. mod.= 0.529 id.= 2.950 dev= -2.42
> sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1
> B449 HIS C . - B450 HIS H3 . mod.= 0.835 id.= 2.950 dev= -2.11
> sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1
> B450 HIS C . - B451 HIS H3 . mod.= 0.932 id.= 2.9
Dear Joanna,
There might be an unnecessary TER card in your PDB file between
residues 430 and 431 of chain A. Could you check that? The log file
suggests that residues after 430 are being recognised as a non-polymer
part.
Best regards,
Keitaro
On Mon, 3 Feb 2025 at 20:12, Joanna Zukowska
<000100
Dear Charis,
Please see: https://www.wwpdb.org/news/news?year=2023#654a801dd78e004e766a96bd
Because wwPDB has changed these atoms names, the monomer library was
updated accordingly. More than 800 monomers were affected. We have
added the old atom names in _chem_comp_atom.alt_atom_id to help
progr
Dear Marco,
> Refmac: Input coordinate file is not complete
Probably the CRYST1 record (unit cell and space group information) is
missing in your pdb file. You could copy this from another pdb file
(and may need to correct it).
Best regards,
Keitaro
On Wed, 28 Feb 2024 at 09:54, Marco Bravo wr
Hi,
XRDa https://xrda.pdbj.org/ archives raw crystallography datasets for
both PDB and non-PDB entries (e.g. https://xrda.pdbj.org/entry/93), as
well as MicroED datasets (e.g. https://xrda.pdbj.org/entry/140).
Best regards,
Keitaro
On Thu, 19 Oct 2023 at 05:48, Kay Diederichs
wrote:
>
> There i
Dear Ai,
Are you trying to make phosphodiester bonds in the main chain? Do your
modified nucleotides follow the standard atom names (P, OP1, OP2, ...,
O3')? If so, you can just change the group name (_chem_comp.group) to
RNA (or DNA). Otherwise you could either change atom names to follow
the stan
gards,
Keitaro
On Thu, 17 Aug 2023 at 16:03, Keitaro Yamashita
wrote:
>
> Hi,
>
> I assume the planarity you mentioned is what is discussed in Moriarty
> et al (2020) https://doi.org/10.1107/S2059798320013534
>
> As shown there, it is known to have some deviation. In Refm
Hi,
I assume the planarity you mentioned is what is discussed in Moriarty
et al (2020) https://doi.org/10.1107/S2059798320013534
As shown there, it is known to have some deviation. In Refmac (or in
the CCP4 monomer library) it is restrained using a torsion angle with
5 degree sigma instead of the
In the monomer library, pyr-SER and pyr-THR links are defined for the
O-glycosylation. A monomer should belong to the "pyranose" group in
the library (or in a user-provided dictionary).
Best regards,
Keitaro
On Fri, 14 Jul 2023 at 09:22, Jon Agirre
<17a7df66b7b3-dmarc-requ...@jiscmail.ac.uk>
ith running CCP4 programs on the
>> command line. Any assistance would be appreciated!
>>
>> Interestingly, when I use the "LINK" and change the type to "peptide" in
>> Coot only the linkage to the preceding residue is broken during refinement,
&
Because of non-standard atom names, group names of some monomers were
changed to NON-POLYMER. In this case the hydrogen atom is only the
problem, so changing group to peptide works unless you have hydrogen.
Moreover, in CSO, the problematic hydrogen is removed when forming a
peptide link. The detai
Dear Massimo,
This was a bug in Refmac and has been fixed in Refmac5.8.0385 which
will be hopefully released with the next CCP4 update.
However, local NCS restraints do not impose restraints on B-factors,
so you do not have to worry about that.
Best regards,
Keitaro
On Thu, 13 Oct 2022 at 14:05
As Refmac5.8.0349 is used, I am almost sure CCP4 8.0 is used. By the
way I would recommend to apply CCP4 update 002 (latest), as a LIBG
(base pair/stacking restraints) related bug was fixed in Refmac.
There might be something wrong with 4D4, but the problem is related to
OP3 atoms in nucleotides t
Dear Ian,
For the moment in Refmac5 we need to use insertion codes to handle
microheterogeneity. LINKR records are also needed in the header. So
7a5v.pdb should be changed like this:
954a955,957
LINKRTHR A 279 LYS A 279A gap
LINKRC VAL A 2
Dear Kay,
I also tested this using a publicly available data of thaumatin
https://zenodo.org/record/10271
(resolution ~1.4 Å, wavelength= 0.97625 Å).
The camera distance from header is 265.27 mm. I tested this original
distance and some shifts (+1, +2, +4, ..., +32 mm) with different
versions of X
t-squares scaled FC+FMASK
>
> regards
> Garib
>
> On 16 Apr 2012, at 16:01, Keitaro Yamashita wrote:
>
> Dear Garib,
>
> Thank you very much for your quick reply.
>
> I tried mskout option and the output looked almost the same as the map
> generated by FC_ALL - FC.
constant
>
>
>
> Regards
> Garib
>
>
> On 16 Apr 2012, at 15:09, Keitaro Yamashita wrote:
>
> Dear Garib,
>
> Is there REFMAC option to output solvent mask information (e.g. Fmask
> and PHImask in mtz to check with Coot)?
>
> I tried to generate i
Dear Garib,
Is there REFMAC option to output solvent mask information (e.g. Fmask
and PHImask in mtz to check with Coot)?
I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL).
But I'm not sure that FC_ALL = FC + FMASK is correct or not.
Keitaro
2012/4/16 Garib N Murshudov :
Dear Charles,
Internet Explorer and VLC player (thanks, Francis) work for me, but
the streaming stops every few minutes in both ways.
The website should be reloaded each time.
I would be very happy if video archives of talks are available on the web!
Thank you for your consideration,
Keitaro
Thank you for replies.
I understand that real space refinement using maps generated by REFMAC
doesn't affect cross validation.
I found the documentation of REFMAC about this topic.
http://www.ysbl.york.ac.uk/refmac/data/refmac_keywords.html#mapcalc
Oops, I should have found this earlier.
Thanks
Dear all,
I'm very interested in this topic.
I have a question about the default behaviors in output reflection
files of each refinement softwares.
Are test set reflections excluded from the columns for calculating
electron density maps?
I found in phenix.refine documentation the option
electron_
R
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Keitaro Yamashita
> Sent: Sunday, February 06, 2011 2:10 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] adding gaussian noise to an mtz data column
>
> Dear James,
>
Dear James,
I'm very interested in your crystallographic R package.
Is it available to the public?
Thanks in advance,
Keitaro
2011/2/4 James Foadi :
> If you fancy using R (and its endless ways of generating random deviates),
> then you could use part of the crystallographic package we are deve
ween them.
>
> Your case: Do you see some sort of modulation of intensities in your images?
> Something like weak strong intensities along c axis? Or do you see elongated
> peaks in the images.
>
> regards
> Garib
>
>
>
>
> On 9 Dec 2010, at 01:11, Keitaro Ya
hudov :
> In refmac you can remove vdw interactions between chains using the following
> command
>
> It is an example:
>
> vdwr exclude between chains A B
>
> or between resdues:
>
> vdwr exclude between residues first residue 123 chain A second residue 155
> c
nergy among symmetry
related atoms, which I want refmac5 to ignore.
K. Yamashita
2010/12/9 Ed Pozharski :
> On Thu, 2010-12-09 at 01:09 +0900, Keitaro Yamashita wrote:
>> When I tried to refine using Refmac5, the output told many vdw
>> repulsions with symmetry mates
>
> What
Dear all,
I'm refining complex structure against X-ray diffraction data with
packing disorder.
(Some domains overlap with their symmetry mates (4-fold), so their
occupancies are set to 0.25)
I'd like to know whether refinement programs can exclude any
interaction among symmetry mates from geometr
er indexing in
> iMosflm means that the matrix, symmetry and mosaic spread are all available,
> so it can be easier doing it this way.
>
> There's a very old script under our "FAQ" page for producing a series of
> images - see http://www.mrc-lmb.cam.ac.uk/harry/mosf
> (creates a ppm)
> or
> create_image prediction on binary true filename image.jpg (creates a
> jpeg, default)
> then
> return (redirects input back to the normal Mosflm commands)
>
> It's also possible to do this from the normal Mosflm command line or put it
Dear all,
I would like to make a picture of diffraction photograph with (hkl) indexes.
I found it in Fig. 1 in the paper: Acta Cryst. (2009). D65, 553-559
http://dx.doi.org/10.1107/S0907444909010725
Direct link to the figure:
http://journals.iucr.org/d/issues/2009/06/00/dz5158/dz5158fig1.html
Ca
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