Re: [ccp4bb] Missing double bonds in the ligand

[Paul Emsley]

The ligand is acetamido-thiadiazole-2-sulfonamide and has code AZM - do 
your PDB atom names match the CCD?




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Re: [ccp4bb] [External] Re: [ccp4bb] Missing double bonds in the ligand

[Srivastava, Dhiraj]

You can make molecule in chemdraw or chemdraw 3d with proper bond order and 
save it in sdf or .mol format or any other format compatible with schrodinger. 
Schrodinger should be able to read .sdf or .mol format.

Dhiraj



From: CCP4 bulletin board  on behalf of Nigel Moriarty 

Sent: Thursday, July 7, 2022 7:30 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [External] Re: [ccp4bb] Missing double bonds in the ligand

Joel

You'll need to be more specific than ".cif" files. CIF can be used for models, 
data and restraints. Read more here.

http://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2013_01.pdf#page=6

If you are referring to the restraints CIF, it is possible but I'm not sure 
which software uses it.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909  Web  : CCI.LBL.gov
ORCID : orcid.org/-0001-8857-9464


On Thu, Jul 7, 2022 at 3:06 PM Joel Tyndall 
mailto:joel.tynd...@otago.ac.nz>> wrote:

Does the Schrodinger software read a .cif file? The bond order should be 
embedded in there.



From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Nigel Moriarty
Sent: Friday, 8 July 2022 7:47 am
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Missing double bonds in the ligand



Further reading



https://en.wikipedia.org/wiki/The_Treachery_of_Images



https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2016_01.pdf#page=10


Cheers



Nigel



---

Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging

Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909  Web  : 
CCI.LBL.gov

ORCID : 
orcid.org/-0001-8857-9464





On Thu, Jul 7, 2022 at 12:42 PM Robbie Joosten 
mailto:robbie_joos...@hotmail.com>> wrote:

Dear Anil,



Bond orders are not captured in PDB files explicitly. The way bonds are shown 
depends on the program and possibly additional information sources (i.e. 
molecular restraint or topology files).

So this is just a "problem" with Schrödinger.



Cheers,

Robbie



On 7 Jul 2022 21:00, "Dr. Anil Kumar Marapaka" 
mailto:anilmarap...@gmail.com>> wrote:

Dear CCP4 Users,

We are working on a ligand-bound structure and would like to look at 
protein-ligand interactions using Schrodinger.

Molecule structure is:

When we load the ligand-fitted PDB file into Schrodinger, the molecule appears 
to be flat like it should be in the structure but it removed all the double 
bonds in the ligand where the above shown original molecular structure has 
double bonds in it.

When we load the same PDB file into pymol and look at the ligand it shows 
correctly



We would appreciate if any insight or suggestions for why this may be happening 
and how to ensure the ligand shows properly when the PDB is loaded into 
Schrodinger. Would this be an issue with Schrodinger software or with the PDB 
file?

I can be available by direct email for troubleshooting at 

Re: [ccp4bb] Missing double bonds in the ligand

[Nigel Moriarty]

Joel

You'll need to be more specific than ".cif" files. CIF can be used for
models, data and restraints. Read more here.

http://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2013_01.pdf#page=6

If you are referring to the restraints CIF, it is possible but I'm not sure
which software uses it.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909  Web  : CCI.LBL.gov
ORCID : orcid.org/-0001-8857-9464


On Thu, Jul 7, 2022 at 3:06 PM Joel Tyndall 
wrote:

> Does the Schrodinger software read a .cif file? The bond order should be
> embedded in there.
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Nigel
> Moriarty
> *Sent:* Friday, 8 July 2022 7:47 am
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Missing double bonds in the ligand
>
>
>
> Further reading
>
>
>
> https://en.wikipedia.org/wiki/The_Treachery_of_Images
> 
>
>
>
>
> https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2016_01.pdf#page=10
> 
>
>
> Cheers
>
>
>
> Nigel
>
>
>
> ---
>
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
>
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709 Email : nwmoria...@lbl.gov
> Fax   : 510-486-5909  Web  : CCI.LBL.gov
> 
>
> ORCID : orcid.org/-0001-8857-9464
> 
>
>
>
>
>
> On Thu, Jul 7, 2022 at 12:42 PM Robbie Joosten 
> wrote:
>
> Dear Anil,
>
>
>
> Bond orders are not captured in PDB files explicitly. The way bonds are
> shown depends on the program and possibly additional information sources
> (i.e. molecular restraint or topology files).
>
> So this is just a "problem" with Schrödinger.
>
>
>
> Cheers,
>
> Robbie
>
>
>
> On 7 Jul 2022 21:00, "Dr. Anil Kumar Marapaka" 
> wrote:
>
> Dear CCP4 Users,
>
> We are working on a ligand-bound structure and would like to look at
> protein-ligand interactions using Schrodinger.
>
> Molecule structure is:
>
> When we load the ligand-fitted PDB file into Schrodinger, the molecule
> appears to be flat like it should be in the structure but it removed all
> the double bonds in the ligand where the above shown original molecular
> structure has double bonds in it.
>
> When we load the same PDB file into pymol and look at the ligand it shows
> correctly
>
>
>
> We would appreciate if any insight or suggestions for why this may be
> happening and how to ensure the ligand shows properly when the PDB is
> loaded into Schrodinger. Would this be an issue with Schrodinger software
> or with the PDB file?
>
> I can be available by direct email for troubleshooting at
> amara...@purdue.edu.
>
>
>
> --
>
>
> *Anil Kumar Marapaka, Ph.D. Post-Doctoral Research Associate *
>
> *Department of Medicinal Chemistry and Molecular Pharmacology (MCMP),*
>
> *Purdue University, West lafayette,*
>
> *Indiana-47907, USA.*
>
> *Mobile 1: +1-765-409-6245 (USA)*
>
> *Mobile 2: +91-995-998-5571 (India)*
>
> *Email 1: amara...@purdue.edu *
>
> *Email 2: anilmarap...@gmail.com *
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 

Re: [ccp4bb] Missing double bonds in the ligand

[Joel Tyndall]

Does the Schrodinger software read a .cif file? The bond order should be 
embedded in there.

From: CCP4 bulletin board  On Behalf Of Nigel Moriarty
Sent: Friday, 8 July 2022 7:47 am
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Missing double bonds in the ligand

Further reading

https://en.wikipedia.org/wiki/The_Treachery_of_Images

https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2016_01.pdf#page=10

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909  Web  : 
CCI.LBL.gov
ORCID : 
orcid.org/-0001-8857-9464


On Thu, Jul 7, 2022 at 12:42 PM Robbie Joosten 
mailto:robbie_joos...@hotmail.com>> wrote:
Dear Anil,

Bond orders are not captured in PDB files explicitly. The way bonds are shown 
depends on the program and possibly additional information sources (i.e. 
molecular restraint or topology files).
So this is just a "problem" with Schrödinger.

Cheers,
Robbie

On 7 Jul 2022 21:00, "Dr. Anil Kumar Marapaka" 
mailto:anilmarap...@gmail.com>> wrote:

Dear CCP4 Users,

We are working on a ligand-bound structure and would like to look at 
protein-ligand interactions using Schrodinger.

Molecule structure is:

When we load the ligand-fitted PDB file into Schrodinger, the molecule appears 
to be flat like it should be in the structure but it removed all the double 
bonds in the ligand where the above shown original molecular structure has 
double bonds in it.

When we load the same PDB file into pymol and look at the ligand it shows 
correctly



We would appreciate if any insight or suggestions for why this may be happening 
and how to ensure the ligand shows properly when the PDB is loaded into 
Schrodinger. Would this be an issue with Schrodinger software or with the PDB 
file?

I can be available by direct email for troubleshooting at 
amara...@purdue.edu.

--
Anil Kumar Marapaka, Ph.D.
Post-Doctoral Research Associate
Department of Medicinal Chemistry and Molecular Pharmacology (MCMP),
Purdue University, West lafayette,
Indiana-47907, USA.
Mobile 1: +1-765-409-6245 (USA)
Mobile 2: +91-995-998-5571 (India)
Email 1: amara...@purdue.edu
Email 2: anilmarap...@gmail.com




To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Missing double bonds in the ligand

[Nigel Moriarty]

Further reading

https://en.wikipedia.org/wiki/The_Treachery_of_Images

https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2016_01.pdf#page=10

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909  Web  : CCI.LBL.gov
ORCID : orcid.org/-0001-8857-9464


On Thu, Jul 7, 2022 at 12:42 PM Robbie Joosten 
wrote:

> Dear Anil,
>
> Bond orders are not captured in PDB files explicitly. The way bonds are
> shown depends on the program and possibly additional information sources
> (i.e. molecular restraint or topology files).
> So this is just a "problem" with Schrödinger.
>
> Cheers,
> Robbie
>
> On 7 Jul 2022 21:00, "Dr. Anil Kumar Marapaka" 
> wrote:
>
> Dear CCP4 Users,
>
> We are working on a ligand-bound structure and would like to look at
> protein-ligand interactions using Schrodinger.
>
> Molecule structure is:
> [image: image.png]
>
> When we load the ligand-fitted PDB file into Schrodinger, the molecule
> appears to be flat like it should be in the structure but it removed all
> the double bonds in the ligand where the above shown original molecular
> structure has double bonds in it.
> [image: image.png]
>
> When we load the same PDB file into pymol and look at the ligand it shows
> correctly
> [image: image.png]
>
>
> We would appreciate if any insight or suggestions for why this may be
> happening and how to ensure the ligand shows properly when the PDB is
> loaded into Schrodinger. Would this be an issue with Schrodinger software
> or with the PDB file?
>
> I can be available by direct email for troubleshooting at
> amara...@purdue.edu.
>
> --
>
> *Anil Kumar Marapaka, Ph.D.Post-Doctoral Research Associate *
>
> *Department of Medicinal Chemistry and Molecular Pharmacology (MCMP),*
>
> *Purdue University, West lafayette,*
> *Indiana-47907, USA.*
> *Mobile 1: +1-765-409-6245 (USA)*
> *Mobile 2: +91-995-998-5571 (India)*
> *Email 1: amara...@purdue.edu *
> *Email 2: anilmarap...@gmail.com *
>
>
>
> --
>
> 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
>



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Re: [ccp4bb] Missing double bonds in the ligand

[Robbie Joosten]

Dear Anil,Bond orders are not captured in PDB files explicitly. The way bonds are shown depends on the program and possibly additional information sources (i.e. molecular restraint or topology files). So this is just a "problem" with Schrödinger.Cheers,RobbieOn 7 Jul 2022 21:00, "Dr. Anil Kumar Marapaka"  wrote:Dear CCP4 Users,We are working on a ligand-bound structure and would like to look at protein-ligand interactions using Schrodinger.Molecule structure is: When we load the ligand-fitted PDB file into Schrodinger, the molecule appears to be flat like it should be in the structure but it removed all the double bonds in the ligand where the above shown original molecular structure has double bonds in it.When we load the same PDB file into pymol and look at the ligand it shows correctlyWe would appreciate if any insight or suggestions for why this may be happening and how to ensure the ligand shows properly when the PDB is loaded into Schrodinger. Would this be an issue with Schrodinger software or with the PDB file?I can be available by direct email for troubleshooting at amara...@purdue.edu.-- Anil Kumar Marapaka, Ph.D.Post-Doctoral Research Associate Department of Medicinal Chemistry and Molecular Pharmacology (MCMP),
Purdue University, West lafayette,Indiana-47907, USA.Mobile 1: +1-765-409-6245 (USA)Mobile 2: +91-995-998-5571 (India)Email 1: amara...@purdue.eduEmail 2: anilmarap...@gmail.com


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[ccp4bb] Senior Lectureship/Lectureship Position at University of Sussex

[Erika Mancini]

Dear all,



We are seeking to recruit a Lecturer/Senior Lecturer (Teaching & Research 
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Imaging, a new 
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Details on the job and how to apply can be found here:

https://www.sussex.ac.uk/about/jobs/senior-lecturer-biochem-biomed-7870


Best wishes,

Erika






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[cid:090812ec-4ae9-4a8d-9b56-e8201387f1d3]




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[ccp4bb] Lectureship Position at University of Essex

[Prischi, Filippo]

Dear all,

We are seeking to recruit a lecturer/assistant professor (Teaching & Research 
permanent contract) to join the School of Life Sciences at University of Essex. 
We encourage applicants with a skillset and research interest in microbiology, 
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For more info and details on how to apply, please follow this link 
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~~
Dr Filippo Prischi
Senior Lecturer in Biochemistry
School of Life Sciences
University of Essex

T.  +44 (0)1206 873370
E.  fpris...@essex.ac.uk
► https://www.essex.ac.uk/people/prisc89105/filippo-prischi



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