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
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