Dear All,
I sincerely appreciate everyone’s contributions and suggestions—the issue has
now been resolved!
Following Oliver's instructions, I used the Grad Web Server to obtain the
coordinates and restraint files for input, then adjusted the conformation using
real-space refinement in Coot. Th
Hi Martin,
I hope you are getting on well with one of the restraints for your molecule.
But if choose
to tweak the restraints to agree with a CSD small molecule structure for
BODIPY, then
I thought I should let you know that the structure you have downloaded YOWVOW
has a high R-factor 10.29%
>
,
Martin
From: CCP4 bulletin board on behalf of Jon
Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Date: Monday, August 19, 2024 at 14:24
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CIF file Cannot Open by Coot
⚠ Caution: External sender
I made your cif into a pdb (attached)
Dear Martin,
My approach to your problem is to download an MOL2 of the small-molecule
compound from WebCSD rather than the small-molecule CIF file. MOL2 files have
the advantage that both the coordinates and the CCDC-curated bond orders are
included in the file. MOL2 files can be read by AceDRG
Monday, August 19, 2024 at 6:43 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CIF file Cannot Open by Coot
Dear All,
Thank you all for your help. I’ve tried several approaches to input this file,
including changing the format to mmCIF, importing it as coordinates, and
checking the restr
Dear all,
The attached is a restraint file generated by aceDRG, using your
713483.txt as the input file. The latest version of aceDRG, currently
not released yet and under the final testing, can generate restraint or
dictionary files of ligands using input files in form of small molecule
cif
> Martin
>>
>> From: CCP4 bulletin board on behalf of Jon Cooper
>> <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk>
>> Date: Monday, August 19, 2024 at 14:24
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] CIF file Cannot Open by Coot
>>
&
On 19/08/2024 14:42, Hu, Wenhao wrote:
Dear Jon,
Thank you so much for all your effort! I really appreciate it. I’ve
just tried to load the files, but unfortunately, it still won’t open
and continues to show the error message I’ve attached here.
Martin,
These are not restraints. They a
ay, August 19, 2024 at 14:24
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] CIF file Cannot Open by Coot
>
> ⚠ Caution: External sender
>
> I made your cif into a pdb (attached) which looks OK. Maybe worth trying with
> that.
>
> Best wishes, Jon Cooper.
> jon.b
of Jon Cooper
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Date: Monday, August 19, 2024 at 14:24
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CIF file Cannot Open by Coot
⚠ Caution: External sender
I made your cif into a pdb (attached) which looks OK. Maybe worth trying with
that.
Dear All,
Thank you all for your help. I’ve tried several approaches to input this file,
including changing the format to mmCIF, importing it as coordinates, and
checking the restraints in the file. However, I am still unable to install the
experimental ligand structure into the protein. It see
On 8/15/24 16:08, Hu, Wenhao wrote:
Hi Paul,
I’ve attached screenshots that show the error message from Coot, along
with the contents of the line that the message refers to. Since this
CIF file contains experimental data and restrains that would be
difficult to rebuild in other software, I’
: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CIF file Cannot Open by Coot
Hi Paul,
Thank you for your reply.
I’ve attached screenshots that show the error message from Coot, along with the
contents of the line that the message refers to. Since this CIF file contains
experimental data and
solutions to successfully import this file into Coot.
Any help you can provide would be greatly appreciated.
Best regards,
Martin
From: Paul Emsley
Sent: Thursday, August 15, 2024 3:09 PM
To: Hu, Wenhao ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CIF file Cannot
On 8/15/24 15:01, Tang, Jiazhi wrote:
--
It happens sometimes when you can not open the downloaded cif files
properly.
One solution is to draw the compound yourself in Chemdraw, copy the
smiles and generate the cif in Elbow within the phenix suit or other
ligand software within ccp4. Just
could cause
some issues.
Regards,
Jiazhi
发件人: CCP4 bulletin board 代表 Martin Hu
发送时间: Thursday, August 15, 2024 2:44:46 PM
收件人: CCP4BB@JISCMAIL.AC.UK
主题: [ccp4bb] CIF file Cannot Open by Coot
Dear [Recipient's Name],
I have downloaded a CIF file of a liga
On 8/15/24 14:44, Martin Hu wrote:
Dear [Recipient's Name],
Dear [Correspondent's Name],
I have downloaded a CIF file of a ligand of interest directly from WebCSD,
which was originally obtained from experimental crystallography research, and
attempted to import it into Coot. However, Coot
Dear [Recipient's Name],
I have downloaded a CIF file of a ligand of interest directly from WebCSD,
which was originally obtained from experimental crystallography research, and
attempted to import it into Coot. However, Coot indicates that it cannot read
the file for some reason. I've also tri
18 matches
Mail list logo
