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Dear Peer,
can you send the output of the command
ls -l /share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
Best,
Tim
On 04/12/2013 04:11 PM, Peer Mittl wrote:
Dear Colleagues,
For some reason Refmac refuses to read the file
Please send an extract - you probably have a format error..
Or do you have 1500 chais?)
Eleanor
On 30 Oct 2012, at 22:43, jp d wrote:
hi,
i have a large pdb file and i keep getting this error with refmac
ERROR: number of chains 1500
i suspect something needs to be done to my pdb
any
hi,
i have a large pdb file and i keep getting this error with refmac
ERROR: number of chains 1500
i suspect something needs to be done to my pdb
any suggestions ?
thanks
jpd
hi,
answering my own question, but maybe this will
save some searching in the future,
the error was related to 3 letter RNA codes
refmac doesn't like that.
jpd
--- On Tue, 10/30/12, jp d yo...@yahoo.com wrote:
From: jp d yo...@yahoo.com
Subject: [ccp4bb] refmac
To: CCP4BB@JISCMAIL.AC.UK
Date
searching in the future,
the error was related to 3 letter RNA codes
refmac doesn't like that.
jpd
--- On Tue, 10/30/12, jp d yo...@yahoo.com wrote:
From: jp d yo...@yahoo.com
Subject: [ccp4bb] refmac
To: CCP4BB@JISCMAIL.AC.UK
Date: Tuesday, October 30, 2012, 3:43 PM
hi,
i have a large
Thank you very much James !
-kiran
From: James Holton jmhol...@lbl.gov
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, September 26, 2012 9:58 PM
Subject: Re: [ccp4bb] Refmac- solvent mask
Yes, it's called a partial structure. You input the mask as
structure
Dear CCP4 users,
Is it possible to specify a solvent mask to the refmac ?
Many thanks in advance for your time and help.
Regards,
-Kiran
Yes, it's called a partial structure. You input the mask as
structure factors and call them FPART in the refmac LABIN input.
http://www.ysbl.york.ac.uk/refmac/docs/keywords/xray-principal.html#labin_fparti_phiparti
Then enable refining the scale and B factor of the partial structure:
: [ccp4bb] Refmac: ADP is non-positive
To: wtempel wtem...@gmail.com
Cc: CCP4BB@jiscmail.ac.uk
On Tuesday, 24 July 2012, wtempel wrote:
CCP4ers,
a log file from Refmac_5.7.0027 presents me with this line:
fromLog
Problem with the ADP of the atom N A 3 ADP is non-positive
CCP4ers,
a log file from Refmac_5.7.0027 presents me with this line:
fromLog
Problem with the ADP of the atom N A 3 ADP is non-positive
-1.7740907E+35
/fromLog
I did not explicitely refine ADPs or TLS.
Should I modify my model when I encounter such a message? If yes, does the
On Tuesday, 24 July 2012, wtempel wrote:
CCP4ers,
a log file from Refmac_5.7.0027 presents me with this line:
fromLog
Problem with the ADP of the atom N A 3 ADP is non-positive
-1.7740907E+35
/fromLog
I did not explicitely refine ADPs or TLS.
Should I modify my model
, respectively. Could refmac just be taking exception to the
missing N atom?
-- Forwarded message --
From: Ethan Merritt merr...@u.washington.edu
Date: Tue, Jul 24, 2012 at 11:27 AM
Subject: Re: [ccp4bb] Refmac: ADP is non-positive
To: wtempel wtem...@gmail.com
Cc: CCP4BB@jiscmail.ac.uk
hello everyone
Does anybody knows why refmac5 will not process any model that
contains thymine in its structure? This problem only happens on my PC
which supports a 2.1.0 version of ccp4i. The error in the log file
says its due to bad value during floating point read. However, this
Hi Uma,
Altering sigma affects the strength of geometry restraints throughout the model
- bonds, angles, etc. Choosing a very low sigma will cause geometry to be more
tightly restrained towards ideal values, which is why you observe
improvements in Coot validation. Note that strengthening the
).
Note that the absence of geometric outliers does not prove that your model is
optimal. If you use too tight restraints you can end up hiding genuine fitting
errors.
Cheers,
Robbie
Date: Fri, 27 Apr 2012 10:04:11 +0200
From: herman.schreu...@sanofi.com
Subject: Re: [ccp4bb] Refmac
not prove that your model
is optimal. If you use too tight restraints you can end up hiding genuine
fitting errors.
Cheers,
Robbie
--
Date: Fri, 27 Apr 2012 10:04:11 +0200
From: herman.schreu...@sanofi.com
Subject: Re: [ccp4bb] Refmac and sigma value
To: CCP4BB
up hiding
genuine fitting errors.
Cheers,
Robbie
--
Date: Fri, 27 Apr 2012 10:04:11 +0200
From: herman.schreu...@sanofi.com
Subject: Re: [ccp4bb] Refmac and sigma value
To: CCP4BB@JISCMAIL.AC.UK
It all will depend on the resolution. At low resolution
Dear All:
I use Refmac5 to refine my structure model.
When I set the sigma value to 0.3 (as recommended from tutorial), the
resulted model has many red-bars by coot validation (geometry, rotamer,
especially, Temp Facotr).
I then lower the sigma value to 0.1, the resulted model is much improved
Hi, Alex:
Which sigma do you mean?
The one for automatic weight, not for Jelly-body refinement.
I did not turn the Jelly-body refinement on.
Thanks
Ros
On Thu, Apr 26, 2012 at 4:08 PM, aaleshin aales...@burnham.org wrote:
Hi Uma,
Which sigma do you mean? The one for Jelly-body
On Sat, Apr 07, 2012 at 08:42:47AM -0700, Bernhard Rupp (Hofkristallrat a.D.)
wrote:
Something the developers might be interested in:
The Refmac_5.6.0117 32-bit windows binaries run native on a win64 3-4x
slower than
those from the linux distribution run
Thanks for benchmarking.
If
Hi Bernhard,
Maybe the paranoia-checkers in windows slow everything down
although I did not see any resources overwhelmed...
I wonder whether the windoze refmac binaries can be used through wine in a
GNU/Linux environment. If yes, then you could possibly differentiate
between the
Hi Nat,
one of my colleagues found (on Linux) that the exp() function provided
by g77 was 20-fold slower than the equivalent in the Intel math library.
I do not know whether this has recently been changed, but the license for
icc-produced executables used to be rather restrictive. If I
I do not know whether this has recently been changed, but the license for
icc-produced executables used to be rather restrictive. If I remember
correctly, you were not allowed to distribute the binaries, full stop.
Nicholas, this restriction applies (and has always applied) only to
Intel's
Hi
I suspect that this is more to do with the amount of memory required,
size of arrays etc; refinement will (in general) be more demanding in
terms of these than an integration program like Mosflm. The last time
I compared the Mosflm performance (which was a few years ago),
running the
Hi Ian,
Nicholas, this restriction applies (and has always applied) only to
Intel's 'evaluation' licence
That's right. With a cost of $9,997.00 for a 3-years/2-seats academic
license,
I couldn't have been talking for anything else ... :-)))
All the best,
Nicholas
--
Nicholas
On Sun, Apr 08, 2012 at 03:59:22PM +0300, Nikolaos Glykos wrote:
Nicholas, this restriction applies (and has always applied) only to
Intel's 'evaluation' licence
That's right. With a cost of $9,997.00 for a 3-years/2-seats academic
license, I couldn't have been talking for anything else ...
That's right. With a cost of $9,997.00 for a 3-years/2-seats academic
license,
I couldn't have been talking for anything else ... :-)))
Hi Nicholas
That sounds like way more than it should be, in fact it sounds like
you've been quoted the cost of the commercial licence and then some!
From
Hi Ian,
That sounds like way more than it should be, in fact it sounds like
you've been quoted the cost of the commercial licence and then some!
From Intel's website the academic licence for icc (Linux/2 seats) is
$570 incl 1 year's support. Renewal of support for subsequent years
will be less
Something the developers might be interested in:
The Refmac_5.6.0117 32-bit windows binaries run native on a win64 3-4x
slower than
those from the linux distribution run
**in a RHEL6.2-64 VMware virtual machine hosted the same windows7/64
system.**
VM/RHEL:
Refmac_5.6.0117: End of
I don't know the state of current software, because I haven't tried
recently, but when I set up my student crystallography workstations a
few years back I noticed many packages (e.g. EPMR, Phaser) that had
potentially long run times (where it is really noticeable) would run on
the identical
On Sat, Apr 7, 2012 at 9:50 AM, Roger Rowlett rrowl...@colgate.edu wrote:
I don't know the state of current software, because I haven't tried
recently, but when I set up my student crystallography workstations a few
years back I noticed many packages (e.g. EPMR, Phaser) that had potentially
Dear users, I was using Refmac 5.5.0102 (ccp4- 6.1.2) for refining the structures, I was supposed to do one more roundof refinement with final model but unfortunately system crashed and i had to install the new version of ccp4 (6.2.0) which has refmac-5.6.0117. So my doubt here is - can I do the
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Dear Kavya,
I would trust the authors of such programs (ccp4-, phenix-,
shelx-collection et al.) to only release new versions of their programs
if they believe that version is an improvement over the previous version
;-) and generally use the latest
Dear Kavya
In principle you should be able to use newer version for old pdb file unless
you have pdb v2 namings for DNA/RNA etc.
New version of ccp4 has more dicitionary elements (1 or so). Older version
was compiled for 3000. That is the reason why old version does not work with
new
robbie_joos...@hotmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, March 6, 2012 4:26 AM
Subject: Re: [ccp4bb] REFMAC Riding Hydrogens
Hi Everyone,
Pavel’s statement is likely a bit of an exaggeration, but he has a
valid (yet hard to prove point). The default in CCP4i
From: Robbie Joosten robbie_joos...@hotmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, March 6, 2012 4:26 AM
Subject: Re: [ccp4bb] REFMAC Riding Hydrogens
Hi Everyone,
Pavel’s statement is likely a bit of an exaggeration, but he has a valid (yet
hard
GUI?
Thanks again,
--Paul
From: Robbie Joosten robbie_joos...@hotmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday, March 6, 2012 4:26 AM
Subject: Re: [ccp4bb] REFMAC Riding Hydrogens
Hi Everyone,
Pavel’s statement is likely a bit
4:26 AM
Subject: Re: [ccp4bb] REFMAC Riding Hydrogens
Hi Everyone,
Pavel’s statement is likely a bit of an exaggeration, but he has a valid (yet
hard to prove point). The default in CCP4i was (and is?) to use hydrogens
only if present in the input file. This is IMO not a safe default
).
Cheers,
Robbie
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel
Afonine
Sent: Monday, March 05, 2012 21:53
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] REFMAC Riding Hydrogens
Dear Tim,
good catch, thanks; I could craft that phrase more carefully! Although
Pavel’s statement is likely a bit of an exaggeration, but he has a valid
(yet hard to prove point). The default in CCP4i was (and is?) to use
hydrogens only if present in the input file. This is IMO not a safe default.
I agree: what I find confusing here is that the current CCP4i default
is
Hello CCP4 community,
I'm posting at large regarding a previously raised issue for REFMAC for which I
cannot find the conclusion in the old threads.
Specifically, does REFMAC add riding hydrogens during default refinement?
Though I've not requested that any hydrogens be added, only used if in
Hi Paul -
Refmac does indeed add riding hydrogens by default; see here:
http://www.ccp4.ac.uk/dist/html/refmac5/keywords/restraints.html#makecif
The REMARK 3 is referring to what you think it is: riding hydrogens have
been added. (They are not, however, written to the output file unless
you
On the interface under Refinement Parameters there are three options
1) Use if present
2) Do not use
3) Generate all
if you are using script then default is generate all (add them riding
positions). You can switch to other options:
make hydr all# generate all - default option
make hydr yes
Hi,
On Mon, Mar 5, 2012 at 11:52 AM, Matthew Franklin mfrank...@nysbc.orgwrote:
Adding the riding hydrogens generally gives you some improvement in R
factors even with a good quality (i.e. stereochemically correct) model.
and here are the results of more or less systematic test that prove
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Dear Pavel,
you may want to add to the structures mentioned in [1] one or two
organic structures present in the Cambridge Database.
Until recently it was customary to ignore hydrogen atoms throughout the
process of crystallographic X-‐ray structure
Dear Tim,
good catch, thanks; I could craft that phrase more carefully! Although
often it may not be quite fair to take phrases out of context: this
newsletter article was written in the context of macromolecular refinement.
And yes, recently may be a broad term -:)
All the best,
Pavel
On Mon,
Dear board,
How do I define base-pairing restraints in DNA in REFMAC 5.7?
Cheers,
Morten
--
Morten K Grøftehauge, PhD
Pohl Group
Durham University
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Dear Morten,
the 'external' keyword as e.g. exploited by Rob Nicholls' prosmart
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ Software-ProSmart could
probably do that. The syntax reads like
exte dist first chain I resi 9 ins . atom N second
Dear All,
When running refmac with twin refinement option it continues
indefinitely at trying gamma equal step. With normal refinement
this problem is not there.
Any idea, how to rectify this?
Jobi
Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed
Pozharski
Sent: Monday, January 02, 2012 7:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and metal on a two-fold?
On Sun, 2012-01-01 at 12:14 -0600, Dima Klenchin wrote:
With Garib's help, I have
-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed
Pozharski
Sent: Monday, January 02, 2012 7:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and metal on a two-fold?
On Sun, 2012-01-01 at 12:14 -0600, Dima Klenchin wrote:
With Garib's help, I have
Hi Bernhard
So what's new? See
http://ccp4bb.blogspot.com/2011/11/pdb-header-info-wrong.html
(17-Nov-11).
Cheers
-- Ian
On 2 January 2012 06:58, Bernhard Rupp (Hofkristallrat a.D.)
hofkristall...@gmail.com wrote:
Dear Developers,
it seems to me that at least Refmac 5.6.0117 does not
with refmac.
Best regards,
Herman
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
George M. Sheldrick
Sent: Monday, January 02, 2012 1:22 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac and metal on a two-fold?
I am surprised
So what's new?
Alzheimer's and late night senile dementia :-)
BR
PS: nice site!
-Original Message-
From: Ian Tickle [mailto:ianj...@gmail.com]
Sent: Monday, January 02, 2012 4:34 AM
To: b...@hofkristallamt.org
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] refmac low resolution
I've seen this happening to water molecules as well (in a somewhat
unpredictable fashion). In the latest refmac versions, you can try
harmonic restraints, although these will only slow down the atom drift,
as the target position is updated every cycle.
Perhaps you can use distance restraints
I've seen this happening to water molecules as well (in a somewhat
unpredictable fashion). In the latest refmac versions, you can try
harmonic restraints, although these will only slow down the atom drift,
as the target position is updated every cycle.
Perhaps you can use distance restraints
Good to know, thanks. I was actually wondering about this recently.
On Sun, Jan 1, 2012 at 1:14 PM, Dima Klenchin klenc...@facstaff.wisc.eduwrote:
I've seen this happening to water molecules as well (in a somewhat
unpredictable fashion). In the latest refmac versions, you can try
harmonic
On Sun, 2012-01-01 at 12:14 -0600, Dima Klenchin wrote:
With Garib's help, I have forced the atom into its position by using
external distance restrains of zero length against the same
symmetry-related atom. The cause is unclear because the same program
handles special positions in another
Dear Developers,
it seems to me that at least Refmac 5.6.0117 does not report the actual
lowest resolution used in refinement, but instead the lowest resolution of
the hkl index range generated by the default cif import script instead.
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION
instead
of simple.
Yep, understood.
Thx, BR
Regards and Happy New Year
Garib
From: Garib Murshudov [mailto:garib.murshu...@gmail.com] On Behalf Of Garib N
Murshudov
Sent: Thursday, December 29, 2011 4:47 PM
To: b...@hofkristallamt.org
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb
...@gmail.com] On Behalf Of Garib
N Murshudov
Sent: Thursday, December 29, 2011 4:47 PM
To: b...@hofkristallamt.org
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refmac Bsol
Partial structure mask bulk solvent parameters. If you use simple scaling
then mask solvent is still on. You can turn it off
Dear Refmac developers group,
I am trying to understand a small detail in the refmac log listing. In the
bulk
solvent section just below the restraint table (I use monitor MANY in
general):
-
Overall :
Partial structure mask bulk solvent parameters. If you use simple scaling then
mask solvent is still on. You can turn it off by Calculate the contribution of
from the solvent region
To turn Babient's bulk solvent you need to use Babinet's scaling instead of
simple.
I hope it helps
regards
Hello,
I have a metal ion sitting on a two-fold. I assigned it an occupancy of 0.5
but Refmac keeps refining it away from that position so that in the end
there is a symmetry-related ion 1.6A away. I thought that this problem has
been rectified long ago? Certainly I had several occasions
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Krisztian Fodor
Sent: 20 December 2011 13:57
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Refmac with TLS terminates early when occupancy
changed
Hello Guys,
I am trying to refine a 3.2 A complex structure with Refmac using TLS.
It seems that I need
Hello Guys,
I am trying to refine a 3.2 A complex structure with Refmac using TLS.
It seems that I need to decrease the occupancy for a 38 amino acid
peptide in the structure. However, after changing the occupancy to 0.50,
Refmac terminates after 4 rounds of TLS refinement.
The only error
Hello all.
Did anyone encounter the following?
Running refmac 5.6.0117/ccp4-6.2/ccp4i-2.1.0, I hoped to obtain, for
pdb_extract, the appropriate output model statistics. When I did not
find the cif file with a modification date similar to my output
coordinates, I noticed a series of
Hi All,
Is it possible to define twin operator and twin fraction in the latest version
of Refmac (i.e., in version 5.6.0117) ?
I tried to define these two keywords in Buccaneer but it fails with an error
message Refmac_5.6.0117: Problem in some of the instructions.
Please help me to fix this.
I am absolutely sure this has been discussed before, and I have just
re-convinced myself that refmac reports the number of reflections in
just the working set, and not the total number of reflections. So my
question is
Is there a reason why the PDB ADIT tool imports the Nwork from the
refmac pdb
work, we may need a closer
look at your input model.
Cheers,
Robbie
Date: Thu, 27 Oct 2011 20:48:49 -0500
From: satys...@wisc.edu
Subject: [ccp4bb] refmac 5.6 ccp4 6.2.0
To: CCP4BB@JISCMAIL.AC.UK
Has anyone had problems with Refmac 5.6? I tried refining our stucture at
1.24 A,
aniso
d'envoi : vendredi 28 octobre 2011 09:42
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0
Hi Kenneth,
This looks like an off-by-one bug in the restraint generation. Typical sources
are weird LINKs, wrong atom names and bad luck. I suggest you make sure you
have the very latest
Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0
Hi Kenneth,
This looks like an off-by-one bug in the restraint generation. Typical
sources are weird LINKs, wrong atom names and bad luck. I suggest you make
sure you have the very latest Refmac and dictionary and try setting up a new
refinement
Just to verify, is this by any chance *unrestrained* refinement?
On Fri, 2011-10-28 at 09:37 +0200, Tim Gruene wrote:
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Dear Kenneth A. Satyshur,
what is your weight set to? If it is set to 'auto', try setting it to a
specific value and lower
Pozharski
[epozh...@umaryland.edu]
Date d'envoi : vendredi 28 octobre 2011 16:00
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0
Just to verify, is this by any chance *unrestrained* refinement?
On Fri, 2011-10-28 at 09:37 +0200, Tim Gruene wrote:
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Dear all,
If those hydrogens are in riding position, their coordinates are
calculated and should not be refined at all, isn't it? Hence they should
appear in the list of deviations at all.
Are the hydrogens present in the PDB file? Does it work to
:00
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0
Just to verify, is this by any chance *unrestrained*
refinement?
On Fri, 2011-10-28 at 09:37 +0200, Tim Gruene wrote:
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Dear Kenneth A. Satyshur,
what is your
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Sorry, should NOT appear in the list of deviations, of course!
- Original Message
Subject: Re: [ccp4bb] refmac 5.6 ccp4 6.2.0
Date: Fri, 28 Oct 2011 17:39:06 +0200
From: Tim Gruene t...@shelx.uni-ac.gwdg.de
Reply-To: Tim Gruene t
:00
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] refmac 5.6 ccp4 6.2.0
Just to verify, is this by any chance *unrestrained* refinement?
On Fri, 2011-10-28 at 09:37 +0200, Tim Gruene wrote:
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Dear Kenneth A. Satyshur,
what is your weight
part de Garib N
Murshudov [ga...@mrc-lmb.cam.ac.uk]
Date d'envoi : vendredi 28 octobre 2011 17:49
À : LEGRAND Pierre
Cc : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] RE : [ccp4bb] refmac 5.6 ccp4 6.2.0
Dear Pierre
Resolution seems to be good enough for full anisotropic refinement. Why don't
you
Has anyone had problems with Refmac 5.6? I tried refining our stucture at 1.24
A,
aniso with H in riding position and it just exploded! I get error in distances
such as
Standard External All
Bonds: 3270 0 3270
I'm running into some geometry problems with my DNA model after refinement with
refmac (version 5.5.0109), and would appreciate any feedback.
The problem is that the angles for many of the glycosidic bonds are 2 to 4
degrees off of the ideal values, and so are several standard deviations
OK, I updated ccp4 to 6.2.0 (and refmac to 5.6.0117) and now the angles coming
out close to the ideal values. Also, I see now the the MODRES in the pdb
header from before was tell future refmac runs to rename those residues - which
confused the newer refmac version as it thought the DT (renamed
Is ' U ' now the standard vs ' U' ? I'm used to right justified letters for
RNA residues in the residue field.
This is with a recent refinement with refmac 5.6.0117 .
And of course this switch in naming convention breaks compatibility with
molprobity (which requires right justified letters
Original message
Date: Mon, 12 Sep 2011 12:23:17 -0600
From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Francis E
Reyes francis.re...@colorado.edu)
Subject: Re: [ccp4bb] refmac and DNA (and now RNA)
To: CCP4BB@JISCMAIL.AC.UK
Is ' U ' now the standard vs ' U' ? I'm used
Hi Garib
Thanks for the quick reply!
Refmac however is writing my pdb's as with the residue letter in the centered
position.
Is the newest pdb requiring centered residue letters for RNA?
F
On Sep 12, 2011, at 1:05 PM, Garib N Murshudov wrote:
Refmac will read right or left justified
Yes, new version of the dictionary uses U. Refmac will read right or left
justified residue names, however pdb may use only one of them.
There are some backward compatibility code/dictionary elements. For example
Ad/Ar are also accepted. However it is encouraged to use new pdb v2.3
Hi Francis
Is that newer version of refmac?
regards
Garib
On 12 Sep 2011, at 20:09, Francis E Reyes wrote:
Hi Garib
Thanks for the quick reply!
Refmac however is writing my pdb's as with the residue letter in the
centered position.
Is the newest pdb requiring centered residue
Le 11/09/2011 00:23, Ed Pozharski a écrit :
On Sat, 2011-09-10 at 08:21 +0200, Miguel Ortiz Lombardía wrote:
A, C and G are RNA nucleotides. T is (mostly) not, its RNA-equivalent
is
uridine phosphate, U.
Right, that was my suspicion. But I thought that RNA bases would be Xr,
not Xd.
On 09/09/11 17:29, Ed Pozharski wrote:
On Thu, 2011-09-08 at 16:58 +0200, Miguel Ortiz Lombardía wrote:
Perhaps the Nd/DN issue was solved between revisions 3470 and 3628 ?
Indeed. I just built the rev 3633 and it works fine. Autobuild scripts
used to have some problems on Lucid, but this
On Sat, 2011-09-10 at 08:21 +0200, Miguel Ortiz Lombardía wrote:
A, C and G are RNA nucleotides. T is (mostly) not, its RNA-equivalent
is
uridine phosphate, U.
Right, that was my suspicion. But I thought that RNA bases would be Xr,
not Xd. Plus, refmac does not complain about missing
On Thu, 2011-09-08 at 16:58 +0200, Miguel Ortiz Lombardía wrote:
Perhaps the Nd/DN issue was solved between revisions 3470 and 3628 ?
Indeed. I just built the rev 3633 and it works fine. Autobuild scripts
used to have some problems on Lucid, but this time it worked perfectly.
This evolved
After switching (finally) to 6.2.0 and therefore to Refmac 5.6.0117 I
have found a problem working with DNA that I have not seen with
6.1.13/5.5.0109. Namely,
- if I use the pdb file produced by Coot (0.7.pre-1.3470) that seems to
output DNA as Ad/Td/Gd/Cd no matter what the input names were,
On 08/09/11 15:35, Ed Pozharski wrote:
After switching (finally) to 6.2.0 and therefore to Refmac 5.6.0117 I
have found a problem working with DNA that I have not seen with
6.1.13/5.5.0109. Namely,
- if I use the pdb file produced by Coot (0.7.pre-1.3470) that seems to
output DNA as
Rex, I think the problem is that the latest version of the dictionary which
contains LBT (and many other new ligands) only works with Refmac 5.6 (but
check with Garib on that!), but that version hasn't yet been compiled for
Windows. Unfortunately Windows versions tend to lag a bit behind Linux
Dear protein crystallographers
We tried downloading the latest version of Refmac for Windows, Refmac 5.5.0071
from the prerelease page on ccp4. However it does not seem to have alpha
lactose in the monomer library. Does anyone know if it is possible to obtain
the latest Refmac version complete
Dear Rex,
you can always get the latest dictionary from Garib's homepage,
http://www.ysbl.york.ac.uk/~garib/refmac/latest_refmac.html
Since they are plain text files they are platform independent (unless Windows
has issues with the directories separating slash, but my guess is that the
windows
On 6/10/11 6:10 PM, Ed Pozharski wrote:
On Fri, 2011-06-10 at 12:48 -0700, Ethan Merritt wrote:
I don't think that combination makes any sense. Whatever anisotropic
is being described by the TLS parameters can also be fully described
by the individual anisotropic U^ij terms. So the TLS
Hi all -
I seem to be encountering a problem with Refmac refinement of a
structure containing anisotropic B factors. I have been using TLS
refinement and individual anisotropic B refinement, which may not be
correct technique, but it does lower my R and Rfree versus aniso B
refinement alone
On Friday, June 10, 2011 12:33:10 pm Matthew Franklin wrote:
Hi all -
I seem to be encountering a problem with Refmac refinement of a
structure containing anisotropic B factors. I have been using TLS
refinement and individual anisotropic B refinement, which may not be
correct technique,
Hi,
I seem to be encountering a problem with Refmac refinement of a
structure containing anisotropic B factors. I have been using TLS
refinement and individual anisotropic B refinement, which may not be
correct technique, but it does lower my R and Rfree versus aniso B
refinement alone
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