Hi Paul,
Thank you for providing that information. Editing the restraints for CSO
corrected the issue! Your assistance is greatly appreciated. I figured I
was missing something :)
Best,
Nick Clark
On Fri, May 26, 2023 at 10:55 PM Paul Emsley
wrote:
>
> On 27/05/2023 03:46, Nicholas Clark
On 27/05/2023 03:46, Nicholas Clark wrote:
Paul,
Yes, it appears that the upper level group is "NON-POLYMER". However,
there is an alias at the bottom that does state polymer.
Hi Nick,
In Coot: Edit -> Restraints... -> CSO -> OK -> Change "Non-POLYMER" to
"peptide" and press enter in
Paul,
Yes, it appears that the upper level group is "NON-POLYMER". However, there
is an alias at the bottom that does state polymer.
Best,
Nick Clark
On Fri, May 26, 2023 at 10:37 PM Paul Emsley
wrote:
>
> On 27/05/2023 03:23, Nicholas Clark wrote:
>
> Hey Paul,
>
> I found the dictionary
On 27/05/2023 03:23, Nicholas Clark wrote:
Hey Paul,
I found the dictionary entry for CSO, it appears to be in the
"peptide" group (under CCP4-8.0->lib->data->monomers->c->CSO.cif):
"loop_
_chem_comp_alias.comp_id
_chem_comp_alias.group
_chem_comp_alias.atom_id
Hey Paul,
I found the dictionary entry for CSO, it appears to be in the "peptide"
group (under CCP4-8.0->lib->data->monomers->c->CSO.cif):
"loop_
_chem_comp_alias.comp_id
_chem_comp_alias.group
_chem_comp_alias.atom_id
_chem_comp_alias.atom_id_standard
CSO *peptide* HN2 H2"
I've attached the
Hey Paul,
I'm not sure how to check that? Would you be able to provide a resource to
check this?
Best,
Nick Clark
On Fri, May 26, 2023 at 9:21 PM Paul Emsley
wrote:
>
> On 27/05/2023 00:43, Nicholas Clark wrote:
>
> I have a cysteine residue that is oxidized and needs to be modeled as CSO.
>
On 27/05/2023 00:43, Nicholas Clark wrote:
I have a cysteine residue that is oxidized and needs to be modeled as
CSO. In the past, when "replace residue" was used to substitute for
CSO, the CSO would "behave" during real-space refinement and
essentially take the place of the Cys. However,
Hi Jon,
Thanks for the reply. They’re going in as HETATMs. I didn’t try changing
them to ATOMs because I checked my previous structure’s PDB file (one that
worked fine) and they were in it as HETATMs.
I have changed them to ATOMs and it’s still “misbehaving” in real space
refinement but shows a
Hello, is the CSO going into the PDB file as ATOM'S or HETATM's?
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Sent from Proton Mail mobile
Original Message
On 27 May 2023, 00:43, Nicholas Clark wrote:
> I have a cysteine residue that is oxidized and needs to be
I have a cysteine residue that is oxidized and needs to be modeled as CSO.
In the past, when "replace residue" was used to substitute for CSO, the CSO
would "behave" during real-space refinement and essentially take the place
of the Cys. However, when Cys is replaced by CSO now the CSO is behaving
I've just registered as a non-member and there's no fee, right?
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
Sent from Proton Mail mobile
Original Message
On 24 May 2023, 09:26, Harry Powell wrote:
> Hi Jon “Preaching to the choir”! Harry > On 23 May 2023, at 23:16,
A Postdoctoral Research Assistant position in Structural Biology is available
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Hello All,
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*Dear all,*
*
We are excited to announce the release of the new version of the PISA
software, developed at PDBe, based on the jsPISA implementation from
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CCP4 core team, enables the calculation of macromolecular
HI Zoe
If, from a terminal with CCP4 configured, you type
dials.image_viewer (path-to-hdf5-master-file)
Where (path-to-hdf5-master-file) is your file location, does it work?
All the i2 message says is “something went wrong” which is not super helpful
As a general rule, I also usually
Hi everyone,
I am currently trying to view images with dials through CCP4i2 (on mac)
I have so far tried using the DUI but when importing files, nothing seems to
happen… there are no error codes appearing as such but no images/experimental
data is imported. I have tried this on both .cbf and
Dear Matt,
What version of CCP4MG are you using? I thought I had fixed this in the
version that is in recent CCP4 8.0, but apologies if this is still causing
problems.
Best wishes,
Stuart
On Thu, 25 May 2023 at 21:54, Matt McLeod wrote:
> Hi all,
>
> I am having a weird issue where the
Very interesting one from Katherine Lonsdale- thank you
On Thu, 25 May 2023 at 21:21, CCP4BB <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> I found these audio clips on the BBC website - might be of interest -
>
> https://www.bbc.co.uk/archive/dame_kathleen_lonsdale/z6v8kmn
>
>
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