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Hi Jenny and Iain,
But my understanding is that Iain's procedure gives the rmsds of the
_aligned_ C-alphas, whereas Jenny actually seems to be more interested
in those that she excludes from the alignment. I may be wrong, but in
these cases, I use lsq
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 pa
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 a106
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 pai
That kind of thing has been suggested a few times, and in principle is
a better way of doing things.
One problem we face, is that we're a collaboration rather than a single
project, and it is not always possible to adopt neat solutions across the
suite. Which is partly why ccp4i was designed to
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
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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 Ma
Hi Tim,
I just had a conversation with somebody who pointed that out to me, that
tells you how much I use the GUI :-)
Thanks,
Juergen
Tim Grune wrote:
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
th
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 "Run&View com file". This o
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: (315)-228
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
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 u
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 fo
The most useful aspect of the ccp4i GUI is its automatic generation of
com files. However, I would prefer the GUI to output a .com file into my
working directory (rather than the obscure location they are saved to
now) every time I run a program so that I can then tinker with it and
add any extra k
Thanks Pierre. Its good to have more than one idea.
I'd had a similar private idea - basically to have a pull-down menu of
all keywords (there's a slight issue that ccp4i tasks tend to include
several programs).
My feeling is that segregating the expert options into folder(s) under
global control
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 Lomb
Dear Martyn et al.,
How about putting all the keywords of any program into its GUI, then the
user can click on the ones he/she thinks are needed, to open up the
subkeywords for editing. It might be a case of one horizontal bar for
each and every keyword, and could quickly become tedious when progr
Many interfaces already have an other parameters folder, see e.g. the
folder "Infrequently Used Parameters" in the Molrep GUI. The request
seems to be to:
a) complete this with more parameters for more programs (taking due note
of Kevin's comment)
b) have a Preferences switch that globally hides
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"
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
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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, bu
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 : j
This is timely. We're in the process of a) trying to organise a major
effort to tidy up the existing ccp4i classic (rather than fire-fighting
problems), and b) thinking about designing the next generation. Not sure
which this is. Option b) would be a project over several years.
Can you elucidate
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Dear all,
I'm a well-known luddite as Eleanor says. However, I shamelessly confess
that the CCP4 GUI is great. Not that I think this is necessary here, I'm
sure most people agree with that.
If I write now is because Martynn's e-mail have reminded me
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
... 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:
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 deve
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
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 Chemical
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 excellent
Thanks very much for the replies, and especially for the link to the
previous thread on this topic (Eva).
Just a comment about the ccp4i GUI in general - pretty much all the
students in my department are slowly becoming dependant on the GUI
because it is so much easier to use for those brought up
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 "REFERE
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 som
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
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