Hi all,
during concentrating my protein, using Amicon Ultra centrifugal filter devices,
5000g, 4C, I lost large amount of my protein (75%). I heard the same story from
one of my colleagues too. It seems the membrane of the Amicon tube ate my
protein.
Why this happen and how to recover my prote
itional
2-fold axis. But not fully understand the symmetry in details in this case.
Your help and teaching are highly appreciated.
Yanming Zhang
All UNIX gurus,
I need to change 300 image file names sequentially, such as:
XXX_10001.img to XXX_101.img
XXX_10002.img to XXX_102.img
Obviously, using UNIX 'mv' to work on 300 files is stupid. Anyone can give me a
very simple UNIX shell file to finish the job quickly? Thank y
Hi, all,
If I have a large molecule, say 2000 aa, the coot ramachandran plot will
be lots of outliers. Now I want to do things one step at a time, i.e
checking the outliers by residue ranges such as, 1--500, 501--1000, so on.
Can COOT do this? I remember Xfit has this function. Thanks
Yanming
Hello,
I want to make a movie to show the process of ligand
switch. In the movie, the first ligand will gradually be replaced by the
second ligand(Include the conformation change such as the bond rotation
when the second is approaching). possible to make this movie? I will use
Pymol+eMovie to
Hello,
I did the replacement soaking and it was successful. Now I want to
superimpose the two maps to show (I hate to show off but I have to) the
map diffrence of the ligand region to demonstrate that the replacement
soaking was a success. Is there a way to superimpose the two maps?
The two
Dear All,
I set up drops using RTISCC:1Lambda protein complex+1Lambda reservoir.
But I am not sure how much another ligand(50mM) I should add into the
drop. Any suggestion? Thank you very much.
Yanming
Hi All,
Maybe, I should not have asked this question:
Can anybody give me the hints (or point to the references) on the impact
of His tag on crystallization experiments. In perticular:
1, With or without His tag, which one is better for crystallization?
2, If I successfully crystallized N-termi
Dear all,
Sorry I did not make it clear in my first email. Now my question can boil
down to:
IS IT POSSIBLE TO ONLY ZOOM ONE OBJECT AND KEEP ALL THE OTHER OBJECTS
UN-ZOOMED IN PYMOL?
thanks
Yanming
On Mon, 29 Oct 2007, Yanming Zhang wrote:
Hi, all,
I want to make a pymol figure wich
Hi, all,
I want to make a pymol figure wich can show the pretty density of a
ligand. But we don't want to show the detailed chemical info of the
ligand. If I use a
large enough sphere_scale for the ligand, the chemical info will be hidden
but the density map will be disrupted. If I use a sma
Hi, Joe,
1,Try SHARP and then check the quality of the map. If good, continue,
if bad, need re-examine your data. I Think SHARP is good for your case.
2, Do not give up the possibility of twinning. A lower symmetry plus a
nearly perfect twin operator might mislead to a higher symmetry.
Yanmin
Hi, All,
After lunching pymol, if I drag the Xterm window produced by PYMOL using
mouse, my computer will suddenly freeze, the keyboard seems no longer
functioning. The only thing I can do is to re-boot my Linux system.
This problem makes it almost impossible for me to use PYMOL on my LINUX
Hi,
Thank you all the repliers who kindly offer their hands after my
PREVIOUS posting message. I received around 12 messages in total and the
concensus reply is:
P422 POINT GROUP WITH ONLY ONE MOLECULE IN ONE A.U.(peak (90 45 180)
indicates P422 with the 2-fold crystallographic symmetry alon
Hi ,
Please help me on this structure:
Data 1.8A: cell 84.892 84.892 172.580 90 90 90 with tetrahedral index
Space group: P43212 or P43, Final refinement Rfree indicates P43 is better
so most likely P43(also the systematic absence indicate P43 is it)
Matthew coeffient indicates: P43 3mol/a.u(2.5
a lower
value -- either using Extensions->Set Matrix (Refinement Weight) or in your
.coot file:
(set-matrix )
There's also a coot-bb, btw.
JED
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of
Yanming Zhang
Sent: 29 May 2007 01:50
To: CCP4BB
Hi,
I use coot almost around the clock. One thing troubles me is that:
when clicking on 'real space refine zone', coot seems only care about the
'real space'(Electron density), sometimes it will bring the model to
the density no matter whether the density was already claimed by other
model at
Hi, All,
I have image files with the format of extention .sfrm. I have to
re-process the dataset. But HKL2000 is unavailable in my group and mosflm
seems can not handle this format. Can you tell me:
Which data process program can handle .sfrm format to survive the
re-processing of the data?
Dear All,
lately I have a fantacy toward ccp4mg. But either from
ccp4i or typing 'ccp4mg' directly from the prompt(Linux),
I got the following error message:
Loading fonts..
...DONE
Starting graphics thread..
...DONE
Parsing command line..
...DONE
Redirecting output to /home/yzhang/.CCP4MG/c
07 03:51:50 -0500
Von: Yanming Zhang <[EMAIL PROTECTED]>
An: CCP4BB@JISCMAIL.AC.UK
CC:
Betreff: [ccp4bb] Very weird
Dear all,
I am sorry to trouble you again because I am facing a very weird
situation:
Three copies from Phaser are the right solutions based upon:
1, Rfree 42% R 39%
2, No pa
Dear all,
I am sorry to trouble you again because I am facing a very weird
situation:
Three copies from Phaser are the right solutions based upon:
1, Rfree 42% R 39%
2, No packing clash
3, The packing within the 3 makes good sense
4, Density evenly distributed among the 3 copies even without N
Dear All,
After I send out the 'SOS' for my multi-copy problem, I have received many
good suggestions and tips. Many thanks to all of you.
Now my problem has been solved:
1, There are only 4 molecules in a.u, even the solvent containt is high,
it is not uncommon for a data with low resolution
spacegroup with fewer molecules in the asymm unit?
What does the self rotation show?
Yanming Zhang wrote:
Dear All,
Maybe this is a trivial question:
My data should have 6 molecules in one assymetric unit. MR could find out
4 molecules. After this, no matter how hard I have tried, no more
Dear All,
Maybe this is a trivial question:
My data should have 6 molecules in one assymetric unit. MR could find out
4 molecules. After this, no matter how hard I have tried, no more
molecules can be found. At this stage, I suppose that all other copies are
dis-ordered. And go ahead to do r
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