Downloading Results of ConSurf Jobs.
Using and Customizing the Downloaded Files.
Making Presentations Showing ConSurf Results.
Why download results from ConSurf?
- When a fast Internet connection is not always convenient or available,
you will be able to review your downloaded and saved results quickly and easily.
This may be especially desirable when
you wish to show the results to an audience in
- Saving your results will keep them available after they have been
removed from the server.
You can re-run the job, of course, but saving the results avoids the
time required to re-run the job.
- It is relatively easy to customize the display of your downloaded
ConSurf results. For example, you can change the initial background
color, the entire conservation color scheme, or even the control panel
How to download this ConSurf result:
- Decide where, on your computer, you want to put your downloaded
ConSurf results, and create a folder (directory) for them. We recommend
that this folder be named consurf/pdb_only.
If you use a different folder name,
substitute that name wherever consurf/pdb_only is mentioned below.
If you have downloaded Protein Explorer (PE),
a folder (directory) named
my_molecules/pipes/consurf/pdb_only was created
automatically. Use it.
If you later decide to create an HTML ("web browser") page with links to
your ConSurf results, putting them here
will make it easier.
(See instructions below.)
- Click on MDL at the lower right of the molecular image
at the top of this page. On the menu that opens, select
File, Save Molecule As. Save the
file into consurf/pdb_only.
We strongly recommend that you keep the original filename, of the form
1xxx_consurf0000000000_pipe.pdb, where "1xxx" is the PDB identification
code, "0000000000" is the ConSurf job number, and the ending "_pipe.pdb"
is required by Protein Explorer. These names alphabetize by PDB code,
and within jobs for the same PDB code, by job number.
from the filename may
prevent the result from being displayed correctly in PE.
(using Netscape 4.8 in Classic under OSX)
the PDB filename
cannot exceed 31 characters in length.
The default filename above is exactly 31 characters in length.
Rename it if you wish, but don't make it longer!
for more information.
Using this page to save the PDB file ensures that the filename will
If you save the file directly from PE itself
(rather than from this page), the filename will
not be correct.
- The previous step saves only the visualization result, but not
the ConSurf Job Status Page nor the several text files linked to it,
including "Amino Acid Conservation Scores", "PSI-BLAST Output",
"The Homologues found by PSI-BLAST (in FASTA format)",
"Multiple Sequence Alignment (in Clustal format)",
and "Phylogenetic Tree". If you want to save these,
Using your downloaded ConSurf results.
- The simplest way to use your downloaded ConSurf result files is
to start Empty Protein Explorer (PE). You will need to use
Protein Explorer version 2.78 or higher, and
downloaded copy of PE, or
Netscape 4.8 with PE on-line. (See * below for why.)
Look for the Empty Explorer
link on PE's FrontDoor (middle gray box). After PE has started, you
will see the "Load Molecule"
Use the Browse button
there to select your downloaded ConSurf PDB file, then click Load.
The last ten PDB files loaded with the Browse button into Empty PE
appear on the pull-down menu Select Previously Loaded PDB File
in Empty PE's Load Molecule control panel. The second time you want to
load one of the last ten, simply pick it from the menu and you won't
have to find it again in the browse dialog.
* Why do you need a downloaded copy of PE, or Netscape 4.8? The
browsers have a security barrier that precludes displaying a local PDB file
when PE is on-line. Internet Explorer can do this, but cannot easily access the ConSurf
results in the PDB file. Netscape 4.8 can do both. When PE is run from
a local (downloaded) copy, the Gecko browsers work fine.
- Optionally, you can make an HTML ("web browser") page
with links to your saved ConSurf results. This enables you to add some
description to each result, and to order the results as you wish.
An example of such a page is the saved
ConSurf Examples included with Protein Explorer.
Changing the conservation color scheme in your downloaded ConSurf results
ConSurf's Color Scheme
Color Scheme Inspired by MSA3D
- ConSurf uses a series of nine colors from turquoise
through white through burgandy to represent conservation grades from
variable through conserved, respectively.
Changing this color scheme in your downloaded PDB file
is relatively simple. At right is shown
an alternative color scheme inspired by
(in which grades 4, 5, and 6 use the same color).
Presenting ConSurf-colored molecular views.
The easiest way to present a ConSurf result is to bookmark the job
result page. However, your job will remain on the ConSurf server for
a limited time. Below are methods for saving the results on your computer,
and using them in presentations.
- Static Snapshots:
It is easy to copy any ConSurf view and paste it into a presentation
(such as MS Powerpoint or
Open Office Impress).
Rotating Views Method I: Saved ConSurf PDB File.
Saving and using ConSurf PDB files, detailed above, is the
easiest method for including a rotatable, ConSurf-colored molecular
view in a presentation. (If your presentation is in Powerpoint, you would
need to pop the PE window in front to show the ConSurf view, then pop Powerpoint back
in front afterwards.) With this
method, you can show a ConSurf result exactly as it was first shown to you
by the ConSurf server, but you don't need an Internet connection, nor
do you have to depend on the result still being on the ConSurf server.
Also, if you prefer, you could
customize the color-scheme (details above).
Here are examples
of saved ConSurf PDB files.
Rotating Views Method II: MolSlides.
- If you want simply a rotatable ConSurf-colored view (or
several), perhaps among other non-ConSurf molecular views, then
MolSlides are ideal. Making MolSlides takes a bit more
effort than method I above, but is still relatively easy. Once you
have made them, you can show them (off-line or on-line) without
having to run PE, using either
Here is a sample of
ConSurf views saved as MolSlides.
MolSlides are appropriate when
you don't need the ConSurf control panel, or the complexity of PE,
but just one (or more) pre-selected
ConSurf-colored molecular views (perhaps among other views) in a set of slides.
- A MolSlide can be inserted into a Powerpoint slide (Windows
only), but this is technically fussy.
For more information, please see
- You are not limited to presenting the preset molecular views produced by
ConSurf. Instructions for customizing the molecular view within PE
are linked at the bottom ConSurf's
"Customize this molecular view -- Explore this structure".
You can save any customized molecular view into a MolSlide.
- To save ConSurf views for later presentation:
Find the link
Save This View .. below PE's
box. Click it when you see the view you want to save.
In the dialog that opens, click Add a new MolSlide.
Follow instructions there. You will be able to save your views for
display in either MDL
Chime or Jmol. Full details are at
Rotating Views Method III: PiPEs.
PE includes a mechanism for
in Protein Explorer (PiPEs).
Building PiPEs is much more technical than saving MolSlides, but gives
you much more control.
A downloaded ConSurf PDB file is already
one "chapter" of a PiPE, and can simply be included among other chapters.
Alternatively, you could insert one (or more) ConSurf-colored molecular
views among non-ConSurf views within a single PiPE chapter.
Protein Explorer automatically records the commands used to generate
each successive molecular view. You can save one or more molecular views
during a PE session, including the default ConSurf view or a customized
by clicking the button Save this view..
box. In the dialog that opens, scroll down below the MolSlides
section, and save a Chime command script.
Click the Help.. button below the message box
for a complete introduction to using PE's Recorder.
Your saved molecular views can be incorporated into a
in Protein Explorer (PiPE).
Changing the PE control panel used by your saved ConSurf results
Technically-savvy users will be interested to know that it is also
possible to customize the
panel PE uses for ConSurf.
Feedback to Eric Martz.