Hello,
To answer the question of Dilip, you can change starting sequence
numbers in ESPript by editing the MSA file as explained in the doc
http://espript.ibcp.fr/ESPript/ESPript/esp_userguide.php
We got in touch with him by mail to answser his question in more details.
We take this opportunity to announce the release of the new version of
our webserver ENDScript, which is associated to ESPript.
http://endscript.ibcp.fr
This new version supports automatic generation of PyMOL scripts that
allows analysis of sequence and structure conservation for a chosen PDB
file.
Output examples from selected PDB entries are illustrated here.
http://espript.ibcp.fr/ESPript/ENDscript/end_gallery.php
ESPript has also been upgraded with a new interface.
Links from T-Coffee and to Jalview are supported.
Cheers
Patrice and Xavier
Le 04/02/2014 08:38, Dilip Badjugar a écrit :
Hi Martyn,
Thank you very much for you suggestions, it worked out for me. But, if I
have multiple sequences in alignment, how should I go in that case?
Thanking you in advance
DCB
On Tue, Feb 4, 2014 at 12:14 AM, MARTYN SYMMONS <
martainn_oshioma...@btinternet.com> wrote:
Hi Dilip
the numbering can be given for the top and the bottom sequence only in
ESPRIPT
you enter the command to produce these in the SPECIAL COMMANDS AND
CHARACTERS BOX. You only get this box on the server input page if you
select the ADV version in the header - this is the ADVANCED version of
the input page.
The relevant commands start with Y for the top numbering and Z for the
bottom numbering
so in the box you enter (say):
Y D 1-1000
Z D 1-1000
as separate lines
which are understood as
Y - give top numbering
D - make it black * (B is blue, R is red - there is a guide alongside
the box to the colour codes)
1-1000 - number the range 1 to 1000 (or what ever you want... I guess
you can change colour for ranges within the sequence)
Notice you cannot change the order of the sequences in the MSA in ESPRIPT
- I usually do it manually if I want a particular sequence at the top and
bottom.
Hope this helps
all the best
Martyn
(hmmm well that is 'Dubh' in Gaidhlig...)
------------------------------
*From:* Dilip Badjugar <dilip....@gmail.com>
*To:* CCP4BB@JISCMAIL.AC.UK
*Sent:* Saturday, 1 February 2014, 5:49
*Subject:* [ccp4bb] MSA with starting amino acid numbers
Dear users,
I know one server for having the secondary structure over MSA i.e.
Espript. But I want to incorporate the staring amino acid for protein. I
could not find this option in the tutorial. Is it the post editing is the
only way to add the amino acid numbers or there are other server which
allow me to do so?
Thanking you in advance.
DCB
--
Mr.Dilip C. Badgujar,
Senior Research Fellow,
ACTREC,
Tata Memorial Center,
Sector-22, Kharghar,
Navi Mumbai.
Pin-410210
--
BioCrystallography and Structural Biology of Therapeutical Targets Group
Institut de Biologie et Chimie des Proteines, FR3302
Molecular and Structural Bases for Infectious Diseases, UMR 5086
7 passage du Vercors
69367 Lyon Cedex 07 - France
tel: (0|33) 4 72722624
fax: (0|33) 4 72722616
