Dear Filipa and Nicholas,
I confirm that in the current CCP4 version 8.0.019, refmacat is integrated in the ccp4i2
refinement task - now the task is called "Refmacat/Refmac5".
Cheers,
Martin
On 29/04/2024 17:30, Nicholas Clark
<0000b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote:
Hi Filipa,
I had a similar issue with "CSO". To visualize the peptide bond in Coot,
you need to change the restraints applied to "2CO". To do this in Coot,
go to "Edit->Restraints" select 2CO and under "group" change this to
"peptide" (make sure to hit enter) then click ok. This should allow you
to visualize the peptide bond.
To get refinement to work properly, I had to use refmacat (which at the
time was command line only, not sure if this is still the case). I'm not
sure if the same requirement will apply for you too. The Refmacat CCP4
website
(https://cloud.ccp4.ac.uk/manuals/html-taskref/doc.task.Refmac.html
<https://cloud.ccp4.ac.uk/manuals/html-taskref/doc.task.Refmac.html>)
seems like it's been fully integrated but someone else would know better
than I.
Best,
Nick Clark
On Mon, Apr 29, 2024 at 10:14 AM Filipa Engrola
<0000ce14ef297227-dmarc-requ...@jiscmail.ac.uk
<mailto:0000ce14ef297227-dmarc-requ...@jiscmail.ac.uk>> wrote:
Dear community,
I am trying to model 2 alternate Cys conformations, one of them
"CYS" (occ 0.6), but the other "2CO" (Chemical identity:
_https://www.rcsb.org/ligand/2CO
<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rcsb.org%2Fligand%2F2CO&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7Cd4317bc7064c4d240ec008dc6856b39e%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638499968861707741%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=UubmJKkvQam6ukRIC%2F5onlDdiYW64nr5%2F%2BWwrtSj70I%3D&reserved=0>;_
occ 0.4).
I can place the residue with alt conformation but not connect it
with the rest of the polypeptide chain (Photo attached).
Using Coot 0.9.8.92, and Refmac5, I have tried:
i) calculate>Modelling>Make Link
After refinement, I get no link.
or
ii) calculate>Modelling>Rebuild Fragment using DB Loop"
It works to connect only "CYS".
I cannot add an alternate conformation and mutate ONLY one to the
desired "2CO", it mutates both of them.
Does anyone have any suggestions? :)
Thank you in advance!
Best,
Filipa.
image.png
--
Filipa Engrola
PhD Candidate
NOVA School of Science and Technology (FCT NOVA) @UCIBIO
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--
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical Sciences
955 Main Street, RM 5130
Buffalo, NY 14203
Cell: 716-830-1908
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