Re: [ccp4bb] To Trim or Not to To Trim

[Bernhard Lechtenberg]

I found the poll I wrote about earlier. This actually is way older than I had 
expected (2011). You can see the poll results (which was run by Ed Pozharski) 
and discussion at the time here in the CCP4BB archive:
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg20268.html

In brief, the results of 240 respondents were:
Delete the atoms 43%
Let refinement take care of it by inflating B-factors41%
Set occupancy to zero12%
Other 4%


Bernhard

From: CCP4 bulletin board  on behalf of Debanu Das 

Date: Friday, 10 March 2023 at 2:56 pm
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] To Trim or Not to To Trim
We dealt with this in-depth during structural genomics days when we deposited 
over 1500 novel, high-quality, experimentally-phased structures into the PDB. 
Think it’s prudent to trim/truncate side chains without reliable density.

Non-structural biologists using PDB structures without expert help can err in 
any of these scenarios: misinterpreting most common/random rotamer, zero 
occupancy atoms, B-factors, etc.

What is the value of populating the PDB, which is a structural model 
repository, with such information that is not there, i.e., reliable structural 
model?

Any trained crystallographer/structural biologist can easily add in side chain 
information if needed for modeling/computational chemistry reasons.

Best regards,
Debanu

On Thu, Mar 9, 2023 at 6:50 PM Jurgen Bosch 
mailto:jxb...@case.edu>> wrote:
I’d say no trimming to side chains for the following reason: There are 
non-structural biologists using PDB files and if atoms are missing they don’t 
know what to do. A better approach is where no side chain density allows 
support of placement, pick the most common rotamer and set the occupancy to 
zero for those atoms lacking density support. More work for you but more 
accurate in my opinion.

Jürgen


___
Jürgen Bosch, PhD, MBA
Center for Global Health & Diseases
Case Western Reserve University
Cleveland, OH 44106
https://www.linkedin.com/in/jubosch/


CEO & Co-Founder at InterRayBio, LLC




On Mar 9, 2023, at 9:45 PM, Bernhard Lechtenberg 
<968307750321-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Hi Rhys,

I am also all for leaving side chains and letting the B-factors deal with the 
weak/absent density.

I don’t think there is a consensus, but I kind of remember that somebody did a 
poll a few years ago and if I remember correctly the main approaches were the 
one described above, or trimming the side-chains.

Bernhard

Bernhard C. Lechtenberg PhD
NHMRC Emerging Leadership Fellow
Laboratory Head
Ubiquitin Signalling Division​​
E lechtenber...@wehi.edu.au
T +61 3 9345 2217


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Rhys Grinter 
<22087c81e8c6-dmarc-requ...@jiscmail.ac.uk>
Date: Friday, 10 March 2023 at 12:26 pm
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] To Trim or Not to To Trim
Hi All,

I'm trying to crowdsource an opinion on how people deal with modelling side 
chains with poorly resolved electron or cryoEM density.

My preference is to model the sidechain and allow the B-factors to go high in 
refinement to represent that the side chain is flexible. However, I'm aware 
that some people truncate sidechains if density is not present to justify 
modelling. I've also seen models where the sidechain is modelled but with zero 
occupancy if density isn't present.

Is there a consensus and justifying arguments for why one approach is better?

Cheers,

Rhys




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Re: [ccp4bb] To Trim or Not to To Trim

[Jon Cooper]

Hello, yes, the trimming and occupancy tricks can be confusing and they can be 
a bit of a cheeky way to improve the model statistics. I prefer to build the 
whole side chain and if you can't see all or part of it, then that's just too 
bad, but I have erred.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 10 Mar 2023, 01:25, Rhys Grinter wrote:

> Hi All,
>
> I'm trying to crowdsource an opinion on how people deal with modelling side 
> chains with poorly resolved electron or cryoEM density.
>
> My preference is to model the sidechain and allow the B-factors to go high in 
> refinement to represent that the side chain is flexible. However, I'm aware 
> that some people truncate sidechains if density is not present to justify 
> modelling. I've also seen models where the sidechain is modelled but with 
> zero occupancy if density isn't present.
>
> Is there a consensus and justifying arguments for why one approach is better?
>
> Cheers,
>
> Rhys
>
> ---
>
> 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] To Trim or Not to To Trim

[Debanu Das]

We dealt with this in-depth during structural genomics days when we
deposited over 1500 novel, high-quality, experimentally-phased structures
into the PDB. Think it’s prudent to trim/truncate side chains without
reliable density.

Non-structural biologists using PDB structures without expert help can err
in any of these scenarios: misinterpreting most common/random rotamer, zero
occupancy atoms, B-factors, etc.

What is the value of populating the PDB, which is a structural model
repository, with such information that is not there, i.e., reliable
structural model?

Any trained crystallographer/structural biologist can easily add in side
chain information if needed for modeling/computational chemistry reasons.

Best regards,
Debanu

On Thu, Mar 9, 2023 at 6:50 PM Jurgen Bosch  wrote:

> I’d say no trimming to side chains for the following reason: There are
> non-structural biologists using PDB files and if atoms are missing they
> don’t know what to do. A better approach is where no side chain density
> allows support of placement, pick the most common rotamer and set the
> occupancy to zero for those atoms lacking density support. More work for
> you but more accurate in my opinion.
>
> Jürgen
>
>
> ___
> Jürgen Bosch, PhD, MBA
> Center for Global Health & Diseases
> Case Western Reserve University
> Cleveland, OH 44106
> https://www.linkedin.com/in/jubosch/
>
> CEO & Co-Founder at InterRayBio, LLC
>
>
>
> On Mar 9, 2023, at 9:45 PM, Bernhard Lechtenberg <
> 968307750321-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> Hi Rhys,
>
> I am also all for leaving side chains and letting the B-factors deal with
> the weak/absent density.
>
> I don’t think there is a consensus, but I kind of remember that somebody
> did a poll a few years ago and if I remember correctly the main approaches
> were the one described above, or trimming the side-chains.
>
> Bernhard
>
> *Bernhard C. Lechtenberg* PhD
> NHMRC Emerging Leadership Fellow
> Laboratory Head
> Ubiquitin Signalling Division​​
> E lechtenber...@wehi.edu.au
> T +61 3 9345 2217
>
>
>
> *From: *CCP4 bulletin board  on behalf of Rhys
> Grinter <22087c81e8c6-dmarc-requ...@jiscmail.ac.uk>
> *Date: *Friday, 10 March 2023 at 12:26 pm
> *To: *CCP4BB@JISCMAIL.AC.UK 
> *Subject: *[ccp4bb] To Trim or Not to To Trim
> Hi All,
>
> I'm trying to crowdsource an opinion on how people deal with modelling
> side chains with poorly resolved electron or cryoEM density.
>
> My preference is to model the sidechain and allow the B-factors to go high
> in refinement to represent that the side chain is flexible. However, I'm
> aware that some people truncate sidechains if density is not present to
> justify modelling. I've also seen models where the sidechain is modelled
> but with zero occupancy if density isn't present.
>
> Is there a consensus and justifying arguments for why one approach is
> better?
>
> Cheers,
>
> Rhys
>
>
> --
>
> 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] To Trim or Not to To Trim

[Debanu Das]

In fact, for non-SBs using the PDB, it is far likelier that they will
recognize truncated side chains and thus seek help or know what to do
themselves, compared to recognizing incorrectly modeled rotamers (as they
won’t be checking electron density likely) and atoms with zero occupancy
and B-factors, which could lead to fairly incorrect biological
interpretations.
Best,
Debanu

On Thu, Mar 9, 2023 at 7:55 PM Debanu Das  wrote:

> We dealt with this in-depth during structural genomics days when we
> deposited over 1500 novel, high-quality, experimentally-phased structures
> into the PDB. Think it’s prudent to trim/truncate side chains without
> reliable density.
>
> Non-structural biologists using PDB structures without expert help can err
> in any of these scenarios: misinterpreting most common/random rotamer, zero
> occupancy atoms, B-factors, etc.
>
> What is the value of populating the PDB, which is a structural model
> repository, with such information that is not there, i.e., reliable
> structural model?
>
> Any trained crystallographer/structural biologist can easily add in side
> chain information if needed for modeling/computational chemistry reasons.
>
> Best regards,
> Debanu
>
> On Thu, Mar 9, 2023 at 6:50 PM Jurgen Bosch  wrote:
>
>> I’d say no trimming to side chains for the following reason: There are
>> non-structural biologists using PDB files and if atoms are missing they
>> don’t know what to do. A better approach is where no side chain density
>> allows support of placement, pick the most common rotamer and set the
>> occupancy to zero for those atoms lacking density support. More work for
>> you but more accurate in my opinion.
>>
>> Jürgen
>>
>>
>> ___
>> Jürgen Bosch, PhD, MBA
>> Center for Global Health & Diseases
>> Case Western Reserve University
>> Cleveland, OH 44106
>> https://www.linkedin.com/in/jubosch/
>>
>> CEO & Co-Founder at InterRayBio, LLC
>>
>>
>>
>> On Mar 9, 2023, at 9:45 PM, Bernhard Lechtenberg <
>> 968307750321-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>> Hi Rhys,
>>
>> I am also all for leaving side chains and letting the B-factors deal with
>> the weak/absent density.
>>
>> I don’t think there is a consensus, but I kind of remember that somebody
>> did a poll a few years ago and if I remember correctly the main approaches
>> were the one described above, or trimming the side-chains.
>>
>> Bernhard
>>
>> *Bernhard C. Lechtenberg* PhD
>> NHMRC Emerging Leadership Fellow
>> Laboratory Head
>> Ubiquitin Signalling Division​​
>> E lechtenber...@wehi.edu.au
>> T +61 3 9345 2217
>>
>>
>>
>> *From: *CCP4 bulletin board  on behalf of Rhys
>> Grinter <22087c81e8c6-dmarc-requ...@jiscmail.ac.uk>
>> *Date: *Friday, 10 March 2023 at 12:26 pm
>> *To: *CCP4BB@JISCMAIL.AC.UK 
>> *Subject: *[ccp4bb] To Trim or Not to To Trim
>> Hi All,
>>
>> I'm trying to crowdsource an opinion on how people deal with modelling
>> side chains with poorly resolved electron or cryoEM density.
>>
>> My preference is to model the sidechain and allow the B-factors to go
>> high in refinement to represent that the side chain is flexible. However,
>> I'm aware that some people truncate sidechains if density is not present to
>> justify modelling. I've also seen models where the sidechain is modelled
>> but with zero occupancy if density isn't present.
>>
>> Is there a consensus and justifying arguments for why one approach is
>> better?
>>
>> Cheers,
>>
>> Rhys
>>
>>
>> --
>>
>> 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
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
> --
> ---
> LinkedIn: www.linkedin.com/in/debanudas
> Cal Alumni: cal.berkeley.edu/debanudas
>
-- 
---
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Cal Alumni: cal.berkeley.edu/debanudas



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Re: [ccp4bb] To Trim or Not to To Trim

[Bernhard Lechtenberg]

Hi Rhys,

I am also all for leaving side chains and letting the B-factors deal with the 
weak/absent density.

I don’t think there is a consensus, but I kind of remember that somebody did a 
poll a few years ago and if I remember correctly the main approaches were the 
one described above, or trimming the side-chains.

Bernhard

Bernhard C. Lechtenberg PhD
NHMRC Emerging Leadership Fellow
Laboratory Head
Ubiquitin Signalling Division​​
E lechtenber...@wehi.edu.au
T +61 3 9345 2217


From: CCP4 bulletin board  on behalf of Rhys Grinter 
<22087c81e8c6-dmarc-requ...@jiscmail.ac.uk>
Date: Friday, 10 March 2023 at 12:26 pm
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] To Trim or Not to To Trim
Hi All,

I'm trying to crowdsource an opinion on how people deal with modelling side 
chains with poorly resolved electron or cryoEM density.

My preference is to model the sidechain and allow the B-factors to go high in 
refinement to represent that the side chain is flexible. However, I'm aware 
that some people truncate sidechains if density is not present to justify 
modelling. I've also seen models where the sidechain is modelled but with zero 
occupancy if density isn't present.

Is there a consensus and justifying arguments for why one approach is better?

Cheers,

Rhys




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] To Trim or Not to To Trim

[Jurgen Bosch]

I’d say no trimming to side chains for the following reason: There are 
non-structural biologists using PDB files and if atoms are missing they don’t 
know what to do. A better approach is where no side chain density allows 
support of placement, pick the most common rotamer and set the occupancy to 
zero for those atoms lacking density support. More work for you but more 
accurate in my opinion.

Jürgen


___
Jürgen Bosch, PhD, MBA
Center for Global Health & Diseases
Case Western Reserve University
Cleveland, OH 44106
https://www.linkedin.com/in/jubosch/

CEO & Co-Founder at InterRayBio, LLC



> On Mar 9, 2023, at 9:45 PM, Bernhard Lechtenberg 
> <968307750321-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi Rhys,
>  
> I am also all for leaving side chains and letting the B-factors deal with the 
> weak/absent density.
>  
> I don’t think there is a consensus, but I kind of remember that somebody did 
> a poll a few years ago and if I remember correctly the main approaches were 
> the one described above, or trimming the side-chains.
>  
> Bernhard
>  
> Bernhard C. Lechtenberg PhD
> NHMRC Emerging Leadership Fellow
> Laboratory Head
> Ubiquitin Signalling Division​​
> E lechtenber...@wehi.edu.au 
> T +61 3 9345 2217
>  
>  
> From: CCP4 bulletin board  on behalf of Rhys Grinter 
> <22087c81e8c6-dmarc-requ...@jiscmail.ac.uk>
> Date: Friday, 10 March 2023 at 12:26 pm
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [ccp4bb] To Trim or Not to To Trim
> 
> Hi All,
>  
> I'm trying to crowdsource an opinion on how people deal with modelling side 
> chains with poorly resolved electron or cryoEM density.
>  
> My preference is to model the sidechain and allow the B-factors to go high in 
> refinement to represent that the side chain is flexible. However, I'm aware 
> that some people truncate sidechains if density is not present to justify 
> modelling. I've also seen models where the sidechain is modelled but with 
> zero occupancy if density isn't present. 
>  
> Is there a consensus and justifying arguments for why one approach is better?
>  
> Cheers,
>  
> Rhys
>  
>  
> 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] Structural alignment and classification

[Debanu Das]

Try POSA and FATCAT from Godzik group for structural clusters/trees and
multiple/flexible structure alignments:

https://academic.oup.com/nar/article/48/W1/W60/5848494

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086100/

https://posa.godziklab.org/
https://fatcat.godziklab.org/

Best regards,
Debanu

On Thu, Mar 9, 2023 at 3:57 PM Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Coot's ssm superposition does give the C-alpha rmsd, though, most easily
> seen if you run it from a terminal window? I guess it can't be miles
> different from a least-squares fit ;-?
>
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>
>
>  Original Message 
> On 9 Mar 2023, 13:55, Paul Emsley < pems...@mrc-lmb.cam.ac.uk> wrote:
>
>
> On 06/03/2023 07:35, Armando Albert wrote: > I want to align several
> structures we obtained from a fragment screening campaign and cluster them
> according to RMSD. > To what end, may I ask? I would use LSQKAB, parse the
> log files for the RMSD and create an input file for R. (One cannot just do
> this in Coot, because, for LSQ fitting, Coot only returns the
> transformation matrix, not any fitting statistics - in retrospect this is
> obviously an oversight.) Paul.
>  To
> unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This
> message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing
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Re: [ccp4bb] Structural alignment and classification

[Jon Cooper]

Coot's ssm superposition does give the C-alpha rmsd, though, most easily seen 
if you run it from a terminal window? I guess it can't be miles different from 
a least-squares fit ;-?

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 9 Mar 2023, 13:55, Paul Emsley wrote:

> On 06/03/2023 07:35, Armando Albert wrote: > I want to align several 
> structures we obtained from a fragment screening campaign and cluster them 
> according to RMSD. > To what end, may I ask? I would use LSQKAB, parse the 
> log files for the RMSD and create an input file for R. (One cannot just do 
> this in Coot, because, for LSQ fitting, Coot only returns the transformation 
> matrix, not any fitting statistics - in retrospect this is obviously an 
> oversight.) Paul. 
>  To 
> unsubscribe from the CCP4BB list, click the following link: 
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message 
> was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by 
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[ccp4bb] To Trim or Not to To Trim

[Rhys Grinter]

Hi All,

I'm trying to crowdsource an opinion on how people deal with modelling side
chains with poorly resolved electron or cryoEM density.

My preference is to model the sidechain and allow the B-factors to go high
in refinement to represent that the side chain is flexible. However, I'm
aware that some people truncate sidechains if density is not present to
justify modelling. I've also seen models where the sidechain is modelled
but with zero occupancy if density isn't present.

Is there a consensus and justifying arguments for why one approach is
better?

Cheers,

Rhys



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Re: [ccp4bb] Structural alignment and classification

[Paul Emsley]

On 06/03/2023 07:35, Armando Albert wrote:

I want to align several structures we obtained from a fragment screening 
campaign and cluster them according to RMSD.


To what end, may I ask?

I would use LSQKAB, parse the log files for the RMSD and create an input 
file for R.


(One cannot just do this in Coot, because, for LSQ fitting, Coot only 
returns the transformation matrix, not any fitting statistics - in 
retrospect this is obviously an oversight.)



Paul.



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[ccp4bb] Virtual Crash Course - Understanding PDBx/mmCIF | May 3rd | REGISTER NOW!

[Gregg Crichlow]

Use PDB data to their full extent: Understanding PDBx/mmCIF 

Wednesday, May 3rd 2023 | 1:00 PM EDT 

Registration: go.rutgers.edu/u3vpwjet  


* This RCSB Protein Data Bank (PDB) virtual course will be broadcast on Zoom. 
Please fill out the registration form to receive the Zoom link. Registration 
will be available online from March 1, 2023 to May 3, 2023. 

LEARNING OBJECTIVES 

Understand the basics of PDBx/mmCIF data dictionary and file format that 
underpin archiving of more than 200,000 experimentally determined 
three-dimensional biostructures in the PDB. Learn about software tools for 
generating and working with PDBx/mmCIF files, and programmatic access for 
harvesting PDB data. Main topics: 

 * PDBx/mmCIF format description and examples 
 * PDBx/mmCIF data model 
 * Software tools for generating, editing, and visualizing PDBx/mmCIF files 
 * PDBx/mmCIF dictionary extensions, including ModelCIF for computed 
   structure models (CSM) from AI/ML 
 * Parsing data from PDBx/mmCIF files for your research 



WHO SHOULD ATTEND 

Professionals and graduate students interested in learning about strategies to 
take full advantage of PDB data in the fields of: 

 * Structural biology 
 * Cheminformatics and computational chemistry 
 * Bioinformatics and computational biology 



PROGRAM | Download Printable Program 

 


1:00–1:10 PM Welcome
Stephen K. Burley, M.D., D.Phil. 
Director, RCSB PDB and Founding Director, 
Institute for Quantitative Biomedicine, Rutgers University 

1:10–1:25 PM Introduction and course objectives 
Gregg Crichlow, Ph.D., RCSB PDB, Rutgers University

1:25–1:45 PM PDBx/mmCIF format - Not your parents’ legacy PDB format 
Ezra Peisach, Ph.D., RCSB PDB, Rutgers University 

1:45–2:05 PM PDBx/mmCIF data files - Lifting the lid off the black box 
Brian Hudson, Ph.D., RCSB PDB, Rutgers University 

2:05–2:50 PM Programmatic data access and analysis using PDBx/mmCIF files 
Irina Persikova, Ph.D. and Chenghua Shao, Ph.D., 
RCSB PDB, Rutgers University 

2:50–3:00 PM Closing remarks and acknowledgements 
Stephen K. Burley, M.D., D.Phil. 


Development and management of the PDBx/mmCIF data dictionary is a collaborative 
effort involving RCSB PDB, Worldwide Protein Data Bank (wwPDB, wwPDB.org 
) partners, and members of the wwPDB PDBx/mmCIF Working 
Group (wwpdb.org/task/mmcif ). 


CO-ORGANIZERS 

RCSB PDB Biocurators: Gregg Crichlow, Justin Flatt, Sutapa Ghosh, Brian Hudson, 
Yuhe Liang, Ezra Peisach, Irina Persikova, Monica Sekharan, Chenghua Shao, 
Jasmine Young 
(Rutgers, The State University of New Jersey). 


QUESTIONS

Contact Michelle Sanghera msangh...@iqb.rutgers.edu 

 
CO-SPONSORS 

RCSB Protein Data Bank 
rcsb.org 
RCSB PDB is managed by Rutgers, UCSD/SDSC, and UCSF. 
RCSB PDB is supported by grants from the NSF (DBI-1832184), the US DoE 
(DE-SC0019749), and the NIH (R01GM133198). 
RCSB PDB is a founding member of the wwPDB. 

Institute for Quantitative Biomedicine 
iqb.rutgers.edu 



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