Hello, everyone,
I've a protein sequence of known domain. Based on structure alignment,
I've got a alignment of those with known structures. Then how to add my
sequence to the alignment?Any suggestions?
Regards,
Yuan SHANG
Dear Yuan SHANG,
you can use Jalview do create and edit an alignment with your sequence.
Jalview is available at http://www.jalview.org/, and I quite liked it when I
worked with it.
Tim
On Mon, May 31, 2010 at 04:29:48PM +0800, 商元 wrote:
Hello, everyone,
I've a protein sequence of known
Dear Colleagues,
Call is open for proposals for the PX (Protein Crystallography) beamlines of
the Swiss Light Source, SLS.
Deadline for proposal submission: Tuesday, June 15, 2010 (00:00 (midnight)).
Submission: All submissions will be handled by the SLS Digital Users Office
(DUO) /contact:
Hello everyone,
I collected a x-ray crystal data at around 3-4A resolution and processed
with HKL2000.
The space group, P6, C2, C222, P2, P1, were possible when indexing.
I tried all these space groups.
However, when first cycle of scaling without using rejection, chi square
values of the
Dear Yuan,
the MUSCLE program can do that for you. It is capable of doing
profile-profile and profile-sequence alignments.
http://www.drive5.com/muscle/muscle_userguide3.8.html#_Toc260497021
Section 2.10 of the manual should be what you want.
Cheers,
Thomas
On Mon, May 31, 2010 at 01:46, Tim
Paul,
Does your lower resolution structure have the same unit cell as the
model used for MR? If your two crystals are the same except for the
presence of the ligand, then you need to make sure to keep the same
Rfree set for both. Otherwise, some reflections that were previous in
the
This reminded me another thing... Did you create the free-R flags
considering twinning? This is very important.
Pavel.
On 5/31/10 12:43 PM, Gregory Bowman wrote:
Paul,
Does your lower resolution structure have the same unit cell as the
model used for MR? If your two crystals are the same
Does anyone know of a program that can calculate the theoretical PI of
metal-bound proteins? All that I’ve seen are programs that only account for
the protein sequence. Any information is helpful. Sorry for the basic
non-ccp4 question.
LH
Lori B. Horton, Predoctoral Fellow
Baylor
