Dear Nick,
Sorry for this. Refmacat is a replacement for the refmac5 command, so
it is totally unfriendly to the people who never used Refmac as a
command. But it is great you managed to use it!
Best regards,
Keitaro
On Mon, 29 May 2023 at 22:11, Nicholas Clark wrote:
>
> Keitaro,
>
> Please di
Keitaro,
Please disregard my previous email. After informing myself on how Refmac is
executed from command line (via online websites & log files from GUI Refmac
runs) and many trial and error executions, I was able to execute refmac5
from command line and was able to recycle the code for execution
Hi Keitaro,
Thanks for the response. Is there documentation somewhere on how to run
refmacat (like an example for Crystallographic data refinement, I found the
one for CryoEM data but )? I have made multiple attempts to get this to run
on my end but when I input the command I get "Waiting for inpu
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
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 wrot
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 the
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 en
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
_chem_comp_alias.atom_id_stand
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 fi
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, when
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 modeled
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
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