Re: [ccp4bb] Efficient way of showing residue conservation

[Jason Vertrees]

Hi Yuri,

> I once saw a figure showing the protein as surface, but instead of having it 
> coloured by atom type
> or potential, it was shown by percent conservation in the family. Something 
> like red highly conserved, all the way to white, not conserved at all...
> Now, I assume the figure was done by uploading aligned sequnces of several 
> members of a family, and the colouring
> the generated surface accordingly.
> Does anyone know a way to do this more elegantly than what I tried doing?
> ps. I quit colouring them manually after I remebered my protein was 407 aa 
> long...

PyMOL can do this pretty easily now. First you need to calculate an
alignment, then you need to do the coloring. The alignment step is
done like this:

align protA, protB, object=aln

I then wrote a script to automate the coloring of residues by
conservation in the sequence alignment. You can find the script on the
PyMOLWiki, here http://pymolwiki.org/index.php/Color_by_conservation.
The script does a couple other useful things like showing the
conservation not only by color but by cartoon putty radius, and
expanding the alpha-carbon conservation to surface colors. You can
find an example to copy/paste into PyMOL on that page.

Hope this helps.

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

Re: [ccp4bb] Efficient way of showing residue conservation

[xaravich ivan]

I  input the alignment in ESPript. Add the template PDB file and it
makes a Bcol.pdb file where temperature factors are replaced my
sequence similarity. I open this file in Pymol in Surface and color
B-Factors as rainbow.

Ivan

On 12/7/11, Yuri Pompeu  wrote:
> I once saw a figure showing the protein as surface, but instead of having it
> coloured by atom type
> or potential, it was shown by percent conservation in the family. Something
> like red highly conserved, all the way to white, not conserved at all...
> Now, I assume the figure was done by uploading aligned sequnces of several
> members of a family, and the colouring
> the generated surface accordingly.
> Does anyone know a way to do this more elegantly than what I tried doing?
> ps. I quit colouring them manually after I remebered my protein was 407 aa
> long...
>

Re: [ccp4bb] Efficient way of showing residue conservation-thank you everyone

[Yuri]

On Thu, 8 Dec 2011 09:19:57 +, Mads Gabrielsen wrote:

I believe Charlie Bond's ALINE
(http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/) will let 
you
make a nicely coloured sequence alignement, and then write out a 
Pymol

script which will colour the surface by conservation.

Mads
--
Mads Gabrielsen, PhD
Institute of Infection, Immunology and Inflammation
College of Medical, Veterinary and Life Sciences
University of Glasgow

Room B216 /L303
GBRC
120 University place
G12 8TA


Phone: 0141 3307264 / 6180

E-mail: mads.gabriel...@glasgow.ac.uk





On 08/12/2011 05:26, "Yuri Pompeu"  wrote:

I once saw a figure showing the protein as surface, but instead of 
having

it coloured by atom type
or potential, it was shown by percent conservation in the family.
Something like red highly conserved, all the way to white, not 
conserved

at all...
Now, I assume the figure was done by uploading aligned sequnces of
several members of a family, and the colouring
the generated surface accordingly.
Does anyone know a way to do this more elegantly than what I tried 
doing?
ps. I quit colouring them manually after I remebered my protein was 
407

aa long...


--
Yuri Pompeu

Re: [ccp4bb] Efficient way of showing residue conservation

[Mads Gabrielsen]

I believe Charlie Bond's ALINE
(http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/) will let you
make a nicely coloured sequence alignement, and then write out a Pymol
script which will colour the surface by conservation.

Mads
-- 
Mads Gabrielsen, PhD
Institute of Infection, Immunology and Inflammation
College of Medical, Veterinary and Life Sciences
University of Glasgow

Room B216 /L303
GBRC
120 University place
G12 8TA


Phone: 0141 3307264 / 6180

E-mail: mads.gabriel...@glasgow.ac.uk





On 08/12/2011 05:26, "Yuri Pompeu"  wrote:

>I once saw a figure showing the protein as surface, but instead of having
>it coloured by atom type
>or potential, it was shown by percent conservation in the family.
>Something like red highly conserved, all the way to white, not conserved
>at all...
>Now, I assume the figure was done by uploading aligned sequnces of
>several members of a family, and the colouring
>the generated surface accordingly.
>Does anyone know a way to do this more elegantly than what I tried doing?
>ps. I quit colouring them manually after I remebered my protein was 407
>aa long...

Re: [ccp4bb] Efficient way of showing residue conservation

[Petr Leiman]

Coot is beyond competition (is there any nowadays?), but it cannot do what Yuri 
Pompeu asked about. 

Petr

On Dec 8, 2011, at 10:10 AM, Francois Berenger wrote:

> On 12/08/2011 05:11 PM, Petr Leiman wrote:
>> Dear Bostjan,
>> 
>> There is Chimera for almost anything you can think of.
> 
> Not coot, you are sure?
> 
> Because (i) Chimera is not part of CCP4 and (ii) usually
> coot does everything on this mailing list. :)
> 
> > Search for "Structure-Based Sequence Alignment" on this page:
>> http://www.cgl.ucsf.edu/chimera/features.html
>> 
>> Petr
>> 
>> 
>> 
>> On Dec 8, 2011, at 6:39 AM, Bostjan Kobe wrote:
>> 
>>> Consurf will do this for you.
>>> 
>>> Bostjan
>>> 
>>> ---
>>> Bostjan Kobe
>>> NHMRC Research Fellow
>>> Professor of Structural Biology
>>> School of Chemistry and Molecular Biosciences
>>> 
>>> and Institute for Molecular Bioscience (Division of Chemistry and
>>> Structural Biology) and Centre for Infectious Disease Research
>>> 
>>> 
>>> Cooper Road
>>> University of Queensland
>>> Brisbane, Queensland 4072
>>> Australia
>>> Phone: +61 7 3365 2132
>>> Fax: +61 7 3365 4699
>>> E-mail: b.k...@uq.edu.au
>>> URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe
>>> Office: Building 76 Room 329
>>> Notice: If you receive this e-mail by mistake, please notify me, and do
>>> not make any use of its contents. I do not waive any privilege,
>>> confidentiality or copyright associated with it. Unless stated otherwise,
>>> this e-mail represents only the views of the Sender and not the views of
>>> The University of Queensland.
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On 8/12/11 3:26 PM, "Yuri Pompeu"  wrote:
>>> 
 I once saw a figure showing the protein as surface, but instead of having
 it coloured by atom type
 or potential, it was shown by percent conservation in the family.
 Something like red highly conserved, all the way to white, not conserved
 at all...
 Now, I assume the figure was done by uploading aligned sequnces of
 several members of a family, and the colouring
 the generated surface accordingly.
 Does anyone know a way to do this more elegantly than what I tried doing?
 ps. I quit colouring them manually after I remebered my protein was 407
 aa long...

Re: [ccp4bb] Efficient way of showing residue conservation

[Francois Berenger]

On 12/08/2011 05:11 PM, Petr Leiman wrote:

Dear Bostjan,

There is Chimera for almost anything you can think of.


Not coot, you are sure?

Because (i) Chimera is not part of CCP4 and (ii) usually
coot does everything on this mailing list. :)

> Search for "Structure-Based Sequence Alignment" on this page:

http://www.cgl.ucsf.edu/chimera/features.html

Petr



On Dec 8, 2011, at 6:39 AM, Bostjan Kobe wrote:


Consurf will do this for you.

Bostjan

---
Bostjan Kobe
NHMRC Research Fellow
Professor of Structural Biology
School of Chemistry and Molecular Biosciences

and Institute for Molecular Bioscience (Division of Chemistry and
Structural Biology) and Centre for Infectious Disease Research


Cooper Road
University of Queensland
Brisbane, Queensland 4072
Australia
Phone: +61 7 3365 2132
Fax: +61 7 3365 4699
E-mail: b.k...@uq.edu.au
URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe
Office: Building 76 Room 329
Notice: If you receive this e-mail by mistake, please notify me, and do
not make any use of its contents. I do not waive any privilege,
confidentiality or copyright associated with it. Unless stated otherwise,
this e-mail represents only the views of the Sender and not the views of
The University of Queensland.





On 8/12/11 3:26 PM, "Yuri Pompeu"  wrote:


I once saw a figure showing the protein as surface, but instead of having
it coloured by atom type
or potential, it was shown by percent conservation in the family.
Something like red highly conserved, all the way to white, not conserved
at all...
Now, I assume the figure was done by uploading aligned sequnces of
several members of a family, and the colouring
the generated surface accordingly.
Does anyone know a way to do this more elegantly than what I tried doing?
ps. I quit colouring them manually after I remebered my protein was 407
aa long...

Re: [ccp4bb] Efficient way of showing residue conservation

[Joel Sussman]

8-Dec-2011   10:40am
Dear Bostjan
Consurf is also interfaced to Proteopedia, http://www.proteopedia.org,  i.e. 
for all structures that have at least several sequences, one can automatically 
see an evolutionarily colored 3D Jmol image of the structures by just pushing 
the ConSurf button.
See, e.g. http://proteopedia.org/wiki/index.php/1hho
the "STRUCTURE OF HUMAN OXYHAEMOGLOBIN AT 2.1 ANGSTROMS RESOLUTION" by Boaz 
Shaanan
and click on button "Evolutionary conservation:  [show]"
best regards,
Joel
On 8 Dec 2011, at 07:39, Bostjan Kobe wrote:

Consurf will do this for you.

Bostjan

---
Bostjan Kobe
NHMRC Research Fellow
Professor of Structural Biology
School of Chemistry and Molecular Biosciences

and Institute for Molecular Bioscience (Division of Chemistry and
Structural Biology) and Centre for Infectious Disease Research


Cooper Road
University of Queensland
Brisbane, Queensland 4072
Australia
Phone: +61 7 3365 2132
Fax: +61 7 3365 4699
E-mail: b.k...@uq.edu.au
URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe
Office: Building 76 Room 329
Notice: If you receive this e-mail by mistake, please notify me, and do
not make any use of its contents. I do not waive any privilege,
confidentiality or copyright associated with it. Unless stated otherwise,
this e-mail represents only the views of the Sender and not the views of
The University of Queensland.





On 8/12/11 3:26 PM, "Yuri Pompeu" 
mailto:yuri.pom...@ufl.edu>> wrote:

I once saw a figure showing the protein as surface, but instead of having
it coloured by atom type
or potential, it was shown by percent conservation in the family.
Something like red highly conserved, all the way to white, not conserved
at all...
Now, I assume the figure was done by uploading aligned sequnces of
several members of a family, and the colouring
the generated surface accordingly.
Does anyone know a way to do this more elegantly than what I tried doing?
ps. I quit colouring them manually after I remebered my protein was 407
aa long...

Re: [ccp4bb] Efficient way of showing residue conservation

[Boaz Shaanan]

Just to add on others' tips: Consurf is interfaced to Chimera.

   Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710






From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yuri Pompeu 
[yuri.pom...@ufl.edu]
Sent: Thursday, December 08, 2011 7:26 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Efficient way of showing residue conservation

I once saw a figure showing the protein as surface, but instead of having it 
coloured by atom type
or potential, it was shown by percent conservation in the family. Something 
like red highly conserved, all the way to white, not conserved at all...
Now, I assume the figure was done by uploading aligned sequnces of several 
members of a family, and the colouring
the generated surface accordingly.
Does anyone know a way to do this more elegantly than what I tried doing?
ps. I quit colouring them manually after I remebered my protein was 407 aa 
long...

Re: [ccp4bb] Efficient way of showing residue conservation

[Petr Leiman]

Do I feel stupid! My previous message about Chimera should have been addresses 
to Yuri Pompeu, but not to Bostjan Kobe.

Sincerely,

Petr


On Dec 8, 2011, at 6:26 AM, Yuri Pompeu wrote:

> I once saw a figure showing the protein as surface, but instead of having it 
> coloured by atom type
> or potential, it was shown by percent conservation in the family. Something 
> like red highly conserved, all the way to white, not conserved at all...
> Now, I assume the figure was done by uploading aligned sequnces of several 
> members of a family, and the colouring
> the generated surface accordingly. 
> Does anyone know a way to do this more elegantly than what I tried doing?
> ps. I quit colouring them manually after I remebered my protein was 407 aa 
> long...

Re: [ccp4bb] Efficient way of showing residue conservation

[Petr Leiman]

Dear Bostjan,

There is Chimera for almost anything you can think of. Search for 
"Structure-Based Sequence Alignment" on this page:
http://www.cgl.ucsf.edu/chimera/features.html

Petr



On Dec 8, 2011, at 6:39 AM, Bostjan Kobe wrote:

> Consurf will do this for you.
> 
> Bostjan
> 
> ---
> Bostjan Kobe
> NHMRC Research Fellow
> Professor of Structural Biology
> School of Chemistry and Molecular Biosciences
> 
> and Institute for Molecular Bioscience (Division of Chemistry and
> Structural Biology) and Centre for Infectious Disease Research
> 
> 
> Cooper Road
> University of Queensland
> Brisbane, Queensland 4072
> Australia
> Phone: +61 7 3365 2132
> Fax: +61 7 3365 4699
> E-mail: b.k...@uq.edu.au
> URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe
> Office: Building 76 Room 329
> Notice: If you receive this e-mail by mistake, please notify me, and do
> not make any use of its contents. I do not waive any privilege,
> confidentiality or copyright associated with it. Unless stated otherwise,
> this e-mail represents only the views of the Sender and not the views of
> The University of Queensland.
> 
> 
> 
> 
> 
> On 8/12/11 3:26 PM, "Yuri Pompeu"  wrote:
> 
>> I once saw a figure showing the protein as surface, but instead of having
>> it coloured by atom type
>> or potential, it was shown by percent conservation in the family.
>> Something like red highly conserved, all the way to white, not conserved
>> at all...
>> Now, I assume the figure was done by uploading aligned sequnces of
>> several members of a family, and the colouring
>> the generated surface accordingly.
>> Does anyone know a way to do this more elegantly than what I tried doing?
>> ps. I quit colouring them manually after I remebered my protein was 407
>> aa long...

Re: [ccp4bb] Efficient way of showing residue conservation

[Bostjan Kobe]

Consurf will do this for you.

Bostjan

---
Bostjan Kobe
NHMRC Research Fellow
Professor of Structural Biology
School of Chemistry and Molecular Biosciences

and Institute for Molecular Bioscience (Division of Chemistry and
Structural Biology) and Centre for Infectious Disease Research


Cooper Road
University of Queensland
Brisbane, Queensland 4072
Australia
Phone: +61 7 3365 2132
Fax: +61 7 3365 4699
E-mail: b.k...@uq.edu.au
URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe
Office: Building 76 Room 329
Notice: If you receive this e-mail by mistake, please notify me, and do
not make any use of its contents. I do not waive any privilege,
confidentiality or copyright associated with it. Unless stated otherwise,
this e-mail represents only the views of the Sender and not the views of
The University of Queensland.





On 8/12/11 3:26 PM, "Yuri Pompeu"  wrote:

>I once saw a figure showing the protein as surface, but instead of having
>it coloured by atom type
>or potential, it was shown by percent conservation in the family.
>Something like red highly conserved, all the way to white, not conserved
>at all...
>Now, I assume the figure was done by uploading aligned sequnces of
>several members of a family, and the colouring
>the generated surface accordingly.
>Does anyone know a way to do this more elegantly than what I tried doing?
>ps. I quit colouring them manually after I remebered my protein was 407
>aa long...

Re: [ccp4bb] Efficient way of showing residue conservation

[James Stroud]

Usually you put a statistic like this in the tempFactor field (B) and then 
color by "B-factor" in pymol or similar.

I'm certain there is a facility for filling this entry somewhere. If not, then 
a fairly trivial server is waiting for someone to create it and claim the glory.

Google something like "alignment b-factor" or "clustal b-factor". That's my 
best guess.

James


On Dec 7, 2011, at 10:26 PM, Yuri Pompeu wrote:

> I once saw a figure showing the protein as surface, but instead of having it 
> coloured by atom type
> or potential, it was shown by percent conservation in the family. Something 
> like red highly conserved, all the way to white, not conserved at all...
> Now, I assume the figure was done by uploading aligned sequnces of several 
> members of a family, and the colouring
> the generated surface accordingly. 
> Does anyone know a way to do this more elegantly than what I tried doing?
> ps. I quit colouring them manually after I remebered my protein was 407 aa 
> long...