Hi Stefanie,
Why can you only use "taken" three letter codes? In the "output monomer"
box, you should be able to enter whatever you'd like for the "Three letter
code for output monomer". In the attached image, this is shown as "DRG" but
can be changed to any 3 letter code of your choice.
Hi Marco,
"Superpose" in *Coot* will also take any associated ligands along during
the superposition. You can do this under "Calculate-> SSM Superpose". Be
sure to check "move copy of moving structure". The one that moves will show
as "copy of xxx", with xxx being the name of the one that was
Hi Harry,
I did stumble upon this python mmCIF handler for modelCIF:
https://github.com/ihmwg/python-modelcif/blob/main/examples/README.md
Maybe this will have something of use to your efforts?
Best,
Nick Clark
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
uot;
Best,
Nick
-- Forwarded message -----
From: Nicholas Clark
Date: Fri, Feb 23, 2024 at 8:03 AM
Subject: Re: [ccp4bb] mmCIF files from PDB format for AlphaFill
To: Harry Powell
Cc: Harry Powell
Hi Harry,
MAXIT binaries are located here:
https://sw-tools.rcsb.org/apps/MAXIT/b
Harry,
After a little digging, it seems this was previously reported as an issue
to AlphaFold… see:
https://github.com/google-deepmind/alphafold/issues/252
There are a few options others recommended or got to work in the comments.
Notably, MAXIT was used:
“Huiwenke:
MineProt
Hi Harry,
Have you tried MAXIT from the PDB? It can be installed locally:
https://sw-tools.rcsb.org/apps/MAXIT/index.html
Best,
Nick Clark
Nicholas D. Clark (He/Him)
PhD Candidate
Malkowski Lab
University at Buffalo
Department of Structural Biology
Jacob's School of Medicine & Biomedical
Hi Javier,
For a few years (during an industry job) we regularly cloned directly into
BL21 (we made our own high competency cells) and confirmed via expression
before plasmid sequencing. Only after sequencing did we transform into a
cloning strain for miniprep and “long term storage”.
We didn’t
Maria,
Apologies for the second email. I forgot that "Prepare files for
deposition" also merges the CCP4 formatted files into an MTZ. If I recall
correctly, I used "CONVERT2MTZ" in the command line to complete the merging
of the CCP4 files to generate the necessary MTZ for deposition.
Hi Maria,
I'm not sure if anyone has replied to this chain. However, I had a similar
issue when I was trying to prepare files for deposition in the past. You
can use the PDB file and upload it to https://pdb-extract.wwpdb.org/ to
generate the CIF file for deposition.
Best,
Nick Clark
On Tue,
Hi Morgan,
Have you tried MMS?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157405/
If you can reproducibly grow crystals MMS might give you hits in different
conditions during screening. I’ve used this successfully multiple times for
crystals that wouldn’t optimize with standard methods. We
Hello Harry,
I have successfully used the HH-Suite in the recent past. I might be able
to assist you. You can contact me off-list, since this isn’t directly
related to CCP4.
Best,
Nick Clark
On Mon, Nov 13, 2023 at 7:15 AM Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
(Å)*
>>
>> 28.9
>>
>> *Number of non-hydrogen atoms*
>>
>> 4302
>>
>> *Macromolecules*
>>
>> 4086
>>
>> *Ligands*
>>
>> 94
>>
>> *Solvent*
>>
>> 124
>>
>> *Protein residues*
>>
This is why I said this is somewhat subjective.
I would agree I/sigI of 0.6+ and cc1/2 of 0.5+
in high res shell is fine but these values are overall, as the resolution
range is 23-2.6 angstroms.
On Thu, Nov 2, 2023 at 12:16 PM Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Mandar,
It would also be helpful if you could share the statistics in the highest
resolution shell. But to me (which is admittedly a bit subjective), as
noted by Eleanor, the R-merge seems a bit high and the your I/sigma and
CC1/2 seem a bit low. Which doesn’t really matter if you can build a
code for execution of
refmacat.
Best,
Nick Clark
On Mon, May 29, 2023 at 1:48 PM Nicholas Clark wrote:
> 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
> Refmac would work, if "refmacat" (explained in the paper) is used. The
> command is already available in the latest CCP4 update, but not from
> the interfaces at the moment.
>
> Best regards,
> Keitaro
>
> On Sat, 27 May 2023 at 04:02, Nicholas Clark wrote:
> >
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
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,
>
ptide* HN2 H2"
I've attached the file I have for your reference, as I may not be looking
in the correct place. Also, if I'm looking in the wrong file location,
please let me know.
Best,
Nick Clark
On Fri, May 26, 2023 at 10:04 PM Nicholas Clark
wrote:
> Hey Paul,
>
> I'm not sure how
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 mo
ent from Proton Mail mobile
>
>
>
> Original Message ----
> On 27 May 2023, 00:43, Nicholas Clark < ndcla...@buffalo.edu> wrote:
>
>
> I have a cysteine residue that is oxidized and needs to be modeled as CSO.
> In the past, when "replace residue&quo
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
Jinhua,
As Michael stated, ticking "keep delete active" will prevent the window
from closing. Additionally, if you accidentally forget to do this, Coot
does not actually crash. The window gets "hidden" or "minimized". If you
right click on the XQuartz icon, you will see the window at the top of
Hi Medhanjali,
In Coot, there are two additional options for "automated" correction of
Ramachandran outliers. You can find them under "Calculate".
For the entire structure in the "Calculate->all molecule" tab, select
Refine/Improve Ramachandran Plot. For a specific region, you can use the
-- Forwarded message -
From: Nicholas Clark
Date: Mon, Feb 6, 2023 at 6:44 AM
Subject: Re: [ccp4bb] Issues with Coot and PyMOL on MacOS Ventura 13.2
To: Julia Griese
Julia,
I have the same issue with PyMOL. After it opens the blank session, if you
return to the file explorer
Mirek,
Yes, this is a known issue (I read about it previously either here or on
the Coot webpage, I can't recall which).
The only "workaround" is to check the "keep delete active" box before you
begin deleting. It took me a bit to realize this, so I'll share: The window
is still open and can be
Phenix in the past, and I’m assuming still, does not recognize “link
records”. You’ll likely need to generate the peptide in AceDRG, making sure
to link the carboxy- and amino-termini, and include the cif during
refinement.
This was the only way I was able to get Phenix to properly refine an
I had the same issue in the past. To resolve this issue, point Phenix (in
settings -> Graphics, if I recall correctly) to the Coot location in CCP4.
As you suspected, Coot does not know where the Restraint Library is when
opened from Phenix.
Best,
Nick Clark
On Sun, Aug 7, 2022 at 2:00 AM Cryo
Hi Dale,
I recently updated Phenix and CCP4 on iOS had a similar issues with
Phenix/Coot.
I fixed the issues with the restraint dictionary by directing Phenix to the
new location for Coot (in the CCP4 program libraries) in the Phenix
settings. This resolved the lack of restraints for every amino
Dr. Pearl,
I have used the pre-built installer here:
http://scottlab.ucsc.edu/xtal/wiki/index.php/Stand-Alone_Coot
This worked on my Mac running Monterey OS with an intel i7.
Best regards,
Nick Clark
On Fri, Feb 11, 2022 at 4:53 PM Laurence Pearl
wrote:
> Does anyone know where I can
Reza,
Thus far, it seems we’ve all assumed this was an AlphaFold or RobettaFold
model. If this is not indeed the case, it may be worthwhile to “validate”
your mode by running your sequence through one of these two and using the
validation from them.
The AlphaFold DB can be found here, with a
The Molprobity server can be run online and only requires the coordinates
in PDB format: http://molprobity.biochem.duke.edu/.
Best,
Nick Clark
On Mon, Dec 20, 2021 at 11:10 AM Reza Khayat wrote:
> Hi,
>
>
> Can anyone suggest how to validate a predicted structure? Something
> similar to
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