[Chimera-users] Label secondary structure elements
sette at uniroma2.it
Thu May 7 04:50:09 PDT 2015
thanks a lot.
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
Il 07/05/2015 13.33, Repic Matej ha scritto:
> 2dlabels seem appropriate for the job.
> Matej Repic
> Ecole Polytechnique Fédérale de Lausanne
> SB - ISIC - LCBC
> 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:
>>> 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 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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