I like the consurf coloring scheme the best. I forget things so I had to write
down the instructions which I copied off of some website which I can't seem to
find at the moment. The other program is ESPript which I've also included my
cheat sheet.
Mapping conservation onto your structure (ConSurf):
Here we will map sequence conservation among species onto a structure so that
you can visualize areas of conservation
Create alignment file
1. Open your preferred internet browser and go to Clustalw
(www.ebi.ac.uk/clustalw)
2. copy sequences into the "sequence box" in Clustalw
The following format (FASTA) MUST be used as an input:
>yeast (name followed by any text and carriage return)
acgtacgtagc (sequence with or without carriage returns.)
>human (next sequence name - must have unique first words)
ataagtac
. . . .
3. submit (you can choose to get results emailed back to you or you will be
allowed to open
a window containing you results)
4. Save the aln file in a place you wont forget
Generating pdb file with conservation values replacing B-values
Go to http://consurf.tau.ac.il/index.html
How to load in pymol
explanation
http://consurf.tau.ac.il/gallery/1217929900/pyMOL_instructions.html
this is from the web site, the key is that you have to download a consurf strip
# Download the PDB_FILE updated with ConSurf's colors.
(a) PDB_FILE showing Insufficient Data
(b) PDB_FILE hiding Insufficient Data
# Download the file consurf_new.py.
# Start PyMOL.
# Load the pdb file; In the PyMOL viewer window type:
PyMOL>"load PDB_FILE"
(no quotes) and hit return.
# Run the script to define ConSurf's color; Type:
PyMOL>"run consurf_new.py"
(no quotes) and hit return.
# Run the coloring scheme; Type this command:
PyMOL>"colour_consurf"
The other one I've used is ESPript
Mapping conservation onto your structure (ESPript):
Here we will map sequence conservation among species onto a structure so that
you can visualize areas of conservation
Create alignment file
1. Open your preferred internet browser and go to Clustalw
(www.ebi.ac.uk/clustalw)
2. copy sequences into the "sequence box" in Clustalw (make sure your pdb
sequence is the top sequence)
The following format (FASTA) MUST be used as an input:
>yeast (name followed by any text and carriage return)
acgtacgtagc (sequence with or without carriage returns.)
>human (next sequence name - must have unique first words)
ataagtac
. . . .
3. submit (you can choose to get results emailed back to you or you will be
allowed to open
a window containing you results)
4. Save the aln file in a place you wont forget
Generating pdb file with conservation values replacing B-values
7. open ESPrint 2.2 http://espript.ibcp.fr/ESPript/ESPript/
i. Click on execute
ii. Select expert (top EXP)
iii. Browse to your aln sequence file (see figure below)
iv. Two boxes will be available for you to input a pdb file (see the next page
for the second pdb input)
v. Browse to your pdb file in the first "Aligned Sequences" window
vi. In addition you need to input the same pdb file into the
bottom of the two boxes. This box maps secondary structure onto the aa
sequence.
If you do not input a pdb, it will map a structure prediction
which can be quite useful when analyzing a sequence f an unsolved
structure.
There are different algorithms for calculations, choose which you think is
applicable. For more information click on the question mark to get a small
discussion
To submit the job, return to the top of the page and click on Submit (MAKE SURE
THAT THE POP-UP BLOCKER IS OFF)
After a short time a new window will pop up.
The BCOL [xx Kb] will have the pdb file now with conservation values in the
B-value column (the other files are just your starting files
The pdf [xx Kb] file will have the structure alignment in pretty colors with
secondary structure predictions
8. save output pdb file (if you look at the text file, it will have
conservation mapped in the
B-factor column)
9. open output pdb in pymol (again-must be most recent version- 0.97)
10. show surface
11. color by B-factor
fore even more fun type in
cartoon putty
show cartoon
On 1/29/09 3:37 PM, "Nathaniel Echols" <[email protected]> wrote:
On Thu, Jan 29, 2009 at 1:25 PM, Anastassis Perrakis <[email protected]> wrote:
Dear all,
I was wondering what is the state of the art for this old dark art ... are
there any good servers / programs that allow to easily upload your own sequence
alignments or create a 'transparent' alignment (I want to see the alignment
first and not a total black box) and then allow you to write out sequence
conservation based either on identity or in e.g a Dayhoff matrix on the B
factor column for displaying it later in eg Pymol?
To be clear I do not want a structural alignment, but mapping sequence
alignment of eg a family to a single structure of a family member.
ConSurf! You can submit your own Clustal alignment (the MSA program MUSCLE
will also generate this file format). However, I was never able to visualize
the PDB files it generates very well in PyMOL; I ended up extracting a
different, simpler type of score (integers 1-9) from the results and applying
that to the B-factor column instead of the score ConSurf writes.
