Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

[Tom Peat]

Hello All,

I think we are all in agreement that it depends on resolution, or more 
specifically the amount of experimental data one has versus how many atoms one 
has in the model to refine.

There is also no question that structures have become better over the decades 
due to more and better restraints added into the refinement process, and of 
course people paying more attention to such things.

In terms of guidance to questions, such as when to apply grouped, isotropic or 
anisotropic B factors, it would be nice to have something concrete to respond 
with. We have plenty of 'rules of thumb' or heuristics that might be valuable 
to the community that don't have that many years of experience under the belt.

My approach, which may or may not be approved by all, is to say that for those 
dealing with lower resolution structures (3.0 or worse) or with data to 
parameter ratios less than 4, is to try something that groups B factors instead 
of refining every atom with its own B factor. There aren't many ways to do this 
and it would be nice if there were TLS type implementations that allowed one to 
avoid the individual B factors. There are plenty of data sets out there that 
fall into this category, so it might be nice to have more tools to apply in 
these cases.

This isn't to say that adding more restraints can't help the refinement, but it 
isn't necessarily the best initial course of action when starting out with 
limited data. For very limited data, one might start with a single overall B 
factor and only do rigid body refinement of a model.

I think the results from Pavel's experiment would be interesting and it would 
be useful to see the resolution bins that fell out for the various categories.

cheers, tom

From: CCP4 bulletin board  on behalf of Pavel Afonine 

Sent: Sunday, January 7, 2024 11:28 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

You don't often get email from pafon...@gmail.com. Learn why this is 
important
Hi All,

I believe it depends on the resolution. At sufficiently low resolution, it may 
not be too unreasonable to assume that the main chain atoms of a residue have 
the same B factors, and its side chain atoms also share the same B factor 
(different from the main chain). Why? Simply because your low-resolution data 
cannot resolve the B-factor difference between, for example, CA and C atoms! 
This is much like expecting low to almost zero deviations from ideal bonds and 
angles at low resolution, because your low-res data simply cannot resolve a 
fraction of an Angstrom deviation in bond lengths.

The bottom line, in my opinion, is that there is no black-and-white answer to 
the "grouped vs. individual" B-factor refinement question. Depending on a) the 
data resolution, and b) your experimentation with both individual and group 
options, you may choose one over the other.

Back in the day (when working on the implementation of B-factor refinement in 
phenix.refine), I conducted a test where I re-refined a sample, consisting of 
about 50,000 models from the PDB, using 1) individual, 2) group with one B per 
residue, and 3) group with two B per residue (one for the main and one for the 
side chain). There were clear clusters of results where each of the three 
parameterizations outperformed the others, and this was heavily 
resolution-dependent. I regret not publishing that result, mostly because I 
thought I could always re-do it any time later.. but as Ben said "Don't put off 
until tomorrow what you can do today"!

Regarding TLS, since someone mentioned it, I prefer to see TLS as a more 
physically realistic atomic vibration model, rather than a magic solution to 
reduce R-factors or a way to decrease the number of refinable parameters 
(which, in fact, is not the case because normally residual isotropic B factors 
are always refined on top of TLS anyway, in Phenix at least).

All the best!
Pavel

On Sat, Jan 6, 2024 at 3:41 PM Robbie Joosten 
mailto:robbie_joos...@hotmail.com>> wrote:
Hi Tom,

I think restraints do change the data/parameter ratio, but how much is not 
straightforward. In, at least, the context of the Hamilton test restraints 
change the degrees of freedom which translates into a change of the effective 
data/parameter ratio. It is treated as adding extra observations albeit with 
some unknown weight. Ethan Merritt's way of handeling this unknown weight 
(which we implemented in bselect) is setting an upper limit for the weight and 
thus bracketing the value.

Lets assume we have glycol. Adding individual B-factors instead of one overall 
B adds 3 extra parameters. We also add B-factor restraints: 3 bonded atom 1-2 
restraints plus 2 angled atoms 1-3 restraints (in Refmac's implementation). So 
3 extra parameters, 5 extra restraints. These restraints can at best nullify 
the effect of the extra parameters so their 

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

[Pavel Afonine]

Hi All,

I believe it depends on the resolution. At sufficiently low resolution, it
may not be too unreasonable to assume that the main chain atoms of a
residue have the same B factors, and its side chain atoms also share the
same B factor (different from the main chain). Why? Simply because your
low-resolution data cannot resolve the B-factor difference between, for
example, CA and C atoms! This is much like expecting low to almost zero
deviations from ideal bonds and angles at low resolution, because your
low-res data simply cannot resolve a fraction of an Angstrom deviation in
bond lengths.

The bottom line, in my opinion, is that there is no black-and-white answer
to the "grouped vs. individual" B-factor refinement question. Depending on
a) the data resolution, and b) your experimentation with both individual
and group options, you may choose one over the other.

Back in the day (when working on the implementation of B-factor refinement
in phenix.refine), I conducted a test where I re-refined a sample,
consisting of about 50,000 models from the PDB, using 1) individual, 2)
group with one B per residue, and 3) group with two B per residue (one for
the main and one for the side chain). There were clear clusters of results
where each of the three parameterizations outperformed the others, and this
was heavily resolution-dependent. I regret not publishing that result,
mostly because I thought I could always re-do it any time later.. but as
Ben said "Don't put off until tomorrow what you can do today"!

Regarding TLS, since someone mentioned it, I prefer to see TLS as a more
physically realistic atomic vibration model, rather than a magic solution
to reduce R-factors or a way to decrease the number of refinable parameters
(which, in fact, is not the case because normally residual isotropic B
factors are always refined on top of TLS anyway, in Phenix at least).

All the best!
Pavel

On Sat, Jan 6, 2024 at 3:41 PM Robbie Joosten 
wrote:

> Hi Tom,
>
> I think restraints do change the data/parameter ratio, but how much is not
> straightforward. In, at least, the context of the Hamilton test restraints
> change the degrees of freedom which translates into a change of the
> effective data/parameter ratio. It is treated as adding extra observations
> albeit with some unknown weight. Ethan Merritt's way of handeling this
> unknown weight (which we implemented in bselect) is setting an upper limit
> for the weight and thus bracketing the value.
>
> Lets assume we have glycol. Adding individual B-factors instead of one
> overall B adds 3 extra parameters. We also add B-factor restraints: 3
> bonded atom 1-2 restraints plus 2 angled atoms 1-3 restraints (in Refmac's
> implementation). So 3 extra parameters, 5 extra restraints. These
> restraints can at best nullify the effect of the extra parameters so their
> effective weight is maximum 3/5, but probably less. The weight of the
> restraints must be somewhere between 0 (e.g when the B-factor restraint
> weight in Refmac is set to zero) and 0.6 (the restraint weight is huge).
> Assuming that the restraints do something, the degrees of freedom go up
> with less than 3 for our glycol refinement. How much less is related to the
> restraint weight we set in Refinement.
>
> Cheers,
> Robbie
>
>
>
>
> On 6 Jan 2024 23:26, Tom Peat  wrote:
>
> Hello Robbie,
>
> Thanks for the stats and description of what has been done.
> I think this puts us back into the realm of restraints versus constraints
> and what is possible when trying to reduce the number of parameters to be
> refined. Although grouped B-factors don't capture the reality of side
> chains being more mobile, it is a constraint that reduces the number of
> parameters being refined and helps highlight regions of the structure which
> are more mobile (which a flat or average B-factor would not do).
> Making tighter restraints on the system as a whole doesn't change the
> data/parameter ratio, which can lead to its own issues, but is certainly
> better than just letting things go wild.
> As is often the outcome, we state 'it depends on your individual
> situation' and generally suggest looking at various possibilities until one
> finds some compromise which works. Not as intellectually gratifying as
> having a cut and dry answer to these questions that come up rather
> frequently.
> Thanks again for the stats and description.
> cheers, tom
>
> --
> *From:* Robbie Joosten 
> *Sent:* Sunday, January 7, 2024 8:24 AM
> *To:* Tom Peat ; CCP4BB@JISCMAIL.AC.UK <
> CCP4BB@JISCMAIL.AC.UK>
> *Subject:* RE: [ccp4bb] Can Refmac5 refine temperature factor residue by
> group?
>
> [You don't often get email from robbie_joos...@hotmail.com. Learn why
> this is important at https://aka.ms/LearnAboutSenderIdentification ]
>
> Hi Tom,
>
> At 3A the median number of reflections per atom is 3.4 which is indeed
> lower than 4. So in unrestrained refinement the data/parameter ratio is
> indeed worse than 1. This 

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

[Robbie Joosten]

Hi Tom,I think restraints do change the data/parameter ratio, but how much is not straightforward. In, at least, the context of the Hamilton test restraints change the degrees of freedom which translates into a change of the effective data/parameter ratio. It is treated as adding extra observations albeit with some unknown weight. Ethan Merritt's way of handeling this unknown weight (which we implemented in bselect) is setting an upper limit for the weight and thus bracketing the value. Lets assume we have glycol. Adding individual B-factors instead of one overall B adds 3 extra parameters. We also add B-factor restraints: 3 bonded atom 1-2 restraints plus 2 angled atoms 1-3 restraints (in Refmac's implementation). So 3 extra parameters, 5 extra restraints. These restraints can at best nullify the effect of the extra parameters so their effective weight is maximum 3/5, but probably less. The weight of the restraints must be somewhere between 0 (e.g when the B-factor restraint weight in Refmac is set to zero) and 0.6 (the restraint weight is huge). Assuming that the restraints do something, the degrees of freedom go up with less than 3 for our glycol refinement. How much less is related to the restraint weight we set in Refinement. Cheers,RobbieOn 6 Jan 2024 23:26, Tom Peat  wrote:




Hello Robbie, 




Thanks for the stats and description of what has been done. 

I think this puts us back into the realm of restraints versus constraints and what is possible when trying to reduce the number of parameters to be refined. Although grouped B-factors don't capture the reality of side chains being more mobile, it is a constraint
 that reduces the number of parameters being refined and helps highlight regions of the structure which are more mobile (which a flat or average B-factor would not do). 

Making tighter restraints on the system as a whole doesn't change the data/parameter ratio, which can lead to its own issues, but is certainly better than just letting things go wild. 

As is often the outcome, we state 'it depends on your individual situation' and generally suggest looking at various possibilities until one finds some compromise which works. Not as intellectually gratifying as having a cut and dry answer to these questions
 that come up rather frequently. 

Thanks again for the stats and description. 

cheers, tom 




From: Robbie Joosten 
Sent: Sunday, January 7, 2024 8:24 AM
To: Tom Peat ; CCP4BB@JISCMAIL.AC.UK 
Subject: RE: [ccp4bb] Can Refmac5 refine temperature factor residue by group?
 


[You don't often get email from robbie_joos...@hotmail.com. Learn why this is important at

https://aka.ms/LearnAboutSenderIdentification ]

Hi Tom,

At 3A the median number of reflections per atom is 3.4 which is indeed lower than 4. So in unrestrained refinement the data/parameter ratio is indeed worse than 1. This is where the effect of the restraints really matter and starting from a flat B-factor model
 is interesting. This is what pdb-redo does if there are fewer than 4 reflections per atom. In such cases first TLS model are refined, one-group-per-chain (yes, that has room for improvement) plus any user-provided grouping. The TLS model that performs best
 in refinement is then kept (or no TLS model at all if they don't work). Given this TLS model, the structure model is refined with isotropic B-factors and flat B-factors. Both refinement results are then tested by a program called "bselect" that performs the
 Hamilton test plus some fallback test. The "best" model is then chosen. If this involves isotropic B-factors, the B-factor restraint weight is then optimised.

Some stats:
Of the 1958 cases in the databank, 573 are refined with a flat B-factor model (2.9 reflections/atom on average), 520 with isotropic B-factors and tighter-than-default restraint weights (3.8 reflections/atom on average), 612 with isotropic B-factors and looser-than-default
 weights (4.1 reflections/atom on average), the rest is isotropic with default weights (3.8 ref/atom).

So there is a trend given the number of reflections per atom but it is not that strong for individual cases. Testing is needed. I won't claim that this is the best protocol for each of the cases, but I guess they are decent starting points for most.

Cheers,
Robbie

> -Original Message-
> From: Tom Peat 
> Sent: Saturday, January 6, 2024 21:42
> To: CCP4BB@JISCMAIL.AC.UK; Robbie Joosten
> 
> Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by
> group?
>
> It appears that Zhonghao might be worried about his data to parameter ratio.
> At 3 A, one can easily be in a situation where one has fewer reflections than
> four times the number of atoms (X, Y, Z plus B).
> I like the idea of starting out with the average B (or even Wilson B) and then
> doing TLS as that should reduce the number of parameters being refined.
> Best regards, tom
>
> 
>
> From: CCP4 bulletin board  on behalf of Robbie
> Joosten 
> Sent: 

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

[Tom Peat]

Hello Robbie,

Thanks for the stats and description of what has been done.
I think this puts us back into the realm of restraints versus constraints and 
what is possible when trying to reduce the number of parameters to be refined. 
Although grouped B-factors don't capture the reality of side chains being more 
mobile, it is a constraint that reduces the number of parameters being refined 
and helps highlight regions of the structure which are more mobile (which a 
flat or average B-factor would not do).
Making tighter restraints on the system as a whole doesn't change the 
data/parameter ratio, which can lead to its own issues, but is certainly better 
than just letting things go wild.
As is often the outcome, we state 'it depends on your individual situation' and 
generally suggest looking at various possibilities until one finds some 
compromise which works. Not as intellectually gratifying as having a cut and 
dry answer to these questions that come up rather frequently.
Thanks again for the stats and description.
cheers, tom


From: Robbie Joosten 
Sent: Sunday, January 7, 2024 8:24 AM
To: Tom Peat ; CCP4BB@JISCMAIL.AC.UK 
Subject: RE: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

[You don't often get email from robbie_joos...@hotmail.com. Learn why this is 
important at https://aka.ms/LearnAboutSenderIdentification ]

Hi Tom,

At 3A the median number of reflections per atom is 3.4 which is indeed lower 
than 4. So in unrestrained refinement the data/parameter ratio is indeed worse 
than 1. This is where the effect of the restraints really matter and starting 
from a flat B-factor model is interesting. This is what pdb-redo does if there 
are fewer than 4 reflections per atom. In such cases first TLS model are 
refined, one-group-per-chain (yes, that has room for improvement) plus any 
user-provided grouping. The TLS model that performs best in refinement is then 
kept (or no TLS model at all if they don't work). Given this TLS model, the 
structure model is refined with isotropic B-factors and flat B-factors. Both 
refinement results are then tested by a program called "bselect" that performs 
the Hamilton test plus some fallback test. The "best" model is then chosen. If 
this involves isotropic B-factors, the B-factor restraint weight is then 
optimised.

Some stats:
Of the 1958 cases in the databank, 573 are refined with a flat B-factor model 
(2.9 reflections/atom on average), 520 with isotropic B-factors and 
tighter-than-default restraint weights (3.8 reflections/atom on average), 612 
with isotropic B-factors and looser-than-default weights (4.1 reflections/atom 
on average), the rest is isotropic with default weights (3.8 ref/atom).

So there is a trend given the number of reflections per atom but it is not that 
strong for individual cases. Testing is needed. I won't claim that this is the 
best protocol for each of the cases, but I guess they are decent starting 
points for most.

Cheers,
Robbie

> -Original Message-
> From: Tom Peat 
> Sent: Saturday, January 6, 2024 21:42
> To: CCP4BB@JISCMAIL.AC.UK; Robbie Joosten
> 
> Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by
> group?
>
> It appears that Zhonghao might be worried about his data to parameter ratio.
> At 3 A, one can easily be in a situation where one has fewer reflections than
> four times the number of atoms (X, Y, Z plus B).
> I like the idea of starting out with the average B (or even Wilson B) and then
> doing TLS as that should reduce the number of parameters being refined.
> Best regards, tom
>
> 
>
> From: CCP4 bulletin board  on behalf of Robbie
> Joosten 
> Sent: Saturday, January 6, 2024 8:13 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by
> group?
>
>   You don't often get email from robbie_joos...@hotmail.com. Learn
> why this is important 
>
>
> One wonders who those "many people" are. You may not want to use them
> as your go-to reference for refinement techniques.
>
> Anyway, Refmac cannot do grouped B-factor refinement, but you are not
> missing out on anything. As Eleanor implied, one-per-residue B-factors give
> unrealistic results. You are much better off using isotropic B-factors with 
> tight
> restraints (Refmac's default is already quite tight). Add TLS in your 
> refinement
> to see if that helps.
> If you have a really poor data/parameter ratio you could go for a flat 
> B-factor
> model and try to capture most of the B-factor in the TLS model. This is
> typically not needed at 3A, but there are exceptions (low solvent -more
> atoms-  or low completeness -fewer reflections- are factors to consider). If
> you do go for a flat B-factor model, you need to define sensible TLS groups.
> This takes some trial and error.
>
> pdb-redo has decent algorithms to select the B-factor model and weight 

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

[Krieger, James M]

Hi Robbie and everyone,

Perhaps some clustering of the structure could be used to define TLS groups 
rather than using chains. A spectral clustering based on Gaussian network model 
normal modes seems to work fairly well for defining dynamical domains, for 
example. In some cases these may be groups of chains and in some cases parts of 
one chain or parts of groups. I guess this needs careful testing too but having 
the testing different options presumably means that it’s ok to include some 
that may only help sometimes.

Best wishes
James

> On 6 Jan 2024, at 22:25, Robbie Joosten  wrote:
>
> Hi Tom,
>
> At 3A the median number of reflections per atom is 3.4 which is indeed lower 
> than 4. So in unrestrained refinement the data/parameter ratio is indeed 
> worse than 1. This is where the effect of the restraints really matter and 
> starting from a flat B-factor model is interesting. This is what pdb-redo 
> does if there are fewer than 4 reflections per atom. In such cases first TLS 
> model are refined, one-group-per-chain (yes, that has room for improvement) 
> plus any user-provided grouping. The TLS model that performs best in 
> refinement is then kept (or no TLS model at all if they don't work). Given 
> this TLS model, the structure model is refined with isotropic B-factors and 
> flat B-factors. Both refinement results are then tested by a program called 
> "bselect" that performs the Hamilton test plus some fallback test. The "best" 
> model is then chosen. If this involves isotropic B-factors, the B-factor 
> restraint weight is then optimised.
>
> Some stats:
> Of the 1958 cases in the databank, 573 are refined with a flat B-factor model 
> (2.9 reflections/atom on average), 520 with isotropic B-factors and 
> tighter-than-default restraint weights (3.8 reflections/atom on average), 612 
> with isotropic B-factors and looser-than-default weights (4.1 
> reflections/atom on average), the rest is isotropic with default weights (3.8 
> ref/atom).
>
> So there is a trend given the number of reflections per atom but it is not 
> that strong for individual cases. Testing is needed. I won't claim that this 
> is the best protocol for each of the cases, but I guess they are decent 
> starting points for most.
>
> Cheers,
> Robbie
>
>> -Original Message-
>> From: Tom Peat 
>> Sent: Saturday, January 6, 2024 21:42
>> To: CCP4BB@JISCMAIL.AC.UK; Robbie Joosten
>> 
>> Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by
>> group?
>>
>> It appears that Zhonghao might be worried about his data to parameter ratio.
>> At 3 A, one can easily be in a situation where one has fewer reflections than
>> four times the number of atoms (X, Y, Z plus B).
>> I like the idea of starting out with the average B (or even Wilson B) and 
>> then
>> doing TLS as that should reduce the number of parameters being refined.
>> Best regards, tom
>>
>> 
>>
>> From: CCP4 bulletin board  on behalf of Robbie
>> Joosten 
>> Sent: Saturday, January 6, 2024 8:13 PM
>> To: CCP4BB@JISCMAIL.AC.UK 
>> Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by
>> group?
>>
>>You don't often get email from robbie_joos...@hotmail.com. Learn
>> why this is important 
>>
>>
>> One wonders who those "many people" are. You may not want to use them
>> as your go-to reference for refinement techniques.
>>
>> Anyway, Refmac cannot do grouped B-factor refinement, but you are not
>> missing out on anything. As Eleanor implied, one-per-residue B-factors give
>> unrealistic results. You are much better off using isotropic B-factors with 
>> tight
>> restraints (Refmac's default is already quite tight). Add TLS in your 
>> refinement
>> to see if that helps.
>> If you have a really poor data/parameter ratio you could go for a flat 
>> B-factor
>> model and try to capture most of the B-factor in the TLS model. This is
>> typically not needed at 3A, but there are exceptions (low solvent -more
>> atoms-  or low completeness -fewer reflections- are factors to consider). If
>> you do go for a flat B-factor model, you need to define sensible TLS groups.
>> This takes some trial and error.
>>
>> pdb-redo has decent algorithms to select the B-factor model and weight for
>> Refmac. You could use that as a starting point for your model.
>>
>> HTH,
>> Robbie
>>
>>
>>
>> On 6 Jan 2024 03:13, "chenzhonghao...@163.com"
>>  wrote:
>>
>>
>>Dear Prof. Dr. Dodson and all CCP4 community,
>>
>>
>>
>>  Thanks for your reply.
>>
>>
>>
>> Just now, I used baverage. I found that it can average the B factor but
>> not refine it.
>>
>>  This function does not fit my requirement, because my resolution is
>> low as 3 A.
>>
>> Many people said that Refmac5 overrefines the structure if I used
>> isotropic temperature refinement.
>>
>>
>>
>>Did refmac5 or other programs in CCP4 have similar functions like
>> one_adp_group_per_residue or 

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

[Robbie Joosten]

Hi Tom,

At 3A the median number of reflections per atom is 3.4 which is indeed lower 
than 4. So in unrestrained refinement the data/parameter ratio is indeed worse 
than 1. This is where the effect of the restraints really matter and starting 
from a flat B-factor model is interesting. This is what pdb-redo does if there 
are fewer than 4 reflections per atom. In such cases first TLS model are 
refined, one-group-per-chain (yes, that has room for improvement) plus any 
user-provided grouping. The TLS model that performs best in refinement is then 
kept (or no TLS model at all if they don't work). Given this TLS model, the 
structure model is refined with isotropic B-factors and flat B-factors. Both 
refinement results are then tested by a program called "bselect" that performs 
the Hamilton test plus some fallback test. The "best" model is then chosen. If 
this involves isotropic B-factors, the B-factor restraint weight is then 
optimised.

Some stats:
Of the 1958 cases in the databank, 573 are refined with a flat B-factor model 
(2.9 reflections/atom on average), 520 with isotropic B-factors and 
tighter-than-default restraint weights (3.8 reflections/atom on average), 612 
with isotropic B-factors and looser-than-default weights (4.1 reflections/atom 
on average), the rest is isotropic with default weights (3.8 ref/atom). 

So there is a trend given the number of reflections per atom but it is not that 
strong for individual cases. Testing is needed. I won't claim that this is the 
best protocol for each of the cases, but I guess they are decent starting 
points for most. 

Cheers,
Robbie

> -Original Message-
> From: Tom Peat 
> Sent: Saturday, January 6, 2024 21:42
> To: CCP4BB@JISCMAIL.AC.UK; Robbie Joosten
> 
> Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by
> group?
> 
> It appears that Zhonghao might be worried about his data to parameter ratio.
> At 3 A, one can easily be in a situation where one has fewer reflections than
> four times the number of atoms (X, Y, Z plus B).
> I like the idea of starting out with the average B (or even Wilson B) and then
> doing TLS as that should reduce the number of parameters being refined.
> Best regards, tom
> 
> 
> 
> From: CCP4 bulletin board  on behalf of Robbie
> Joosten 
> Sent: Saturday, January 6, 2024 8:13 PM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by
> group?
> 
>   You don't often get email from robbie_joos...@hotmail.com. Learn
> why this is important 
> 
> 
> One wonders who those "many people" are. You may not want to use them
> as your go-to reference for refinement techniques.
> 
> Anyway, Refmac cannot do grouped B-factor refinement, but you are not
> missing out on anything. As Eleanor implied, one-per-residue B-factors give
> unrealistic results. You are much better off using isotropic B-factors with 
> tight
> restraints (Refmac's default is already quite tight). Add TLS in your 
> refinement
> to see if that helps.
> If you have a really poor data/parameter ratio you could go for a flat 
> B-factor
> model and try to capture most of the B-factor in the TLS model. This is
> typically not needed at 3A, but there are exceptions (low solvent -more
> atoms-  or low completeness -fewer reflections- are factors to consider). If
> you do go for a flat B-factor model, you need to define sensible TLS groups.
> This takes some trial and error.
> 
> pdb-redo has decent algorithms to select the B-factor model and weight for
> Refmac. You could use that as a starting point for your model.
> 
> HTH,
> Robbie
> 
> 
> 
> On 6 Jan 2024 03:13, "chenzhonghao...@163.com"
>  wrote:
> 
> 
>   Dear Prof. Dr. Dodson and all CCP4 community,
> 
> 
> 
> Thanks for your reply.
> 
> 
> 
>Just now, I used baverage. I found that it can average the B factor but
> not refine it.
> 
> This function does not fit my requirement, because my resolution is
> low as 3 A.
> 
>Many people said that Refmac5 overrefines the structure if I used
> isotropic temperature refinement.
> 
> 
> 
>   Did refmac5 or other programs in CCP4 have similar functions like
> one_adp_group_per_residue or two_adp_groups_per_residue in Phenix?
> 
> 
> 
>Any help would be highly appreciated!
> 
> 
> 
> 
> 
> 
>   chenzhonghao...@163.com
> 
> 
>   From: Eleanor Dodson  requ...@jiscmail.ac.uk>
>   Date: 2024-01-05 23:48
>   To: CCP4BB 
>   Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor
> residue by group?
> 
>   Hmmm -  I am not sure about the value of this - one expects
> the longer floppier side chains to have very different B values for the CB 
> than
> the OE2..
> 
>   The program BAVERAGE gives you a 

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

[Tom Peat]

It appears that Zhonghao might be worried about his data to parameter ratio. At 
3 A, one can easily be in a situation where one has fewer reflections than four 
times the number of atoms (X, Y, Z plus B).
I like the idea of starting out with the average B (or even Wilson B) and then 
doing TLS as that should reduce the number of parameters being refined.
Best regards, tom


From: CCP4 bulletin board  on behalf of Robbie Joosten 

Sent: Saturday, January 6, 2024 8:13 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

You don't often get email from robbie_joos...@hotmail.com. Learn why this is 
important

One wonders who those "many people" are. You may not want to use them as your 
go-to reference for refinement techniques.

Anyway, Refmac cannot do grouped B-factor refinement, but you are not missing 
out on anything. As Eleanor implied, one-per-residue B-factors give unrealistic 
results. You are much better off using isotropic B-factors with tight 
restraints (Refmac's default is already quite tight). Add TLS in your 
refinement to see if that helps.
If you have a really poor data/parameter ratio you could go for a flat B-factor 
model and try to capture most of the B-factor in the TLS model. This is 
typically not needed at 3A, but there are exceptions (low solvent -more atoms-  
or low completeness -fewer reflections- are factors to consider). If you do go 
for a flat B-factor model, you need to define sensible TLS groups. This takes 
some trial and error.

pdb-redo has decent algorithms to select the B-factor model and weight for 
Refmac. You could use that as a starting point for your model.

HTH,
Robbie



On 6 Jan 2024 03:13, "chenzhonghao...@163.com"  wrote:

Dear Prof. Dr. Dodson and all CCP4 community,



  Thanks for your reply.



 Just now, I used baverage. I found that it can average the B factor but not 
refine it.

  This function does not fit my requirement, because my resolution is low as 3 
A.

 Many people said that Refmac5 overrefines the structure if I used isotropic 
temperature refinement.



Did refmac5 or other programs in CCP4 have similar functions like 
one_adp_group_per_residue or two_adp_groups_per_residue in Phenix?



 Any help would be highly appreciated!




chenzhonghao...@163.com

From: Eleanor Dodson
Date: 2024-01-05 23:48
To: CCP4BB
Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

Hmmm -  I am not sure about the value of this - one expects the longer floppier 
side chains to have very different B values for the CB than the OE2..

The program BAVERAGE gives you a plot of mean B value residue by residue..



baverage - averages B over main and side chain atoms

SYNOPSIS¶
baverage XYZIN foo_in.pdb RMSTAB foo_out1.tab XYZOUT foo_out2.pdb
[Keyworded input]
DESCRIPTION¶

A very simple minded program to read a PDB file, tabulate to RMSTAB the average 
B values residue by residue (main chain and side chain separately) and the RMS 
deviation of the B values from this mean. It also outputs a PDB file with 
outlying B factors reset to lie within the given range.

On Fri, 5 Jan 2024 at 03:08, 
chenzhonghao...@163.com 
mailto:chenzhonghao...@163.com>> wrote:
Dear CCP4 community,

 I found that Refmac5 refined the temperature factor only by four modes (see 
the bottom of the attached figure). However, no
grouped B-factor (one or two per residue instead of one per atom) was found.

 Actually, PHENIX and CNS can do it. But we are not familiar with both 
software. I want to know whether Refmac5 refines one or
two group B per residue (for side and main chains) grouped temperature factor?

 Any help would be highly appreciated

 Thanks in advance.

best,


 Zhonghao Chen










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[ccp4bb] How do I restrain B values?

[Eleanor Dodson]

I thought it was possible to stop B values on bonded atoms from fluctuating
wildly?
But I am quite unable to follow the newly formatted documentation..



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Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

[Robbie Joosten]

One wonders who those "many people" are. You may not want to use them as your go-to reference for refinement techniques.Anyway, Refmac cannot do grouped B-factor refinement, but you are not missing out on anything. As Eleanor implied, one-per-residue B-factors give unrealistic results. You are much better off using isotropic B-factors with tight restraints (Refmac's default is already quite tight). Add TLS in your refinement to see if that helps. If you have a really poor data/parameter ratio you could go for a flat B-factor model and try to capture most of the B-factor in the TLS model. This is typically not needed at 3A, but there are exceptions (low solvent -more atoms-  or low completeness -fewer reflections- are factors to consider). If you do go for a flat B-factor model, you need to define sensible TLS groups. This takes some trial and error.pdb-redo has decent algorithms to select the B-factor model and weight for Refmac. You could use that as a starting point for your model.HTH,RobbieOn 6 Jan 2024 03:13, "chenzhonghao...@163.com"  wrote:




Dear Prof. Dr. Dodson and all CCP4 community,
 
  Thanks for your reply.
 
 Just now, I used baverage. I found that it
can average the B factor but not refine it.
  This function does not fit my
requirement, because my resolution is low as 3 A. 
 Many people said that Refmac5
overrefines the structure if I used isotropic temperature refinement.
 
Did refmac5 or other programs in CCP4 have similar
functions like one_adp_group_per_residue or two_adp_groups_per_residue in Phenix?
 
 Any help would be highly appreciated!
 


chenzhonghao...@163.com
 From: Eleanor DodsonDate: 2024-01-05 23:48To: CCP4BBSubject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?Hmmm -  I am not sure about the value of this - one expects the longer floppier side chains to have very different B values for the CB than the OE2..The program BAVERAGE gives you a plot of mean B value residue by residue..baverage - averages B over main and side chain atomsSYNOPSIS¶baverage XYZIN foo_in.pdb RMSTAB foo_out1.tab XYZOUT foo_out2.pdb[Keyworded input]DESCRIPTION¶A very simple minded program to read a PDB file, tabulate to RMSTAB the average B values residue by residue (main chain and side chain separately) and the RMS deviation of the B values from this mean. It also outputs a PDB file with outlying B factors reset to lie within the given range.On Fri, 5 Jan 2024 at 03:08, chenzhonghao...@163.com  wrote:Dear CCP4 community, 

 I found that Refmac5 refined the temperature factor only by four modes (see the bottom of the attached figure). However, no
grouped B-factor (one or two per residue instead of one per atom) was found.

 Actually, PHENIX and CNS can do it. But we are not familiar with both software. I want to know whether Refmac5 refines one or
two group B per residue (for side and main chains) grouped temperature factor?

 Any help would be highly appreciated

 Thanks in advance.

best,


 Zhonghao Chen










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