Dear Friends,
I have a question about judging a homology
model. I have three homologous proteins A, B and C of which only A has
3D crystal structure available. Their similarities/identities are
given below.
Pair-wise alignment similarity/identity (%)
A and B
Dear All,
Happy New Year
I am working with a 2.06 Ang resolution structure in F432 space group and
further using REFMAC (also tried Phenix) program for refinement of my
model.
Every thing in the structure seems good, R factor/ R free= 18.59/20.77 but
the structure is too noisy (blobs of differen
Dear CCP4ers
Can anyone recommend their favourite paper, or review, that discusses
anions in protein structures.
Thanks in advance and Happy New Year
Gina
Notice: This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse S
Hi Raja,
1) how big is your protein ?
2) multiple domains ? What's the ID/sim between domains ?
3) Check Xtalpred in case you've overlooked a closer homolog
http://ffas.burnham.org/XtalPred-cgi/xtal.pl
I would not try to predict an intermediate model and then use that to
predict the final mode
On Tue, Jan 5, 2010 at 9:24 AM, Raja Dey wrote:
> Assuming all the above data are right, which of the following way would
> give the best model for C?
>
> 1. Building homology model of C with A as template.
>
> 2.Building homology model of B with A as template and then use B as
> template t
Dear Friends,
I have a question about judging a homology model. I
have three
homologous proteins A, B and C of which only A has 3D crystal structure
available. Their similarities/identities are given below.
Pair-wise alignment similarity/identity (%)
A and B
Dear Katja,
You can find below information from PDB Format Guide,
http://www.wwpdb.org/documentation/format32/remarks2.html#REMARK%20500.
The improper CA-C-CB-N angles for chiral centers are calculated and are
listed in REMARK 500 of PDB file.
It is defined below with 10 degree allowed deviati
Hello again
I am refine my model using TLS and restrained refinement, and I got
below the error message from refmac although the program claim to be
successful. There is no output mtz and pdb files. Any suggestions are
appreciated!
Many thanks!
Jane
***TLS refinement cycle***7
1
Hello again
I am refine my model using TLS and restrained refinement, and I got
below the error message from refmac although the program claim to be
successful. There is no output mtz and pdb files. Any suggestions are
appreciated!
Many thanks!
Jane
***TLS refinement cycle***7
Hi
I think that even post-refining with high resolution data you are unlikely
to refine reliably to the same value within 1 part in 10,000 if you are
making small differences to your processing. The differences you have are
what I would consider to be within experimental error, so I wouldn't worry
Nothing wrong with that approach in principle. You may want to have a
few cycles of rigid body refinement before classical refinement. Just in
case (but the cell parameters are very very close indeed). And the
starting Rfactors should tell you if there is a problem or not.
Fred.
Jane Bailey w
Hi
I was processing my data with XDS several runs, they gave slightly
different cell parameters everytime, eg:
1) 77.100 103.850 116.550 90.00 90.00 90.00 P 21 21 21
2) 77.086 103.821 116.533 90.00 90.00 90.00 P 21 21 21
I have already a refined model from 1), can I use this m
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