Re: [ccp4bb] circular peptide structure refinement

2022-08-15 Thread Matthew Snee 
Hi All

To prevent Phenix removing link records, you can use Readyset to create a 
parameters file based on LINK records, and feed it to the refinement program, 
otherwhise they are deleted.

Best wishes

Matthew.

From: CCP4 bulletin board  on behalf of Nicholas Clark 

Sent: 14 August 2022 16:01
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] circular peptide structure refinement

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 inhibitor 
covalently linked to an active site Cys. Thus, the same procedure may be 
required for your circular peptide.

Best,

Nick Clark

On Sun, Aug 14, 2022 at 1:06 AM Jiang Xu 
mailto:foxj...@gmail.com>> wrote:
Hi Joel,
 Thank you for your reply. I just got time to refine the circular peptide 
structure 1 month later. I use MR to solve the structure. I made the 
link(Calculate-->Modeling-->Make Link) as the guy who replied to my question 
suggested. The link generated is a dashed line but disappeared after refinement 
with Phenix.  It seemed that the program didn't consider the link made in coot 
as a valid bond and intentionally avoided forming a bond between the C atom and 
the N atom. I still don't know how to fix the problem.
Thank you,
Best regards,
Jiang
Lin Chen Lab
University of Southern California

P.S.
coot manually made link between the C and N terminal
[unnamed.jpg]
After refinement
[unnamed (1).jpg]



On Wed, Jul 6, 2022 at 3:29 PM Joel Tyndall 
mailto:joel.tynd...@otago.ac.nz>> wrote:

You will need to add the “link” line to the PDB file so the software recognises 
the covalent bond.

See the pdb file for 6U6K



Hope this helps



J



From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Jiang Xu
Sent: Thursday, 7 July 2022 10:15 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] circular peptide structure refinement



Hello everyone,

   I have a peptide that forms a peptide bond between the N terminal and C 
terminal.  I used X-ray crystallography to solve the structure and found the N 
and C terminals are pretty close to each other with extra electron densities 
clearly showing that they form a peptide bond. However in Coot I could not make 
the peptide bond, the two terminals seem to repel each other when I do real 
space refinement in coot and, couldn't form the peptide bond. Any suggestions 
on how to do it?

Thank you,

Best,

Jiang Xu

Lin Chen Research Group

Molecular and Computational Biology

Department of Biological Sciences

University of Southern California





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--
Nicholas D. Clark
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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Re: [ccp4bb] circular peptide structure refinement

2022-08-14 Thread Nicholas Clark 
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
inhibitor covalently linked to an active site Cys. Thus, the same procedure
may be required for your circular peptide.

Best,

Nick Clark

On Sun, Aug 14, 2022 at 1:06 AM Jiang Xu  wrote:

> Hi Joel,
>  Thank you for your reply. I just got time to refine the circular
> peptide structure 1 month later. I use MR to solve the structure. I made
> the link(Calculate-->Modeling-->Make Link) as the guy who replied to my
> question suggested. The link generated is a dashed line but disappeared
> after refinement with Phenix.  It seemed that the program didn't consider
> the link made in coot as a valid bond and intentionally avoided forming a
> bond between the C atom and the N atom. I still don't know how to fix the
> problem.
> Thank you,
> Best regards,
> Jiang
> Lin Chen Lab
> University of Southern California
>
> P.S.
> coot manually made link between the C and N terminal
> [image: unnamed.jpg]
> After refinement
> [image: unnamed (1).jpg]
>
>
>
> On Wed, Jul 6, 2022 at 3:29 PM Joel Tyndall 
> wrote:
>
>> You will need to add the “link” line to the PDB file so the software
>> recognises the covalent bond.
>>
>>
>> See the pdb file for 6U6K
>>
>>
>>
>> Hope this helps
>>
>>
>>
>> J
>>
>>
>>
>> *From:* CCP4 bulletin board  *On Behalf Of *Jiang
>> Xu
>> *Sent:* Thursday, 7 July 2022 10:15 AM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* [ccp4bb] circular peptide structure refinement
>>
>>
>>
>> Hello everyone,
>>
>>I have a peptide that forms a peptide bond between the N terminal and
>> C terminal.  I used X-ray crystallography to solve the structure and found
>> the N and C terminals are pretty close to each other with extra electron
>> densities clearly showing that they form a peptide bond. However in Coot I
>> could not make the peptide bond, the two terminals seem to repel each other
>> when I do real space refinement in coot and, couldn't form the peptide
>> bond. Any suggestions on how to do it?
>>
>> Thank you,
>>
>> Best,
>>
>> Jiang Xu
>>
>> Lin Chen Research Group
>>
>> Molecular and Computational Biology
>>
>> Department of Biological Sciences
>>
>> University of Southern California
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
>
-- 
Nicholas D. Clark
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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Re: [ccp4bb] circular peptide structure refinement

2022-08-13 Thread Jiang Xu 
Hi Joel,
 Thank you for your reply. I just got time to refine the circular
peptide structure 1 month later. I use MR to solve the structure. I made
the link(Calculate-->Modeling-->Make Link) as the guy who replied to my
question suggested. The link generated is a dashed line but disappeared
after refinement with Phenix.  It seemed that the program didn't consider
the link made in coot as a valid bond and intentionally avoided forming a
bond between the C atom and the N atom. I still don't know how to fix the
problem.
Thank you,
Best regards,
Jiang
Lin Chen Lab
University of Southern California

P.S.
coot manually made link between the C and N terminal
[image: unnamed.jpg]
After refinement
[image: unnamed (1).jpg]



On Wed, Jul 6, 2022 at 3:29 PM Joel Tyndall 
wrote:

> You will need to add the “link” line to the PDB file so the software
> recognises the covalent bond.
>
>
> See the pdb file for 6U6K
>
>
>
> Hope this helps
>
>
>
> J
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Jiang
> Xu
> *Sent:* Thursday, 7 July 2022 10:15 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] circular peptide structure refinement
>
>
>
> Hello everyone,
>
>I have a peptide that forms a peptide bond between the N terminal and C
> terminal.  I used X-ray crystallography to solve the structure and found
> the N and C terminals are pretty close to each other with extra electron
> densities clearly showing that they form a peptide bond. However in Coot I
> could not make the peptide bond, the two terminals seem to repel each other
> when I do real space refinement in coot and, couldn't form the peptide
> bond. Any suggestions on how to do it?
>
> Thank you,
>
> Best,
>
> Jiang Xu
>
> Lin Chen Research Group
>
> Molecular and Computational Biology
>
> Department of Biological Sciences
>
> University of Southern California
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
>



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Re: [ccp4bb] circular peptide structure refinement

2022-07-06 Thread Joel Tyndall 
You will need to add the "link" line to the PDB file so the software recognises 
the covalent bond.

See the pdb file for 6U6K

Hope this helps

J

From: CCP4 bulletin board  On Behalf Of Jiang Xu
Sent: Thursday, 7 July 2022 10:15 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] circular peptide structure refinement

Hello everyone,
   I have a peptide that forms a peptide bond between the N terminal and C 
terminal.  I used X-ray crystallography to solve the structure and found the N 
and C terminals are pretty close to each other with extra electron densities 
clearly showing that they form a peptide bond. However in Coot I could not make 
the peptide bond, the two terminals seem to repel each other when I do real 
space refinement in coot and, couldn't form the peptide bond. Any suggestions 
on how to do it?
Thank you,
Best,
Jiang Xu
Lin Chen Research Group
Molecular and Computational Biology
Department of Biological Sciences
University of Southern California



To unsubscribe from the CCP4BB list, click the following link:
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