Re: [ccp4bb] Lowering R factor from small molecule structure

[Muhammad Umer Faroque Malik]

I can help if share ,, no problem.
Regards
Umer

On Fri, Jun 4, 2021, 7:39 PM Harry Powell - CCP4BB <
193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:

> I’d have to say that Phil is possibly one of the small molecule
> crystallographers who could probably sort this out in a flash - hence my
> last suggestion…
>
> Harry
>
> > On 4 Jun 2021, at 14:40, Phil Jeffrey  wrote:
> >
> > Unlike macromolecular crystallography, small molecule crystallography is
> infrequently starved for data.  So it makes no sense at all to extend your
> data to e.g. I/sigI of 1.0 amd Rmeas > 80% unless you want your R1 to be
> >10% for no good reason or utility, which is what was behind my suggestion
> - test to see if the data cutoff is an issue.  Also about the fastest test
> you can do in SHELXL.
> >
> > > Yes, ANIS and adding hydrogens (in SHELXL) are good things to do -
> with 0.8Å data most small molecule crystallographers would do this as a
> first step after fitting all the non-H atoms.
> >
> > Actually, adding AnisoB's and hydrogens too soon will mess up your
> disorder modeling, so blanket statements like that work for well-behaved
> structures but not so much for more challenging ones.
> >
> > e.g. in one of the the four structures I've done this week, one had
> significant main-molecule disorder so that comes ahead of adding hydrogens,
> and refining unrestrained anisoB (as is the default) for disordered atoms
> is asking for trouble.  It's not as cookie-cutter as you represent, and I
> stick to all my suggestions.
> >
> > Phil Jeffrey
> > Princeton
> >
> > On 6/4/21 4:27 AM, Harry Powell - CCP4BB wrote:
> >> Hi
> >> Yes, ANIS and adding hydrogens (in SHELXL) are good things to do - with
> 0.8Å data most small molecule crystallographers would do this as a first
> step after fitting all the non-H atoms.
> >> One thing I can’t agree with is to cut the resolution of your data
> _unless_ you have a very, very good reason to do so. Normal small molecule
> refinements will use data to ~0.8Å and not use a cut-off based on
> resolution or I/sig(I). A good dataset will often go to higher resolution
> and small molecule crystallographers will be very happy to use these data
> (unless, as I say, they have a very good reason not to), and would
> certainly have to “explain to the referees” why they didn’t if they ignored
> a systematic chunk.
> >> Something else that you might not have thought of - have you actually
> told SHELXL what the reflection data are - i.e., are they F, F^2,
> intensity? It’s perfectly possible to solve a small molecule structure by
> e.g. telling the program you’re giving it F^2 but actually giving it F, but
> refinement would be somewhat less straightforward. SHELXL normally uses F^2
> in refinement, macromolecular programs still normally use F (AFAIK).
> >> What programs did you use for processing the diffraction data?
> >> Of course, lowering the R factor is not the objective of the exercise -
> a lower R-factor is a consequence of having a model that fits the data
> better.
> >> I would be strongly inclined to ask a small molecule crystallographer
> (or someone with a strong background in it) to have a look at your data &
> model - they could probably give you a definitive answer by return of
> e-mail.
> >> Just my two ha’porth
> >> Harry
> >>> On 4 Jun 2021, at 03:10, Jon Cooper <
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> >>>
> >>> Agreed, ANIS is the command to try.
> >>>
> >>> Sent from ProtonMail mobile
> >>>
> >>>
> >>>
> >>>  Original Message 
> >>> On 3 Jun 2021, 20:18, Philip D. Jeffrey < pjeff...@princeton.edu>
> wrote:
> >>>
> >>> R1 of 17% is bad for small molecule.
> >>> 0.8 Å is in the eye of the beholder - if you're using macromolecular
> cutoffs then these might be too aggressive for small molecule-type
> refinement stats - try a more conservative cutoff lie 0.9 and see how that
> changes R1.  However I suspect it's more to do with how your model is
> fitting the data.
> >>>
> >>> Have you refined anisotropic Bfactors ?
> >>> Have you added hydrogens ?
> >>>
> >>> I would suggest non-CCP4 programs like Olex2 or SHELXLE as the
> interface for the refinements - I use the latter and it's somewhat Coot
> like with useful features that are particular to small molecule.  Also
> PLATON has some things (like expand-to-P1 and Squeeze) that, respectively,
> might be useful to explore space group issues and disordered solvent.
> PLATON also has a means to check for some forms of twinning.
> >>>
> >>> Phil Jeffrey
> >>> Princeton
> >>> From: CCP4 bulletin board  on behalf of Jacob
> Summers <60a137e4bf3a-dmarc-requ...@jiscmail.ac.uk>
> >>> Sent: Thursday, June 3, 2021 2:49 PM
> >>> To: CCP4BB@JISCMAIL.AC.UK 
> >>> Subject: [ccp4bb] Lowering R factor from small molecule structure
> >>>  Greetings!
> >>>
> >>> I am currently trying to reduce the R factor of a cyclic small
> molecule peptoid in ShelXle. The max resolution of the molecule is 0.8
> angstroms. The 

Re: [ccp4bb] Lowering R factor from small molecule structure

[Harry Powell - CCP4BB]

I’d have to say that Phil is possibly one of the small molecule 
crystallographers who could probably sort this out in a flash - hence my last 
suggestion…

Harry

> On 4 Jun 2021, at 14:40, Phil Jeffrey  wrote:
> 
> Unlike macromolecular crystallography, small molecule crystallography is 
> infrequently starved for data.  So it makes no sense at all to extend your 
> data to e.g. I/sigI of 1.0 amd Rmeas > 80% unless you want your R1 to be >10% 
> for no good reason or utility, which is what was behind my suggestion - test 
> to see if the data cutoff is an issue.  Also about the fastest test you can 
> do in SHELXL.
> 
> > Yes, ANIS and adding hydrogens (in SHELXL) are good things to do - with 
> > 0.8Å data most small molecule crystallographers would do this as a first 
> > step after fitting all the non-H atoms.
> 
> Actually, adding AnisoB's and hydrogens too soon will mess up your disorder 
> modeling, so blanket statements like that work for well-behaved structures 
> but not so much for more challenging ones.
> 
> e.g. in one of the the four structures I've done this week, one had 
> significant main-molecule disorder so that comes ahead of adding hydrogens, 
> and refining unrestrained anisoB (as is the default) for disordered atoms is 
> asking for trouble.  It's not as cookie-cutter as you represent, and I stick 
> to all my suggestions.
> 
> Phil Jeffrey
> Princeton
> 
> On 6/4/21 4:27 AM, Harry Powell - CCP4BB wrote:
>> Hi
>> Yes, ANIS and adding hydrogens (in SHELXL) are good things to do - with 0.8Å 
>> data most small molecule crystallographers would do this as a first step 
>> after fitting all the non-H atoms.
>> One thing I can’t agree with is to cut the resolution of your data _unless_ 
>> you have a very, very good reason to do so. Normal small molecule 
>> refinements will use data to ~0.8Å and not use a cut-off based on resolution 
>> or I/sig(I). A good dataset will often go to higher resolution and small 
>> molecule crystallographers will be very happy to use these data (unless, as 
>> I say, they have a very good reason not to), and would certainly have to 
>> “explain to the referees” why they didn’t if they ignored a systematic chunk.
>> Something else that you might not have thought of - have you actually told 
>> SHELXL what the reflection data are - i.e., are they F, F^2, intensity? It’s 
>> perfectly possible to solve a small molecule structure by e.g. telling the 
>> program you’re giving it F^2 but actually giving it F, but refinement would 
>> be somewhat less straightforward. SHELXL normally uses F^2 in refinement, 
>> macromolecular programs still normally use F (AFAIK).
>> What programs did you use for processing the diffraction data?
>> Of course, lowering the R factor is not the objective of the exercise - a 
>> lower R-factor is a consequence of having a model that fits the data better.
>> I would be strongly inclined to ask a small molecule crystallographer (or 
>> someone with a strong background in it) to have a look at your data & model 
>> - they could probably give you a definitive answer by return of e-mail.
>> Just my two ha’porth
>> Harry
>>> On 4 Jun 2021, at 03:10, Jon Cooper 
>>> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>>> 
>>> Agreed, ANIS is the command to try.
>>> 
>>> Sent from ProtonMail mobile
>>> 
>>> 
>>> 
>>>  Original Message 
>>> On 3 Jun 2021, 20:18, Philip D. Jeffrey < pjeff...@princeton.edu> wrote:
>>> 
>>> R1 of 17% is bad for small molecule.
>>> 0.8 Å is in the eye of the beholder - if you're using macromolecular 
>>> cutoffs then these might be too aggressive for small molecule-type 
>>> refinement stats - try a more conservative cutoff lie 0.9 and see how that 
>>> changes R1.  However I suspect it's more to do with how your model is 
>>> fitting the data.
>>> 
>>> Have you refined anisotropic Bfactors ?
>>> Have you added hydrogens ?
>>> 
>>> I would suggest non-CCP4 programs like Olex2 or SHELXLE as the interface 
>>> for the refinements - I use the latter and it's somewhat Coot like with 
>>> useful features that are particular to small molecule.  Also PLATON has 
>>> some things (like expand-to-P1 and Squeeze) that, respectively, might be 
>>> useful to explore space group issues and disordered solvent.  PLATON also 
>>> has a means to check for some forms of twinning.
>>> 
>>> Phil Jeffrey
>>> Princeton
>>> From: CCP4 bulletin board  on behalf of Jacob 
>>> Summers <60a137e4bf3a-dmarc-requ...@jiscmail.ac.uk>
>>> Sent: Thursday, June 3, 2021 2:49 PM
>>> To: CCP4BB@JISCMAIL.AC.UK 
>>> Subject: [ccp4bb] Lowering R factor from small molecule structure
>>>  Greetings!
>>> 
>>> I am currently trying to reduce the R factor of a cyclic small molecule 
>>> peptoid in ShelXle. The max resolution of the molecule is 0.8 angstroms. 
>>> The molecule itself fits the density very well, but there are a few 
>>> unexplained densities around the molecule which do not seem to be anything 
>>> in the crystallization 

Re: [ccp4bb] Lowering R factor from small molecule structure

[Muhammad Umer Faroque Malik]

Twinning disorders solvent and hydrogen atoms position with adjustment of
several factors, small molecules are no so complicated as macromolecules.
Regards
Umer

On Fri, Jun 4, 2021, 6:41 PM Phil Jeffrey  wrote:

> Unlike macromolecular crystallography, small molecule crystallography is
> infrequently starved for data.  So it makes no sense at all to extend
> your data to e.g. I/sigI of 1.0 amd Rmeas > 80% unless you want your R1
> to be >10% for no good reason or utility, which is what was behind my
> suggestion - test to see if the data cutoff is an issue.  Also about the
> fastest test you can do in SHELXL.
>
>  > Yes, ANIS and adding hydrogens (in SHELXL) are good things to do -
> with 0.8Å data most small molecule crystallographers would do this as a
> first step after fitting all the non-H atoms.
>
> Actually, adding AnisoB's and hydrogens too soon will mess up your
> disorder modeling, so blanket statements like that work for well-behaved
> structures but not so much for more challenging ones.
>
> e.g. in one of the the four structures I've done this week, one had
> significant main-molecule disorder so that comes ahead of adding
> hydrogens, and refining unrestrained anisoB (as is the default) for
> disordered atoms is asking for trouble.  It's not as cookie-cutter as
> you represent, and I stick to all my suggestions.
>
> Phil Jeffrey
> Princeton
>
> On 6/4/21 4:27 AM, Harry Powell - CCP4BB wrote:
> > Hi
> >
> > Yes, ANIS and adding hydrogens (in SHELXL) are good things to do - with
> 0.8Å data most small molecule crystallographers would do this as a first
> step after fitting all the non-H atoms.
> >
> > One thing I can’t agree with is to cut the resolution of your data
> _unless_ you have a very, very good reason to do so. Normal small molecule
> refinements will use data to ~0.8Å and not use a cut-off based on
> resolution or I/sig(I). A good dataset will often go to higher resolution
> and small molecule crystallographers will be very happy to use these data
> (unless, as I say, they have a very good reason not to), and would
> certainly have to “explain to the referees” why they didn’t if they ignored
> a systematic chunk.
> >
> > Something else that you might not have thought of - have you actually
> told SHELXL what the reflection data are - i.e., are they F, F^2,
> intensity? It’s perfectly possible to solve a small molecule structure by
> e.g. telling the program you’re giving it F^2 but actually giving it F, but
> refinement would be somewhat less straightforward. SHELXL normally uses F^2
> in refinement, macromolecular programs still normally use F (AFAIK).
> >
> > What programs did you use for processing the diffraction data?
> >
> > Of course, lowering the R factor is not the objective of the exercise -
> a lower R-factor is a consequence of having a model that fits the data
> better.
> >
> > I would be strongly inclined to ask a small molecule crystallographer
> (or someone with a strong background in it) to have a look at your data &
> model - they could probably give you a definitive answer by return of
> e-mail.
> >
> > Just my two ha’porth
> >
> > Harry
> >
> >> On 4 Jun 2021, at 03:10, Jon Cooper <
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> >>
> >> Agreed, ANIS is the command to try.
> >>
> >> Sent from ProtonMail mobile
> >>
> >>
> >>
> >>  Original Message 
> >> On 3 Jun 2021, 20:18, Philip D. Jeffrey < pjeff...@princeton.edu>
> wrote:
> >>
> >> R1 of 17% is bad for small molecule.
> >> 0.8 Å is in the eye of the beholder - if you're using macromolecular
> cutoffs then these might be too aggressive for small molecule-type
> refinement stats - try a more conservative cutoff lie 0.9 and see how that
> changes R1.  However I suspect it's more to do with how your model is
> fitting the data.
> >>
> >> Have you refined anisotropic Bfactors ?
> >> Have you added hydrogens ?
> >>
> >> I would suggest non-CCP4 programs like Olex2 or SHELXLE as the
> interface for the refinements - I use the latter and it's somewhat Coot
> like with useful features that are particular to small molecule.  Also
> PLATON has some things (like expand-to-P1 and Squeeze) that, respectively,
> might be useful to explore space group issues and disordered solvent.
> PLATON also has a means to check for some forms of twinning.
> >>
> >> Phil Jeffrey
> >> Princeton
> >> From: CCP4 bulletin board  on behalf of Jacob
> Summers <60a137e4bf3a-dmarc-requ...@jiscmail.ac.uk>
> >> Sent: Thursday, June 3, 2021 2:49 PM
> >> To: CCP4BB@JISCMAIL.AC.UK 
> >> Subject: [ccp4bb] Lowering R factor from small molecule structure
> >>
> >> Greetings!
> >>
> >> I am currently trying to reduce the R factor of a cyclic small molecule
> peptoid in ShelXle. The max resolution of the molecule is 0.8 angstroms.
> The molecule itself fits the density very well, but there are a few
> unexplained densities around the molecule which do not seem to be anything
> in the crystallization conditions. The R1 

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Re: [ccp4bb] Lowering R factor from small molecule structure

[Phil Jeffrey]

Unlike macromolecular crystallography, small molecule crystallography is 
infrequently starved for data.  So it makes no sense at all to extend 
your data to e.g. I/sigI of 1.0 amd Rmeas > 80% unless you want your R1 
to be >10% for no good reason or utility, which is what was behind my 
suggestion - test to see if the data cutoff is an issue.  Also about the 
fastest test you can do in SHELXL.


> Yes, ANIS and adding hydrogens (in SHELXL) are good things to do - 
with 0.8Å data most small molecule crystallographers would do this as a 
first step after fitting all the non-H atoms.


Actually, adding AnisoB's and hydrogens too soon will mess up your 
disorder modeling, so blanket statements like that work for well-behaved 
structures but not so much for more challenging ones.


e.g. in one of the the four structures I've done this week, one had 
significant main-molecule disorder so that comes ahead of adding 
hydrogens, and refining unrestrained anisoB (as is the default) for 
disordered atoms is asking for trouble.  It's not as cookie-cutter as 
you represent, and I stick to all my suggestions.


Phil Jeffrey
Princeton

On 6/4/21 4:27 AM, Harry Powell - CCP4BB wrote:

Hi

Yes, ANIS and adding hydrogens (in SHELXL) are good things to do - with 0.8Å 
data most small molecule crystallographers would do this as a first step after 
fitting all the non-H atoms.

One thing I can’t agree with is to cut the resolution of your data _unless_ you 
have a very, very good reason to do so. Normal small molecule refinements will 
use data to ~0.8Å and not use a cut-off based on resolution or I/sig(I). A good 
dataset will often go to higher resolution and small molecule crystallographers 
will be very happy to use these data (unless, as I say, they have a very good 
reason not to), and would certainly have to “explain to the referees” why they 
didn’t if they ignored a systematic chunk.

Something else that you might not have thought of - have you actually told 
SHELXL what the reflection data are - i.e., are they F, F^2, intensity? It’s 
perfectly possible to solve a small molecule structure by e.g. telling the 
program you’re giving it F^2 but actually giving it F, but refinement would be 
somewhat less straightforward. SHELXL normally uses F^2 in refinement, 
macromolecular programs still normally use F (AFAIK).

What programs did you use for processing the diffraction data?

Of course, lowering the R factor is not the objective of the exercise - a lower 
R-factor is a consequence of having a model that fits the data better.

I would be strongly inclined to ask a small molecule crystallographer (or someone 
with a strong background in it) to have a look at your data & model - they 
could probably give you a definitive answer by return of e-mail.

Just my two ha’porth

Harry


On 4 Jun 2021, at 03:10, Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

Agreed, ANIS is the command to try.

Sent from ProtonMail mobile



 Original Message 
On 3 Jun 2021, 20:18, Philip D. Jeffrey < pjeff...@princeton.edu> wrote:

R1 of 17% is bad for small molecule.
0.8 Å is in the eye of the beholder - if you're using macromolecular cutoffs 
then these might be too aggressive for small molecule-type refinement stats - 
try a more conservative cutoff lie 0.9 and see how that changes R1.  However I 
suspect it's more to do with how your model is fitting the data.

Have you refined anisotropic Bfactors ?
Have you added hydrogens ?

I would suggest non-CCP4 programs like Olex2 or SHELXLE as the interface for 
the refinements - I use the latter and it's somewhat Coot like with useful 
features that are particular to small molecule.  Also PLATON has some things 
(like expand-to-P1 and Squeeze) that, respectively, might be useful to explore 
space group issues and disordered solvent.  PLATON also has a means to check 
for some forms of twinning.

Phil Jeffrey
Princeton
From: CCP4 bulletin board  on behalf of Jacob Summers 
<60a137e4bf3a-dmarc-requ...@jiscmail.ac.uk>
Sent: Thursday, June 3, 2021 2:49 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Lowering R factor from small molecule structure
  
Greetings!


I am currently trying to reduce the R factor of a cyclic small molecule peptoid 
in ShelXle. The max resolution of the molecule is 0.8 angstroms. The molecule 
itself fits the density very well, but there are a few unexplained densities 
around the molecule which do not seem to be anything in the crystallization 
conditions. The R1 factor of the refinement is 17.07% but I am unsure how to 
lower this value. Any ideas on how to better refine this molecule or fill 
densities to lower the R1 factor? I do not have much experience working with 
small molecule refinement or with ShelX.

Thanks so much,
Jacob Summers



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Re: [ccp4bb] Lowering R factor from small molecule structure

[Harry Powell - CCP4BB]

Hi

Yes, ANIS and adding hydrogens (in SHELXL) are good things to do - with 0.8Å 
data most small molecule crystallographers would do this as a first step after 
fitting all the non-H atoms.

One thing I can’t agree with is to cut the resolution of your data _unless_ you 
have a very, very good reason to do so. Normal small molecule refinements will 
use data to ~0.8Å and not use a cut-off based on resolution or I/sig(I). A good 
dataset will often go to higher resolution and small molecule crystallographers 
will be very happy to use these data (unless, as I say, they have a very good 
reason not to), and would certainly have to “explain to the referees” why they 
didn’t if they ignored a systematic chunk.

Something else that you might not have thought of - have you actually told 
SHELXL what the reflection data are - i.e., are they F, F^2, intensity? It’s 
perfectly possible to solve a small molecule structure by e.g. telling the 
program you’re giving it F^2 but actually giving it F, but refinement would be 
somewhat less straightforward. SHELXL normally uses F^2 in refinement, 
macromolecular programs still normally use F (AFAIK).

What programs did you use for processing the diffraction data?

Of course, lowering the R factor is not the objective of the exercise - a lower 
R-factor is a consequence of having a model that fits the data better.

I would be strongly inclined to ask a small molecule crystallographer (or 
someone with a strong background in it) to have a look at your data & model - 
they could probably give you a definitive answer by return of e-mail.

Just my two ha’porth

Harry

> On 4 Jun 2021, at 03:10, Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Agreed, ANIS is the command to try. 
> 
> Sent from ProtonMail mobile
> 
> 
> 
>  Original Message 
> On 3 Jun 2021, 20:18, Philip D. Jeffrey < pjeff...@princeton.edu> wrote:
> 
> R1 of 17% is bad for small molecule.
> 0.8 Å is in the eye of the beholder - if you're using macromolecular cutoffs 
> then these might be too aggressive for small molecule-type refinement stats - 
> try a more conservative cutoff lie 0.9 and see how that changes R1.  However 
> I suspect it's more to do with how your model is fitting the data.
> 
> Have you refined anisotropic Bfactors ?
> Have you added hydrogens ?
> 
> I would suggest non-CCP4 programs like Olex2 or SHELXLE as the interface for 
> the refinements - I use the latter and it's somewhat Coot like with useful 
> features that are particular to small molecule.  Also PLATON has some things 
> (like expand-to-P1 and Squeeze) that, respectively, might be useful to 
> explore space group issues and disordered solvent.  PLATON also has a means 
> to check for some forms of twinning.
> 
> Phil Jeffrey
> Princeton
> From: CCP4 bulletin board  on behalf of Jacob Summers 
> <60a137e4bf3a-dmarc-requ...@jiscmail.ac.uk>
> Sent: Thursday, June 3, 2021 2:49 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [ccp4bb] Lowering R factor from small molecule structure
>  
> Greetings!
> 
> I am currently trying to reduce the R factor of a cyclic small molecule 
> peptoid in ShelXle. The max resolution of the molecule is 0.8 angstroms. The 
> molecule itself fits the density very well, but there are a few unexplained 
> densities around the molecule which do not seem to be anything in the 
> crystallization conditions. The R1 factor of the refinement is 17.07% but I 
> am unsure how to lower this value. Any ideas on how to better refine this 
> molecule or fill densities to lower the R1 factor? I do not have much 
> experience working with small molecule refinement or with ShelX.
> 
> Thanks so much,
> Jacob Summers
> 
> 
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