Dear Nian,
staying within CCP4:
% echo END | pdbset xyzin your.pdb
will print something like
Orthogonal Coordinate limits in output file:
Minimum MaximumCentre Range
On X : 103.67119.61111.64 15.94
On Y : 58.62 93.54
You can use Coot to find the centre of mass. In the scripting window just
type:
in scheme:
(centre-of-mass yourmoleculenumber)
or in python:
centre_of_mass(yourmoleculenumber)
Bernhard
BTW the American spelling of centre (center) should work too...
Dear all,
I was trying to do a NCS
Yes, it is available in the GUI...
Flip
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Peter
Adrian Meyer
Sent: Wednesday, May 09, 2007 23:28
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and B factors
Simon,
REFI BREF OVERALL should do
LSQKAB also tells you the centres of mass of the molecules you are fitting
Look in the log file (Centroid == centre of mass)
CENTROID OF WORKING MOLECULE : -87.717 116.189 1.694
CENTROID OF WORKING MOLECULE :(fractional) -0.180 1.170 0.010
CENTROID OF REFERENCE
Hi Simon,
Well, X-ray crystallography nowadays often, but certainly not always,
amounts to running a set of programs with default settings with a few mouse
clicks in the GUI. The fun part is knowing when you have to deviate from
default, leave the well travelled paths etc.
The GUI is
Just to complete the set, in pdb-mode for emacs, if you do
pdb-increment-centroid 0 0 0 (e.g. to move a molecule to the origin), it
reports the original centroid.
Cheers,
Charlie
--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and
Seems to be a general issue.
Read the editorial in Nature 10 May 2007 Volume 447 Number 7141, pp116.
Under the microscope - The use of 'black box' techniques carries risks.
Colin
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of Flip Hoedemaeker
Sent: 10 May
I would add that I have found the CCP4 development team very receptive
to being informed about specific improvements which could be made, and
even more so to fixes implemented by users themselves.
Perhaps an explicit list of the many limitations which need attention
would be useful to the
... Forgot to say that Simon obviously is right in that the check box
before refine B factors should not be there.
Flip
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Charlie Bond
Sent: Thursday, May 10, 2007 11:40
To: CCP4BB@JISCMAIL.AC.UK
Subject:
The level of detail in the GUI is a matter of constant debate. The
underlying programs are far far richer, so the question is how much to
expose in the GUI. We try to get a balance between ease-of-use and
coverage, but it won't always work. BTW I don't think we ever claimed
that ccp4i (or anything
Dear all,
As somebody already thought about an user-personalized interface, eg. a CCP4
menu where people could drag drop their favorite (or mostly used)
programs?
Cheers,
Stefan
-Message d'origine-
De : CCP4 bulletin board [mailto:[EMAIL PROTECTED] De la part de Martyn
Winn
Envoyé :
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi Martyn,
I was thinking in the less scary widgets-based interface for
not-so-used options. If possible, I think that all options should be
available to the interface. This would make the GUI more consistent, in
a way. I know is a lot more work, but
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Two Ph.D. fellowships and one postdoctoral fellowship are available in
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Src Homology 3 (SH3) domains
Miguel Ortiz Lombardia wrote:
I was thinking in the less scary widgets-based interface for
not-so-used options. If possible, I think that all options should be
available to the interface.
My programs at least have a load of options which I put in for the
purposes of testing out ideas, which
Hi Martyn,
I want to second Miguel: a switch between a basic GUI (could be with
even less options) and an advanced and expert GUI that allows
access to most and all options that can be used in scripts would be
absolutely great! It would allow novice users to do a good job on
standard
I always liked Kevin's comments on little-used options in the DM
documentation
Don't use these unless you really know what you are doing. In which
case you'd better have a better idea of what you
are doing than I do.
Phil
On 10 May 2007, at 13:07, Kevin Cowtan wrote:
Miguel Ortiz
The level of detail in the GUI is a matter of constant debate. The
underlying programs are far far richer, so the question is how much to
expose in the GUI.
How about the simple and elegant way it is done in Refmac?
Tacked under Developers Options is specify an external
keyword script file for
IMO, the GUI is a lifesaver for getting undergraduates involved in
crystallography in an efficient way. While it is possible to teach my
undergraduates to write scripts for CNS, CCP4, and O, it is much, much
easier for them to learn the CCP4 GUI. Sooner or later, real problems
require you to look
Hi Martyn,
how about option c:
in each gui window at the lower left corner have a button called
Display script, or call it Expert Mode if people feel better as
Experts :-) , before running of course. Then people who would like to
edit their stuff could do so before running the script. I
I think a tweak script button or option (before running) would be an
excellent idea.
Cheers,
___
Roger S. Rowlett
Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax:
As long as I have been using the ccp4i (which has been a couple of years
now), this magic button has been there, and it has even been in the 'lower
left corner': When you hold your mouse button on the Run button, a submenu
appears, the second item of which is saying RunView com file. This opens
Hi Martyn:
I never use the GUI and it scares me, so I probably should just STFU, but
that sort of thing has never kept me from pontificating. I often get
emails from people asking how to do something with the GUI and they don't
believe me, because I've developed a reputation as something of a
*PROTEIN CRYSTALLOGRAPHER*
Job # 20546
The X-ray Crystallography Team of the Integrated Center for Structure
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Hopefully my offhand remark wasn't taken as a criticism of ccp4i (it
wasn't meant as such); but seeing as I don't use it, it's not a place
where I could tell someone how to find an option.
As developers, we also have to think about long-term maintainability.
Options, in particular little-used
Hi, All,
I have a question about rmsd calculation.
I have some pdbs (100 residues ) and these pdbs differ pretty much only the
loop region 40-60. Is there any easy way that I can superimpose the fixed
region ( 1-40,60-100) and then calculate the rmsd for the loop?I need to
calculate for each
Hi Jenny,
You can do this in LSQMAN (if I'm understanding your question
correctly...)
You'd first superimpose the residues in the fixed region to give a
superimposed core using the 'EXplicit' command, eg:
LSQMAN ex m1
Range 1 ? (A1-10) a4-10 a19-23 a28-36 a44-51 a53-66 a91-97
Hello,
I'm an undergraduate and recently crystallized and obtained 2.9A
diffraction data for a protein which is predicted to fold into a WD40
7-bladed beta-propeller structure (which has been crudely verified by
cryo-EM by another lab). The space group appears to be I4(1) with
unit cell
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