Hey Dr Afshan,
You can also check the tab menu: Measure>Go to Atoms. There you can enter
the residue number. The particular residue will be selected, and centred.
Thereafter go to the Measure tab, and click residue info. A dialogue box
will pop open, and there you may edit the values. I hope this
I don't know about solving this in Coot but would using a plain text editor on
the PDB file be a way to work around the issue? There is also the
spreadsheet-style PDB editor in i2??
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Original Message
On 27 Jul 2021, 15:21, Afshan Begum wrote:
> Hi E
I recall using CME some time ago (within last couple of years) without
problems. Also, an alternative approach is to incorporate BME as a
separate residue instead - the disulfide bond will be correctly
identified by refmac. I would think ideologically this is more
appropriate - using a different
Dear AfshanMake sure that group name for CME is peptide (or L-peptide). In the new version CME is peptide. I am not sure it was the case in older versions. I attach CME as a peptide. You can add this into your dictionary.Then CME can become part of a peptde. It would also be good to remove all the
Dear Afshan,
I have been struggling with the same irrating "feature" (I would call it
a bug), which was for me one of the reasons to abandon refmac. For some
reason and against PDB standards, refmacs wants linked amino acids to be
consecutively numbered and otherwise decides that they are not lin
Hello Afshan,
Maybe the programm that you use for refinement need specific entry with
restraint for your modified amino acids.
More precisely, i think about the *.cif file for exemple.
HTH.
Nicolas
Le 21/07/11 17:13, Afshan Begum a écrit :
Dear all,
I have facing one problem during the ref
In addition to Fred's suggestion, are you certain about your space group ? I
assume you tried phaser with different space groups turned on ?
Another thing to look at maybe the model you are using for MR has some
extensions that lead to clashes in your crystal packing and therefore the
second mol
Hi,
The R-factor you mention, is it an R-factor before any refinement of the
model ? Like an R-factor at the very beginning of the entire modeling
procedure, right after molecular replacement ?
If this is so: you should always compare such initial R-factors to the
R-factors for the atoms pla
