Hello,
I am not a crystallographer, so I will ask
a maybe stupid question.
When you say "After molecular replacement you should check the result
with the model building program of your choice and correct as many
errors as possible before running a refinement program."
Can this step be automated in some way (without any
human intervention)?
Are there programs to do this?
I am interested even if some program does only one part of the job.
Thanks a lot,
Francois.
Tim Gruene wrote:
Dear Xinghua,
the solvent content provided by yhe Matthews-program is certainly correct.
Whether or not it applies to you protein is a different issue. With only 2
molecules in the asymmetric unit the solvent content rises to 65%, and this is
stll perfectly fine for proteins. So carry out molecular replacement with only
two molecules and start model building and refinement.
Your previous message sounds as though to started refinement directly after
molecular replacement. I would strongly discourage you from this practice (which
somehow seems to be stuck in the heads of many people). After molecular
replacement you should check the result with the model building program of your
choice and correct as many errors as possible before running a refinement
program.
Tim
On Fri, Jun 25, 2010 at 01:54:05PM +0800, xinghua qin wrote:
Hi everyone:
Thanks for all the responses.
The Matthaws-cell content analysis programe in CCP4 package gives the
results: 47% solvent content and 3 molecules in asu with 87% confidence.
the space group is P3121. how to carry out self rotation function? can
phaser do that work? If there areTwo moleculars in asu ,no clashes and the
TF values are above 10.but if three, the clashes are too much and TF valur
is about five.
And how to calculate the solvent content? Is the calculated solvent content
with the Matthews-cell content analysis programe not always right?
Best regards
Xinghua Qin
On Fri, Jun 25, 2010 at 10:42 AM, Vineet Gaur <[email protected]>wrote:
Hi
It would b good if u can mention the solvent content and space group along
with the no. of molecules in asu/
u can carry out self rotation function to check the no of mol in asu
best
vineet
On Fri, Jun 25, 2010 at 6:42 AM, xinghua qin <[email protected]> wrote:
hi CCPeers
The Matthews coefficient of my protein is 3 calculated with
matthews-cell content analysis CCP4 programe with 87% confidence , but when
doing the refinement the third molecular couldn't get into the unit cell
because of too many clashes.Deletion of the clashed AA did not work well,
Then I used two molecules in the unit cell, After refining with Refmac, I
found that the R factor is 0.29, R free is 0.40.I believe the value can be
better with the real space refinement.But the question is that can the
calculated Matthews coefficient be wrong?
Best regards
Xinghua Qin
--
Xinghua Qin
College of Biological Sciences
No.2, Yuan Ming Yuan West Road
Haidian District,Beijing,China,100094
Tel: +86-10-62732672
--
Xinghua Qin
College of Biological Sciences
No.2, Yuan Ming Yuan West Road
Haidian District,Beijing,China,100094
Tel: +86-10-62732672
