.  In the latter case,
>>you can still use the Chimera interface to view the results; this lists
>>pocket volumes and areas calculated with both molecular surface and
>>solvent-accessible surface, number of openings, etc.  More about the
>>Chimera-CASTp interface:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/castp.html>
>> As for display, all of the above are just showing parts of the surface
>>of the protein.  A different approach is to calculate a separate surface
>>of the void space.  There are several programs, mainly separate from
>>Chimera. (For example, CAVER doesn¹t have a Chimera plugin.)
>> (A) Chimera does have a Surfnet tool (in menu under ToolsŠ
>>Surface/Binding Analysis) that you may want to take a look at.
>>Personally, I have had trouble getting a nice display of pocket or
>>tunnel volume with this tool.  I usually get a bunch of smaller blobs
>>instead of the desired one filling the whole pocket.
>> (B) Voss Volume Voxelator <http://3vee.molmovdb.org/> calculates
>>³density² maps filling void spaces, and you can open and view these maps
>>in Chimera¹s Volume Viewer.  Just like other density maps, you could
>>adjust the isosurface level, do coloring, etc.
>> There are probably others.  WIth A or B, you can measure volume
>>enclosed in surfaces with Chimera¹s Measure and Color Blobs tool (in
>>menu under ToolsŠ Surface/Binding Analysis).
>> 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 Apr 30, 2015, at 8:34 PM, Matthias Fellner
>><mfellner at chemistry.otago.ac.nz> wrote:
>>> Good day
>>> I am a PhD student at the University of Otago New Zealand. First I
>>>would like to thank you for this very useful software, I use it for all
>>>my protein crystallography pictures and a lot of analysis as well, I
>>>always cite your citation for sure when I publish using your software.
>>> Normally I get very far with your tutorials but this time I failed to
>>>achieve my goal and I wanted to write a direct question.
>>> I have a protein with an active site pocket. I can display the surface
>>>of the protein and then I see the pocket inside but I am really
>>>interested in the enclosed surface = the active site pocket.
>>> How can I display the ³negative² (enclosed) surface area and possibly
>>>calculate its volume. Can this be done with the pdb file or is such an
>>>analysis only possible based on the electron density. I learned how to
>>>manipulate the density map in chimera, so if this is the only way I
>>>should also be able to do it if you explain the details.
>>> If I get this done I wanted to ask if there is a way to ignore water
>>>molecules from the displaying of surfaces and later calculations or if
>>>I should simply work with a pdb which has the waters removed.
>>> Thank you
>>> Matthias Fellner
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