Dear all,
I am writing because I have a question that concerns coot or ccp4 (don't
know which one). I have 2 maps and one model. One of the map is an
experimental map that has not seen one inch of a model, the second map
is generated after refinement of a molecular replacement model. Same
How about overlapmap in ccp4?
Thanks
Abhinav
Stanford Synchrotron Radiation Lightsource
Joint Center for Structural Genomics
Mail Stop 99
Phone: (650) 926-2992
Fax: (650) 926-3292
Vellieux Frederic wrote:
Dear all,
I am writing because I have a question that concerns coot or ccp4
For a global CC:
Reflaction Data utilities/Phase comparison
For residue by residue:
Map and Mask utilities/Map correlation
Note that the global CC will not be the average of the residue by
residue, since it also correlates over solvent, etc.
Kevin
Vellieux Frederic wrote:
Dear all,
I am
Kevin Cowtan wrote:
For residue by residue:
Map and Mask utilities/Map correlation
Thanks Kevin, indeed this second option was what I was looking for. And
thanks for the other suggestions too. Unfortunately, I do not know all
CCP4i programs by heart :-(
Fred.
First you must be on the same origin
There are various ways to get there - brute force method is to calculate
phases from both models, combine them, and use the reflection utility
phase match to move one to the other by an appropriate origin shift...
Then
Use the GUI map correlation.
It will
Eleanor Dodson wrote:
First you must be on the same origin
There are various ways to get there - brute force method is to
calculate phases from both models, combine them, and use the
reflection utility phase match to move one to the other by an
appropriate origin shift...
Then
Use the GUI
Hi Fred,
you can do all this in PHENIX, using command line or the GUI.
- GUI: from main PHENIX GUI click on Comprehensive validation, the
rest should be obvious.
- also, all these values are computed and available after any
phenix.refine run using PHENIX GUI.
- command line: type
Hi, you may want to try the Bias removal Server at tuna.tamu.edu
HTH,
Sid.
On 2/20/07, Charles W. Carter Jr. [EMAIL PROTECTED] wrote:
Is there a CCP4 program that will calculate residue-by-residue
correlation coefficients for a molecular replacement solution and an
experimentally phased map?
overlapmap does this for any set of coordinates and any map.
Eleanor
Charles W. Carter Jr. wrote:
Is there a CCP4 program that will calculate residue-by-residue
correlation coefficients for a molecular replacement solution and an
experimentally phased map?
Thanks,
Charlie
Is there a CCP4 program that will calculate residue-by-residue
correlation coefficients for a molecular replacement solution and an
experimentally phased map?
Thanks,
Charlie
**UNCrystallographers NOTE new website url**
[EMAIL PROTECTED]
On Tuesday 20 February 2007 11:04, Charles W. Carter Jr. wrote:
Is there a CCP4 program that will calculate residue-by-residue
correlation coefficients for a molecular replacement solution and an
experimentally phased map?
Coot has a validation tool that produces a residue-by-residue
Overlapmap will calculate residue-by-residue CC.
Thanks
Abhinav
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Charles W.
Carter Jr.
Sent: Tuesday, February 20, 2007 11:04 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Real Space Correlation
Sorry, I didn't read the question.
sfcheck wouldn't calculate CC between exp and MR map.
Ed
Edward Berry wrote:
Also sfcheck calculates correlation coefficient for
main chain and side chain of each residue, presented
graphically in row 2 of the figure starting page 3
(example:
Dear all,
We are currently looking into setting up some inexpensive and personal
incubators for crystallization at a stable temperature of ~25C. I
was told that a couple of years back there was an active discussion on
the forum about making some house-hold items into such an incubator,
more
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