rwise). We always try to support as many "standards" as possible,
but there will always be ambiguities.
m
-Original Message-
From: Ian Tickle [mailto:i.tic...@astex-therapeutics.com]
Sent: Fri 6/12/2009 10:45 PM
To: Winn, MD (Martyn)
Cc: CCP4BB@JISCMAIL.AC.UK; Kevin Cowtan; Phil
Apologies, this was a bug introduced by a recent change.
It is fixed and will be in 6.1.2
Martyn
-Original Message-
From: CCP4 bulletin board on behalf of Alejandro Buschiazzo
Sent: Thu 5/21/2009 6:26 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] TLSANL gives zero off-diagonal ANISOU ma
Well, the guys may have distributed a phx-specific configure file, but
otherwise, I think it is USE_DBCCP4I_ON_STARTUP in ~/.CCP4/unix/configure.def
At least it worked for me after the briefest of tests of the Windows equivalent.
Cheers
Martyn
-Original Message-
From: CCP4 bulletin board
Well, I am sure this is not meant to happen. It doesn't seem to happen
with my 6.1 version
First question: are you sure that the project directory really has gone?
Rather than it no longer showing in ccp4i. Check for the directory in a
terminal window.
If it has really gone, then you have t
Part of the reasoning was that arp_waters corresponded to a very old version
of arp/warp It was felt that up-to-date arp/warp and/or findwaters covered
the functionality.
Of course, every implementation does things in a slightly different way, and
each has their fans. Which means it is hard to d
Sounds like a good candidate for (domain-level) TLS to me.
Cheers
Martyn
-Original Message-
From: CCP4 bulletin board on behalf of Nicholas Keep
Sent: Thu 1/8/2009 10:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] NCS restraints of domains
I am refining a low (3A) resolution structur
The current value of maxbat in scala_/parameters.fh is 5000
Mind you, according to CVS this was increased from 1000 to 5000 in 1999!
sortmtz and reindex also have MBATCH=5000. There's no restriction in
the library itself.
Cheers
Martyn
-Original Message-
From: CCP4 bulletin board on beha
At a recent developers' meeting we predicted a release date 2 weeks
from now.*
Meanwhile, the previously announced test release series is pretty stable,
and much better than 6.0.2, so it is worth a try.
HTH
Martyn
* Calculation done assuming: 1) testing reveals 0 problems, 2) none
of our colla
Well, in case of installation difficulties, you can always contact
the friendly and helpful staff at [EMAIL PROTECTED] . ;-)
Unfortunately, our friendly and helpful Mac expert is away at the
moment, but I can try to help. If you follow through to the Mac
download page, you have a few choices.
ROTMAT will also do this. But I am not sure that this is what Phil wants?
The superposition transformation includes a translation, so there is no
locus of points that are left unchanged. You can generate an axis of
rotation for polar angles from the R which will be quite different from t.
You shou
Yes, the Rfreeflag column should be of type I, see e.g. "Output:" section of
http://www.ccp4.ac.uk/dist/html/freerflag.html
And this is what ccp4i expects, see $CCP4/etc/types.def
But not all programs will check it.
In fact, the type changed from W to I in 1995, back in the days when free R was
s
Note the appearance of "Normal Termination" in the middle of the table.
So I think it is this problem:
http://www.ccp4.ac.uk/problems.php#6.0.0-gfortran-unbuffered-22May2006
i.e. the GFORTRAN_UNBUFFERED_ALL one.
Martyn
-Original Message-
From: CCP4 bulletin board on behalf of hari jayar
re refined.
This will cause problems when you try to redo the final refinement: you add
loads of parameters all of a sudden. Using ANISOU records may give you more
reliable information about the B-factors, but not about the refinement.
Cheers,
Robbie Joosten
From: "Winn, MD (Martyn)&quo
Just to point out that the CCP4 wrapper to SSM "superpose" allows you to
specify residue ranges to consider - very useful for multi-domain proteins.
See the -s switches in
http://www.ccp4.ac.uk/dist/html/superpose.html
I'm not clear if this was your issue.
Cheers
Martyn
-Original Message--
> 2) All you need to reproduce the R-factors are the ATOM records and
> structure factor formula (and not ATOM records, PDB header with TLS
> records that sometimes may be lost or manipulated and specific
> converting programs to add TLS contribution). Also note, that not all
> programs extract
Yes, it is down at the moment, due to a hacking event apparently. Don't know
any more.
Martyn
-Original Message-
From: CCP4 bulletin board on behalf of Harry M. Greenblatt
Sent: Wed 3/19/2008 1:28 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] PRODRG?
BS"D
Hi all,
Does anybody know
Refmac (at least 5.2) and TLSANL write a line into the PDB header specifying
what is in the B column:
REMARK 3 ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
Looking at 2qua which used Refmac 5.3, that line isn't there. I don't know at
what stage it has been lost.
Of course, it would be nice
Clearly a few interesting entries .
2) in the context of PX, only the total "B factor" contribution to Fcalc needs
to be positive definite, the TLS component might not be (though it is
satisfying if it is)
3) how do you calculate the "TLS origin" ? The PDB entries should contain the
origi
Yes, it might be the old quotes problem.
Later versions of ccp4i add in quotes around the filenames (to deal with
WIndows paths with spaces) and later versions of Phaser interpret quoted
arguments correctly. But a new gui with an old phaser will cause problems.
Martyn
-Original Message-
F
This is standard gotcha number 17, you are picking up "ncsmask" from XtalView
rather
than the CCP4 one, see
http://www.ccp4.ac.uk/problems/general-probs.php#general_wrong_prog
Basically, you need to fix the path in some way so that the CCP4 one comes
first.
check with "which -a ncsmask"
HTH
Ma
to something that cif2mtz recognises (as long as it is the
same type of column!!)
HTH
Martyn
-Original Message-
From: Björn Kauppi [mailto:[EMAIL PROTECTED]
Sent: Tue 11/6/2007 10:16 AM
To: Winn, MD (Martyn); CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] converting structure factor files
Thanks Ben,
Yes, I am acutely aware that our interface has got out-of-date.
I can add in these little fixes.
If there is sufficient interest, we could talk about updating to
the python version.
Cheers
Martyn
-Original Message-
From: CCP4 bulletin board on behalf of Ben Webb
Sent: Fri
We sometimes find that a local fasta search against the pdb sequence datafile
(for which you need to install fasta package) works better than OCA at EBI, i.e.
finds more matches. We have never tracked down why.
But not sure what you mean by using local OCA server. How have you specified
this
ser
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
If I understand you correctly, the CCP4 program Chainsaw would do
this.
It uses an alignment file, which you could hand-craft to select
mutate or conserve.
Keyword "MODE MIXA" to select the truncate-to-beta option.
HTH
Martyn
-Original Message-
From: CCP4 bulletin board on behalf of [EM
I'd also comment that the absolute values are quite large. Well, I have no
knowledge what groups you've chosen, but for domain-sized groups, typical
values are 1-10 deg**2. Values can be larger for smaller TLS groups. This is
just a rule-of-thumb, but would make me suspicious whether the TLS refine
Yes, I believe York were going to be off-line for a couple
of days following some computer problems.
The Refmac 5.3 source code is also available from our pre-release
page:
http://www.ccp4.ac.uk/prerelease_page.php
As it happens, I updated it on Monday, so it is up-to-date.
Cheers
Martyn
-O
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