Re: [ccp4bb] AW: [ccp4bb] doubt regarding MR search model

2017-09-20 Thread Eleanor Dodson 
Satvik - if you attach your data processing logs I can tell you what to
look out for - too abstract to do without a concrete example to discuss.
Eleanor

On 20 September 2017 at 14:00,  wrote:

> Dear Satvik,
>
>
>
> An R/Rfree of 0.29/0.35 after one round of automatic model building
> indicates that your solution is correct. You can proceed with refinement
> and rebuilding. You can take either the monomer-based or dimer-based
> solution, it does not matter. Personally I would take the monomer-based
> solution since it allowed for some small difference in orientation of the
> monomers within the dimer.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Satvik Kumar
> *Gesendet:* Mittwoch, 20. September 2017 14:40
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* Re: [ccp4bb] doubt regarding MR search model
>
>
>
> Hello,
>
> Thanks all for your valuable suggestions. Two things that stuck me were "one
> gets to know if the space group is correct only after solving the
> structure" and "to try all possible space groups until one lands up with
> the correct solution".
>
> I ran Phaser with "all alternative space groups". The solution is still in
> the same space group P212121. This holds true with both the monomer as well
> as dimer search models. I hope I have checked all orthorhombic space groups
> by doing this as I am unsure what "all alternative space groups" means.
>
> I also ran Zanuda which tells me that the space group P212121 is correct
> in both cases.
>
> Pointless output indicates that "Systematic absence probability: 0.818".
> Can I take this to be convincing or do I need to run other tests?
>
>
>
> I dont know how to check for non-crystallographic symmetry? Please tell me
> how I can do so.
>
>
>
> The model is 60 percent identical to my protein. Also, one round of
> automated model building has brought down the R values. The Rwork,Rfree
> stand at 0.29,0.35 (monomer search model) and 0.30, 0.35 (dimer search
> model). There is good scope for building residues in both cases. But which
> one do I go ahead with is my question.
>
>
>
> Thanks,
>
> Satvik
>
>
>
>
>
> On Tue, Sep 19, 2017 at 11:40 PM, Eleanor Dodson <
> eleanor.dod...@york.ac.uk> wrote:
>
> Well - you haven't said what the sequence identity between model and your
> protein is, nor if you have a non-crystallographic translation.
>
>
>
> With low homology that R factor drop is acceptable and rebuilding can fix
> it, However if there is high homology you might expect better.
>
>
>
> But this sort of conjecture is pretty pointless - check in all
> orthorhombic  space groups as Mark suggests.
>
>
>
> Eleanor
>
>
>
> On 19 September 2017 at 15:16, Mark J van Raaij 
> wrote:
>
> With Rs of 43/48% I don't think you can be sure that your spacegroup is
> right.
>
> You should always try all the spacegroup possibilities until you get a
> solution you are sure is right, i.e. that refines to Rs of around 35% or
> preferably even lower.
>
> More so in the case of screw axes, so try P222, P2122, P2212, P2221,
> P21212, P21221, P22121 and P212121. Phaser can do this automatically for
> you by clicking the right box.
>
> If necessary, then try lower symmetry like P21 and perhaps P1.
>
> Programs like Xanuda can help.
>
>
>
>
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.google.com_-3Fq-3Dcalle-2BDarwin-2B3-26entry-3Dgmail-26source-3Dg&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=WuFY958mWwJOc-_oZdihE6B4h0tlRsfBpLyZ0agnz9E&s=wsbi7Hs3zKGXbwDzjt4Up9v2OvmNaexqb0vzGpBG7j8&e=>
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616 <+34%20915%2085%2046%2016>
> http://wwwuser.cnb.csic.es/~mjvanraaij
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__wwwuser.cnb.csic.es_-7Emjvanraaij&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=WuFY958mWwJOc-_oZdihE6B4h0tlRsfBpLyZ0agnz9E&s=xcDWCasKH3VKSzXrKFpceN-EhF-q4nC9GwjZ338cYrA&e=>
>
> Editor of Acta Crystallographica F, Structural Biology Communications
>
> http://journals.iucr.org/f/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__journals.iucr.org_f_&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=WuFY958mWwJOc-_oZdihE6B4h0tlRsfBpLyZ0ag

[ccp4bb] AW: [ccp4bb] doubt regarding MR search model

2017-09-20 Thread Herman . Schreuder 
Dear Satvik,

An R/Rfree of 0.29/0.35 after one round of automatic model building indicates 
that your solution is correct. You can proceed with refinement and rebuilding. 
You can take either the monomer-based or dimer-based solution, it does not 
matter. Personally I would take the monomer-based solution since it allowed for 
some small difference in orientation of the monomers within the dimer.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Satvik 
Kumar
Gesendet: Mittwoch, 20. September 2017 14:40
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] doubt regarding MR search model

Hello,
Thanks all for your valuable suggestions. Two things that stuck me were "one 
gets to know if the space group is correct only after solving the structure" 
and "to try all possible space groups until one lands up with the correct 
solution".
I ran Phaser with "all alternative space groups". The solution is still in the 
same space group P212121. This holds true with both the monomer as well as 
dimer search models. I hope I have checked all orthorhombic space groups by 
doing this as I am unsure what "all alternative space groups" means.
I also ran Zanuda which tells me that the space group P212121 is correct in 
both cases.
Pointless output indicates that "Systematic absence probability: 0.818". Can I 
take this to be convincing or do I need to run other tests?

I dont know how to check for non-crystallographic symmetry? Please tell me how 
I can do so.

The model is 60 percent identical to my protein. Also, one round of automated 
model building has brought down the R values. The Rwork,Rfree stand at 
0.29,0.35 (monomer search model) and 0.30, 0.35 (dimer search model). There is 
good scope for building residues in both cases. But which one do I go ahead 
with is my question.


Thanks,
Satvik


On Tue, Sep 19, 2017 at 11:40 PM, Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:
Well - you haven't said what the sequence identity between model and your 
protein is, nor if you have a non-crystallographic translation.

With low homology that R factor drop is acceptable and rebuilding can fix it, 
However if there is high homology you might expect better.

But this sort of conjecture is pretty pointless - check in all orthorhombic  
space groups as Mark suggests.

Eleanor

On 19 September 2017 at 15:16, Mark J van Raaij 
mailto:mjvanra...@cnb.csic.es>> wrote:
With Rs of 43/48% I don't think you can be sure that your spacegroup is right.
You should always try all the spacegroup possibilities until you get a solution 
you are sure is right, i.e. that refines to Rs of around 35% or preferably even 
lower.
More so in the case of screw axes, so try P222, P2122, P2212, P2221, P21212, 
P21221, P22121 and P212121. Phaser can do this automatically for you by 
clicking the right box.
If necessary, then try lower symmetry like P21 and perhaps P1.
Programs like Xanuda can help.


Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 
3<https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.google.com_-3Fq-3Dcalle-2BDarwin-2B3-26entry-3Dgmail-26source-3Dg&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=WuFY958mWwJOc-_oZdihE6B4h0tlRsfBpLyZ0agnz9E&s=wsbi7Hs3zKGXbwDzjt4Up9v2OvmNaexqb0vzGpBG7j8&e=>
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij<https://urldefense.proofpoint.com/v2/url?u=http-3A__wwwuser.cnb.csic.es_-7Emjvanraaij&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=WuFY958mWwJOc-_oZdihE6B4h0tlRsfBpLyZ0agnz9E&s=xcDWCasKH3VKSzXrKFpceN-EhF-q4nC9GwjZ338cYrA&e=>
Editor of Acta Crystallographica F, Structural Biology Communications
http://journals.iucr.org/f/<https://urldefense.proofpoint.com/v2/url?u=http-3A__journals.iucr.org_f_&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=WuFY958mWwJOc-_oZdihE6B4h0tlRsfBpLyZ0agnz9E&s=AGltbWDVK377w5vwK7tqER8JFzGUMWMblni0CyuiDUs&e=>

On 19 Sep 2017, at 16:01, Satvik Kumar 
mailto:kumarsatvi...@gmail.com>> wrote:

Hello,
Thanks everyone for your explanations.
I have pasted the pointless output to provide more information.

Best Solution:  space group P 21 21 21

Laue group probability:   0.959

Systematic absence probability: 0.818

Total probability: 0.785

Space group confidence:0.751

Laue group confidence   0.951


Unit cell:   82.10 100.51 157.11 90.00  90.00  90.00

Also based on L-test, pointless says data does not suggest twinning.

Yes, the R values go down when I refine in both cases. After 20 rounds of 
restraine

Re: [ccp4bb] doubt regarding MR search model

2017-09-20 Thread Satvik Kumar 
Hello,

Thanks all for your valuable suggestions. Two things that stuck me were "one
gets to know if the space group is correct only after solving the
structure" and "to try all possible space groups until one lands up with
the correct solution".

I ran Phaser with "all alternative space groups". The solution is still in
the same space group P212121. This holds true with both the monomer as well
as dimer search models. I hope I have checked all orthorhombic space groups
by doing this as I am unsure what "all alternative space groups" means.

I also ran Zanuda which tells me that the space group P212121 is correct in
both cases.

Pointless output indicates that "Systematic absence probability: 0.818".
Can I take this to be convincing or do I need to run other tests?

I dont know how to check for non-crystallographic symmetry? Please tell me
how I can do so.

The model is 60 percent identical to my protein. Also, one round of
automated model building has brought down the R values. The Rwork,Rfree
stand at 0.29,0.35 (monomer search model) and 0.30, 0.35 (dimer search
model). There is good scope for building residues in both cases. But which
one do I go ahead with is my question.




Thanks,
Satvik


On Tue, Sep 19, 2017 at 11:40 PM, Eleanor Dodson 
wrote:

> Well - you haven't said what the sequence identity between model and your
> protein is, nor if you have a non-crystallographic translation.
>
> With low homology that R factor drop is acceptable and rebuilding can fix
> it, However if there is high homology you might expect better.
>
> But this sort of conjecture is pretty pointless - check in all
> orthorhombic  space groups as Mark suggests.
>
> Eleanor
>
> On 19 September 2017 at 15:16, Mark J van Raaij 
> wrote:
>
>> With Rs of 43/48% I don't think you can be sure that your spacegroup is
>> right.
>> You should always try all the spacegroup possibilities until you get a
>> solution you are sure is right, i.e. that refines to Rs of around 35% or
>> preferably even lower.
>> More so in the case of screw axes, so try P222, P2122, P2212, P2221,
>> P21212, P21221, P22121 and P212121. Phaser can do this automatically for
>> you by clicking the right box.
>> If necessary, then try lower symmetry like P21 and perhaps P1.
>> Programs like Xanuda can help.
>>
>>
>> Mark J van Raaij
>> Dpto de Estructura de Macromoleculas
>> Centro Nacional de Biotecnologia - CSIC
>> calle Darwin 3
>> 
>> E-28049 Madrid, Spain
>> tel. (+34) 91 585 4616 <+34%20915%2085%2046%2016>
>> http://wwwuser.cnb.csic.es/~mjvanraaij
>> Editor of Acta Crystallographica F, Structural Biology Communications
>> http://journals.iucr.org/f/
>>
>> On 19 Sep 2017, at 16:01, Satvik Kumar  wrote:
>>
>> Hello,
>>
>> Thanks everyone for your explanations.
>>
>> I have pasted the pointless output to provide more information.
>>
>> Best Solution:  space group P 21 21 21
>>
>> Laue group probability:   0.959
>>
>> Systematic absence probability: 0.818
>>
>> Total probability: 0.785
>>
>> Space group confidence:0.751
>>
>> Laue group confidence   0.951
>>
>>
>> Unit cell:   82.10 100.51 157.11 90.00  90.00  90.00
>>
>> Also based on L-test, pointless says data does not suggest twinning.
>>
>> Yes, the R values go down when I refine in both cases. After 20 rounds of 
>> restrained refinement using the coordinates generated by monomer as search 
>> model, the Rwork and Rfree are 0.43 and 0.48
>>
>> respectively. Refinement using the coordinates generated by using dimer
>> as search model also results in similar R values. I have attached the plots
>> to show that the R values indeed reduce in both cases.
>>
>> Is my space group correct? Do I need to reexamine the space group even
>> though the probability is high?
>>
>> If my space group is indeed correct, how do I decide whether to go ahead
>> with the results generated by the monomer search model or the dimer?
>>
>> Please share your thoughts.
>>
>>
>> Thanks,
>> Satvik
>>
>> On Mon, Sep 18, 2017 at 7:36 PM, Eleanor Dodson <
>> eleanor.dod...@york.ac.uk> wrote:
>>
>>> You need to provide a bit more information.
>>>
>>> First of all about the data processing..
>>>
>>> Is the space group correct?
>>> ways of being misled are:
>>> Non-crystallographic translations with a shift of ~0.5 along an axis -
>>> say a.  This will generate absences in the odd h 0 0 reflections and can
>>> make the space group appear to be P 21 21 21 whilst it is really P 2 21 21..
>>>
>>> Perfect twinning can have the same effect. In an orthorhombix space
>>> group this can usually only occur if two axes have approximately the same
>>> length, but the data processing stats can indicate if that is the case.
>>>
>>> Then - re PHASER. The packing rejection criteria may be set too severely
>>> - that seems the case for your solution.
>>>
>>> Best check on any MR s

Re: [ccp4bb] doubt regarding MR search model

2017-09-19 Thread Eleanor Dodson 
Well - you haven't said what the sequence identity between model and your
protein is, nor if you have a non-crystallographic translation.

With low homology that R factor drop is acceptable and rebuilding can fix
it, However if there is high homology you might expect better.

But this sort of conjecture is pretty pointless - check in all orthorhombic
 space groups as Mark suggests.

Eleanor

On 19 September 2017 at 15:16, Mark J van Raaij 
wrote:

> With Rs of 43/48% I don't think you can be sure that your spacegroup is
> right.
> You should always try all the spacegroup possibilities until you get a
> solution you are sure is right, i.e. that refines to Rs of around 35% or
> preferably even lower.
> More so in the case of screw axes, so try P222, P2122, P2212, P2221,
> P21212, P21221, P22121 and P212121. Phaser can do this automatically for
> you by clicking the right box.
> If necessary, then try lower symmetry like P21 and perhaps P1.
> Programs like Xanuda can help.
>
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616 <+34%20915%2085%2046%2016>
> http://wwwuser.cnb.csic.es/~mjvanraaij
> Editor of Acta Crystallographica F, Structural Biology Communications
> http://journals.iucr.org/f/
>
> On 19 Sep 2017, at 16:01, Satvik Kumar  wrote:
>
> Hello,
>
> Thanks everyone for your explanations.
>
> I have pasted the pointless output to provide more information.
>
> Best Solution:  space group P 21 21 21
>
> Laue group probability:   0.959
>
> Systematic absence probability: 0.818
>
> Total probability: 0.785
>
> Space group confidence:0.751
>
> Laue group confidence   0.951
>
>
> Unit cell:   82.10 100.51 157.11 90.00  90.00  90.00
>
> Also based on L-test, pointless says data does not suggest twinning.
>
> Yes, the R values go down when I refine in both cases. After 20 rounds of 
> restrained refinement using the coordinates generated by monomer as search 
> model, the Rwork and Rfree are 0.43 and 0.48
>
> respectively. Refinement using the coordinates generated by using dimer as
> search model also results in similar R values. I have attached the plots to
> show that the R values indeed reduce in both cases.
>
> Is my space group correct? Do I need to reexamine the space group even
> though the probability is high?
>
> If my space group is indeed correct, how do I decide whether to go ahead
> with the results generated by the monomer search model or the dimer?
>
> Please share your thoughts.
>
>
> Thanks,
> Satvik
>
> On Mon, Sep 18, 2017 at 7:36 PM, Eleanor Dodson  > wrote:
>
>> You need to provide a bit more information.
>>
>> First of all about the data processing..
>>
>> Is the space group correct?
>> ways of being misled are:
>> Non-crystallographic translations with a shift of ~0.5 along an axis -
>> say a.  This will generate absences in the odd h 0 0 reflections and can
>> make the space group appear to be P 21 21 21 whilst it is really P 2 21 21..
>>
>> Perfect twinning can have the same effect. In an orthorhombix space group
>> this can usually only occur if two axes have approximately the same length,
>> but the data processing stats can indicate if that is the case.
>>
>> Then - re PHASER. The packing rejection criteria may be set too severely
>> - that seems the case for your solution.
>>
>> Best check on any MR solution is: does it refine - give it 20 cycles of
>> mindless refinement and see if the R and FreeR go down.
>>
>> Then look at the maps and see if there are obvious corrections to be
>> made..
>>
>> Eleanor
>>
>> On 18 September 2017 at 14:59, Satvik Kumar 
>> wrote:
>>
>>> Dear Crystallographers,
>>>
>>> I am trying to solve a structure in the space group P212121. Based on
>>> Matthews coefficient, there are 4 molecules in the asymmetric unit.
>>>
>>> Based on my limited reading about using of Phaser, I understand that a
>>> single chain should be used as search model even though many copies are
>>> present in asymmetric unit. Am I correct?
>>>
>>> So when I use a single chain as search model and ask Phaser to search
>>> for 4 molecules, Phaser identifies a single solution with a warning "The
>>> top solution from a TF rescoring did not pack" and a warning "Search
>>> request requires more scattering than defined in composition. Composition
>>> increased to accommodate search components". But the final values reported 
>>> "PAK=2
>>> LLG=1065 TFZ==22.6" indicate that phaser has solved the problem.
>>>
>>> Can anyone please explain the meaning of the warning.
>>>
>>> When I inspect the arrangement of the chains (attachment), I observe
>>> minimal contact between the chains and a large cavity in the center. Can a
>>> crystal form this way?
>>>
>>> I have also tried using the dimer as search model and asking phaser to
>>> search for 2 molecules. Even in this

Re: [ccp4bb] doubt regarding MR search model

2017-09-19 Thread Mark J van Raaij 
With Rs of 43/48% I don't think you can be sure that your spacegroup is right.
You should always try all the spacegroup possibilities until you get a solution 
you are sure is right, i.e. that refines to Rs of around 35% or preferably even 
lower.
More so in the case of screw axes, so try P222, P2122, P2212, P2221, P21212, 
P21221, P22121 and P212121. Phaser can do this automatically for you by 
clicking the right box. 
If necessary, then try lower symmetry like P21 and perhaps P1.
Programs like Xanuda can help.


Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://wwwuser.cnb.csic.es/~mjvanraaij
Editor of Acta Crystallographica F, Structural Biology Communications
http://journals.iucr.org/f/

> On 19 Sep 2017, at 16:01, Satvik Kumar  wrote:
> 
> Hello,
> 
> Thanks everyone for your explanations.
> 
> I have pasted the pointless output to provide more information.
> Best Solution:  space group P 21 21 21
>  Laue group probability:   0.959
> Systematic absence probability: 0.818
> Total probability: 0.785
> Space group confidence:0.751
> Laue group confidence   0.951
> 
> Unit cell:   82.10 100.51 157.11 90.00  90.00  90.00
> 
> Also based on L-test, pointless says data does not suggest twinning.
> 
> Yes, the R values go down when I refine in both cases. After 20 rounds of 
> restrained refinement using the coordinates generated by monomer as search 
> model, the Rwork and Rfree are 0.43 and 0.48 
> respectively. Refinement using the coordinates generated by using dimer as 
> search model also results in similar R values. I have attached the plots to 
> show that the R values indeed reduce in both cases. 
> 
> Is my space group correct? Do I need to reexamine the space group even though 
> the probability is high?
> 
> If my space group is indeed correct, how do I decide whether to go ahead with 
> the results generated by the monomer search model or the dimer? 
> 
> Please share your thoughts.
> 
> 
> Thanks,
> Satvik
> 
> On Mon, Sep 18, 2017 at 7:36 PM, Eleanor Dodson  > wrote:
> You need to provide a bit more information.
> 
> First of all about the data processing..
> 
> Is the space group correct?
> ways of being misled are:
> Non-crystallographic translations with a shift of ~0.5 along an axis - say a. 
>  This will generate absences in the odd h 0 0 reflections and can make the 
> space group appear to be P 21 21 21 whilst it is really P 2 21 21..
> 
> Perfect twinning can have the same effect. In an orthorhombix space group 
> this can usually only occur if two axes have approximately the same length, 
> but the data processing stats can indicate if that is the case.
> 
> Then - re PHASER. The packing rejection criteria may be set too severely - 
> that seems the case for your solution.
> 
> Best check on any MR solution is: does it refine - give it 20 cycles of 
> mindless refinement and see if the R and FreeR go down.
> 
> Then look at the maps and see if there are obvious corrections to be made..
> 
> Eleanor
> 
> On 18 September 2017 at 14:59, Satvik Kumar  > wrote:
> Dear Crystallographers,
> 
> I am trying to solve a structure in the space group P212121. Based on 
> Matthews coefficient, there are 4 molecules in the asymmetric unit.
> 
> Based on my limited reading about using of Phaser, I understand that a single 
> chain should be used as search model even though many copies are present in 
> asymmetric unit. Am I correct?
> 
> So when I use a single chain as search model and ask Phaser to search for 4 
> molecules, Phaser identifies a single solution with a warning "The top 
> solution from a TF rescoring did not pack" and a warning "Search request 
> requires more scattering than defined in composition. Composition increased 
> to accommodate search components". But the final values reported "PAK=2 
> LLG=1065 TFZ==22.6" indicate that phaser has solved the problem. 
> 
> Can anyone please explain the meaning of the warning.
> 
> When I inspect the arrangement of the chains (attachment), I observe minimal 
> contact between the chains and a large cavity in the center. Can a crystal 
> form this way?
> 
> I have also tried using the dimer as search model and asking phaser to search 
> for 2 molecules. Even in this case, Phaser finds a single solution but the 
> warning and the advisory still appear as before. The numbers reported reduce 
> a bit to "PAK=1 LLG=722 TFZ==29.2".
> 
> Please help me in understanding these results.
> 
> Thanks,
> Satvik
> 
> 
> 
> 
>

[ccp4bb] AW: [ccp4bb] doubt regarding MR search model

2017-09-19 Thread Herman . Schreuder 
Dear Satvik,

You only know if the space group is correct AFTER you solved your structure. 
With an Rwork/Rfree of 0.43/0.48, the space group is likely not correct. The 
way to solve this is to run MR in all possible space groups. Most, if not all 
MR programs have an option to do this automatically.

For phaser e.g. you have to give the command: SGALTERNATIVE SELECT ALL
If your search model is not too different from the crystallized protein, this 
should work without a problem. Otherwise, you get into the realm of difficult 
molecular replacement and that will be a different story.

Good luck!
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Satvik 
Kumar
Gesendet: Dienstag, 19. September 2017 16:02
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] doubt regarding MR search model

Hello,
Thanks everyone for your explanations.
I have pasted the pointless output to provide more information.

Best Solution:  space group P 21 21 21

Laue group probability:   0.959

Systematic absence probability: 0.818

Total probability: 0.785

Space group confidence:0.751

Laue group confidence   0.951


Unit cell:   82.10 100.51 157.11 90.00  90.00  90.00

Also based on L-test, pointless says data does not suggest twinning.

Yes, the R values go down when I refine in both cases. After 20 rounds of 
restrained refinement using the coordinates generated by monomer as search 
model, the Rwork and Rfree are 0.43 and 0.48
respectively. Refinement using the coordinates generated by using dimer as 
search model also results in similar R values. I have attached the plots to 
show that the R values indeed reduce in both cases.
Is my space group correct? Do I need to reexamine the space group even though 
the probability is high?

If my space group is indeed correct, how do I decide whether to go ahead with 
the results generated by the monomer search model or the dimer?
Please share your thoughts.

Thanks,
Satvik

On Mon, Sep 18, 2017 at 7:36 PM, Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:
You need to provide a bit more information.
First of all about the data processing..
Is the space group correct?
ways of being misled are:
Non-crystallographic translations with a shift of ~0.5 along an axis - say a.  
This will generate absences in the odd h 0 0 reflections and can make the space 
group appear to be P 21 21 21 whilst it is really P 2 21 21..
Perfect twinning can have the same effect. In an orthorhombix space group this 
can usually only occur if two axes have approximately the same length, but the 
data processing stats can indicate if that is the case.
Then - re PHASER. The packing rejection criteria may be set too severely - that 
seems the case for your solution.
Best check on any MR solution is: does it refine - give it 20 cycles of 
mindless refinement and see if the R and FreeR go down.
Then look at the maps and see if there are obvious corrections to be made..
Eleanor

On 18 September 2017 at 14:59, Satvik Kumar 
mailto:kumarsatvi...@gmail.com>> wrote:
Dear Crystallographers,
I am trying to solve a structure in the space group P212121. Based on Matthews 
coefficient, there are 4 molecules in the asymmetric unit.
Based on my limited reading about using of Phaser, I understand that a single 
chain should be used as search model even though many copies are present in 
asymmetric unit. Am I correct?
So when I use a single chain as search model and ask Phaser to search for 4 
molecules, Phaser identifies a single solution with a warning "The top solution 
from a TF rescoring did not pack" and a warning "Search request requires more 
scattering than defined in composition. Composition increased to accommodate 
search components". But the final values reported "PAK=2 LLG=1065 TFZ==22.6" 
indicate that phaser has solved the problem.

Can anyone please explain the meaning of the warning.
When I inspect the arrangement of the chains (attachment), I observe minimal 
contact between the chains and a large cavity in the center. Can a crystal form 
this way?

I have also tried using the dimer as search model and asking phaser to search 
for 2 molecules. Even in this case, Phaser finds a single solution but the 
warning and the advisory still appear as before. The numbers reported reduce a 
bit to "PAK=1 LLG=722 TFZ==29.2".
Please help me in understanding these results.
Thanks,
Satvik

Re: [ccp4bb] doubt regarding MR search model

2017-09-19 Thread Satvik Kumar 
Hello,

Thanks everyone for your explanations.

I have pasted the pointless output to provide more information.

Best Solution:  space group P 21 21 21

Laue group probability:   0.959

Systematic absence probability: 0.818

Total probability: 0.785

Space group confidence:0.751

Laue group confidence   0.951


Unit cell:   82.10 100.51 157.11 90.00  90.00  90.00

Also based on L-test, pointless says data does not suggest twinning.

Yes, the R values go down when I refine in both cases. After 20 rounds
of restrained refinement using the coordinates generated by monomer as
search model, the Rwork and Rfree are 0.43 and 0.48

respectively. Refinement using the coordinates generated by using dimer as
search model also results in similar R values. I have attached the plots to
show that the R values indeed reduce in both cases.

Is my space group correct? Do I need to reexamine the space group even
though the probability is high?

If my space group is indeed correct, how do I decide whether to go ahead
with the results generated by the monomer search model or the dimer?

Please share your thoughts.


Thanks,
Satvik

On Mon, Sep 18, 2017 at 7:36 PM, Eleanor Dodson 
wrote:

> You need to provide a bit more information.
>
> First of all about the data processing..
>
> Is the space group correct?
> ways of being misled are:
> Non-crystallographic translations with a shift of ~0.5 along an axis - say
> a.  This will generate absences in the odd h 0 0 reflections and can make
> the space group appear to be P 21 21 21 whilst it is really P 2 21 21..
>
> Perfect twinning can have the same effect. In an orthorhombix space group
> this can usually only occur if two axes have approximately the same length,
> but the data processing stats can indicate if that is the case.
>
> Then - re PHASER. The packing rejection criteria may be set too severely -
> that seems the case for your solution.
>
> Best check on any MR solution is: does it refine - give it 20 cycles of
> mindless refinement and see if the R and FreeR go down.
>
> Then look at the maps and see if there are obvious corrections to be made..
>
> Eleanor
>
> On 18 September 2017 at 14:59, Satvik Kumar 
> wrote:
>
>> Dear Crystallographers,
>>
>> I am trying to solve a structure in the space group P212121. Based on
>> Matthews coefficient, there are 4 molecules in the asymmetric unit.
>>
>> Based on my limited reading about using of Phaser, I understand that a
>> single chain should be used as search model even though many copies are
>> present in asymmetric unit. Am I correct?
>>
>> So when I use a single chain as search model and ask Phaser to search for
>> 4 molecules, Phaser identifies a single solution with a warning "The top
>> solution from a TF rescoring did not pack" and a warning "Search request
>> requires more scattering than defined in composition. Composition
>> increased to accommodate search components". But the final values reported 
>> "PAK=2
>> LLG=1065 TFZ==22.6" indicate that phaser has solved the problem.
>>
>> Can anyone please explain the meaning of the warning.
>>
>> When I inspect the arrangement of the chains (attachment), I observe
>> minimal contact between the chains and a large cavity in the center. Can a
>> crystal form this way?
>>
>> I have also tried using the dimer as search model and asking phaser to
>> search for 2 molecules. Even in this case, Phaser finds a single solution
>> but the warning and the advisory still appear as before. The numbers
>> reported reduce a bit to "PAK=1 LLG=722 TFZ==29.2".
>>
>> Please help me in understanding these results.
>>
>> Thanks,
>> Satvik
>>
>>
>>
>


Monomer_searchmodel.pdf
Description: Adobe PDF document


Dimer_searchmodel.pdf
Description: Adobe PDF document

Re: [ccp4bb] doubt regarding MR search model

2017-09-18 Thread Randy Read 
Dear Emily,

In this case, I was referring to the difference between 1065 obtained placing 4 
copies of the monomer and 722 obtained placing 2 copies of the dimer.  A 
difference of over 300 is substantial when we feel that an increase of 60 is 
enough to be reasonably convinced that a solution for placing one copy of a 
molecule is correct.  I guess that this value of 60 would be my yardstick for 
“significant” in the sense of “big enough to matter”.  Putting a number to 
“significant” in the sense of “bigger than random” is harder.  There’s an 
argument that the random error in an LLG value is roughly equivalent to the 
square root of the LLG, which would still make this a significant difference.  
That argument could get much more complicated if you started to worry about 
things like the 2-dimer model just being a constrained version of the 4-monomer 
model because the monomers within the dimer are identical!

Not sure if that really helps!

Randy
 
-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

> On 18 Sep 2017, at 17:39, Emilia C. Arturo (Emily)  
> wrote:
> 
> Hello Randy,
> 
> I'm chiming in about the last sentence in your reply:
> 
> 
> Finally, I would suspect that getting a significantly lower LLG for two 
> copies of a dimer means that the dimer in your structure is slightly 
> different from the dimer in the model.
> 
> Will you please be more specific about what you consider "significantly 
> lower" (or higher) for LLG scores? And how does this difference translate to 
> differences among TFZ scores? I have wondered this especially when a Phaser 
> MR result from use of a smaller part (i.e. one domain, 64% of the sequence) 
> of a structure differs by a few units relative to a result from use of a 
> larger part (i.e. two domains, 90% of the sequence) of the protein; the 
> difference in my case was a top TFZ score of 42.5 using the one-domain search 
> model, but a lower TFZ score of 36.9 for the two-domain model. 
> 
> Even more interesting to me is when the TFZ scores vary by quite a bit more 
> between two phaser runs that used two different, but 100% sequence identical, 
> one-domain search models; in this case the top TFZ scores were 18.7 versus 
> 42.5, for the two models that differed only in the coordinate position of ~20 
> out of 290 residues (a lid for the enzyme). 
> 
> Regards,
> 
> Emily.
> 
> 
> Best wishes,
> 
> Randy Read
> 
> -
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical ResearchTel: +44 1223 336500
> Wellcome Trust/MRC Building Fax: +44 1223 336827
> Hills RoadE-mail: 
> rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.   
> www-structmed.cimr.cam.ac.uk
> 
> > On 18 Sep 2017, at 16:24, Andrew Leslie  wrote:
> >
> > Regarding the warning message "The top solution from a TF rescoring did not 
> > pack”, I get this on all the PHASER jobs that I have run recently, but 
> > looking through the PHASER log file I cannot see any evidence for packing 
> > failure.
> >
> > It may be that the failure is buried in an obscure place in the very long 
> > log file, but if I search for “pack” then I get the output summarised 
> > below, all of which, apart from the ADVISORY, suggests to me that there is 
> > no problem at all with the packing.
> >
> > Perhaps someone on the PHASER team can cast light on this.
> >
> > Andrew
> >
> >
> > Extracts from PHASER log file:
> >
> >
> > TRANSLATION FUNCTIONS
> > -
> >
> >Target Function: FAST LETF1
> >Translation Packing Function applied: top peak will pack
> >Translation Packing Cutoff: 50%
> >Sampling:  1.82 Angstroms
> >
> >
> > ===
> > 
> > PACKING FUNCTION
> > 
> >
> >There are 4 solutions to pack
> >Packing analysis
> >0%100%
> >|=| DONE
> >
> > 
> >Packing Table
> >-
> >Solutions accepted if pairwise clashes less than 10 % of trace atoms
> >#in  #out Clash-% Symm TF-SET  ROT TFpk#TFTFZSpaceGroup
> >1Top1  0.741  --   1 11325.94 26.03  P 1
> >22 1.058  --   1 21293.29 24.34  P 1
> >33 0.952  --   1 31245.70 21.88  P 1
> >44 0.847  --   1 41211.49 20.11  P 1
> >
> >4 accepted of 4 solutions
> >   4 pack of 4 accepted solutions
> >
> > ==
> > ---
> > TRANSLATION PACKING
>

Re: [ccp4bb] doubt regarding MR search model

2017-09-18 Thread Emilia C. Arturo (Emily) 
Hello Randy,

I'm chiming in about the last sentence in your reply:


> Finally, I would suspect that getting a significantly lower LLG for two
> copies of a dimer means that the dimer in your structure is slightly
> different from the dimer in the model.
>

Will you please be more specific about what you consider "significantly
lower" (or higher) for LLG scores? And how does this difference translate
to differences among TFZ scores? I have wondered this especially when a
Phaser MR result from use of a smaller part (i.e. one domain, 64% of the
sequence) of a structure differs by a few units relative to a result from
use of a larger part (i.e. two domains, 90% of the sequence) of the
protein; the difference in my case was a top TFZ score of 42.5 using the
one-domain search model, but a lower TFZ score of 36.9 for the two-domain
model.

Even more interesting to me is when the TFZ scores vary by quite a bit more
between two phaser runs that used two different, but 100% sequence
identical, one-domain search models; in this case the top TFZ scores were
18.7 versus 42.5, for the two models that differed only in the coordinate
position of ~20 out of 290 residues (a lid for the enzyme).

Regards,

Emily.


Best wishes,
>
> Randy Read
>
> -
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical ResearchTel: +44 1223 336500
> Wellcome Trust/MRC Building Fax: +44 1223 336827
> Hills Road
> E-mail: rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
> > On 18 Sep 2017, at 16:24, Andrew Leslie 
> wrote:
> >
> > Regarding the warning message "The top solution from a TF rescoring did
> not pack”, I get this on all the PHASER jobs that I have run recently, but
> looking through the PHASER log file I cannot see any evidence for packing
> failure.
> >
> > It may be that the failure is buried in an obscure place in the very
> long log file, but if I search for “pack” then I get the output summarised
> below, all of which, apart from the ADVISORY, suggests to me that there is
> no problem at all with the packing.
> >
> > Perhaps someone on the PHASER team can cast light on this.
> >
> > Andrew
> >
> >
> > Extracts from PHASER log file:
> >
> >
> > TRANSLATION FUNCTIONS
> > -
> >
> >Target Function: FAST LETF1
> >Translation Packing Function applied: top peak will pack
> >Translation Packing Cutoff: 50%
> >Sampling:  1.82 Angstroms
> >
> >
> > ===
> > 
> > PACKING FUNCTION
> > 
> >
> >There are 4 solutions to pack
> >Packing analysis
> >0%100%
> >|=| DONE
> >
> > 
> >Packing Table
> >-
> >Solutions accepted if pairwise clashes less than 10 % of trace atoms
> >#in  #out Clash-% Symm TF-SET  ROT TFpk#TFTFZ
> SpaceGroup
> >1Top1  0.741  --   1 11325.94 26.03  P 1
> >22 1.058  --   1 21293.29 24.34  P 1
> >33 0.952  --   1 31245.70 21.88  P 1
> >44 0.847  --   1 41211.49 20.11  P 1
> >
> >4 accepted of 4 solutions
> >   4 pack of 4 accepted solutions
> >
> > ==
> > ---
> > TRANSLATION PACKING
> > ---
> >
> >Translation Packing Cutoff: 50%
> >All solutions have been packed
> >
> > ==
> >Packing Fast Search Translations...
> >   9871 peaks
> >   500 peaks over 1049.74 checked for packing
> >   Translation peak 1 first to be kept
> >   Done
> >
> > 
> >New Top Packing Fast Translation Function FSS = 2181.37 (TFZ=46.3) at
> Trial #1
> > 
> >
> >Top Peaks Without Clustering
> >Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
> >There was 1 site over 67.5% of top
> >1 peak selected
> >The sites over 67.5% are:
> ># Frac X Frac Y Frac ZFSS   Z-score
> >1  0.719  0.122  0.890 2181.4 46.35
> >
> >Top 1 translations before clustering will be rescored
> >Calculating Likelihood for TF SET #1 of 1 TRIAL #1 of 1
> >0% 100%
> >|==| DONE
> >
> >Packing LLG Translations: pass 1 of 11...
> >   1 peaks
> >   No peaks over 1878.46 - no packing check
> >Packing LLG Translations: pass 2 of 11...
> >   1 peaks
> >   1 peaks over 1878.46 checked for packing
> >   Translation peak 1 first to be kept
> >   Done
> >   Exit: found a peak that packs
> >
> > -==
> >
> > *** AND THEN ***
> > 
> --
> > Advisory: The top solution from a TF rescoring did not pack
> > 
> --
> >
>

Re: [ccp4bb] doubt regarding MR search model

2017-09-18 Thread Randy Read 
Yes, I can see how that message would be confusing!

This comes from a new feature.  Phaser now does a relatively liberal packing 
test as part of rescoring the fast translation results with the full likelihood 
function.  Peaks that are rejected at this stage aren’t counted for the top 
peak height used to define the cutoff for what is stored for the proper packing 
test and eventual rigid-body refinement.  This turns out to be very useful for 
models that are small fragments, particularly helices in Arcimboldo, where the 
initial searches tend to put molecules on top of symmetry axes.

The confusing part is that you get the advisory even if the particular 
translation search where a peak was rejected didn’t even yield a score as high 
as the one that ended up being chosen.

The bit in the log file about increasing the composition suggests that what is 
in your model has more scattering matter than what you defined for the 
corresponding part of the structure in the composition definition.  If the 
change wasn’t big, you don’t need to worry, but if there was a big discrepancy 
it’s worth sorting out where it comes from.

Finally, I would suspect that getting a significantly lower LLG for two copies 
of a dimer means that the dimer in your structure is slightly different from 
the dimer in the model.

Best wishes,

Randy Read

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

> On 18 Sep 2017, at 16:24, Andrew Leslie  wrote:
> 
> Regarding the warning message "The top solution from a TF rescoring did not 
> pack”, I get this on all the PHASER jobs that I have run recently, but 
> looking through the PHASER log file I cannot see any evidence for packing 
> failure.
> 
> It may be that the failure is buried in an obscure place in the very long log 
> file, but if I search for “pack” then I get the output summarised below, all 
> of which, apart from the ADVISORY, suggests to me that there is no problem at 
> all with the packing.
> 
> Perhaps someone on the PHASER team can cast light on this.
> 
> Andrew
> 
> 
> Extracts from PHASER log file:
> 
> 
> TRANSLATION FUNCTIONS
> -
> 
>Target Function: FAST LETF1
>Translation Packing Function applied: top peak will pack
>Translation Packing Cutoff: 50%
>Sampling:  1.82 Angstroms
> 
> 
> ===
> 
> PACKING FUNCTION
> 
> 
>There are 4 solutions to pack
>Packing analysis
>0%100%
>|=| DONE
> 
> 
>Packing Table
>-
>Solutions accepted if pairwise clashes less than 10 % of trace atoms
>#in  #out Clash-% Symm TF-SET  ROT TFpk#TFTFZSpaceGroup 
>1Top1  0.741  --   1 11325.94 26.03  P 1
>22 1.058  --   1 21293.29 24.34  P 1
>33 0.952  --   1 31245.70 21.88  P 1
>44 0.847  --   1 41211.49 20.11  P 1
> 
>4 accepted of 4 solutions
>   4 pack of 4 accepted solutions
> 
> ==
> ---
> TRANSLATION PACKING
> ---
> 
>Translation Packing Cutoff: 50%
>All solutions have been packed
> 
> ==
>Packing Fast Search Translations...
>   9871 peaks
>   500 peaks over 1049.74 checked for packing
>   Translation peak 1 first to be kept
>   Done
> 
> 
>New Top Packing Fast Translation Function FSS = 2181.37 (TFZ=46.3) at 
> Trial #1
> 
> 
>Top Peaks Without Clustering
>Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
>There was 1 site over 67.5% of top
>1 peak selected
>The sites over 67.5% are:
># Frac X Frac Y Frac ZFSS   Z-score
>1  0.719  0.122  0.890 2181.4 46.35
> 
>Top 1 translations before clustering will be rescored
>Calculating Likelihood for TF SET #1 of 1 TRIAL #1 of 1
>0% 100%
>|==| DONE
> 
>Packing LLG Translations: pass 1 of 11...
>   1 peaks
>   No peaks over 1878.46 - no packing check
>Packing LLG Translations: pass 2 of 11...
>   1 peaks
>   1 peaks over 1878.46 checked for packing
>   Translation peak 1 first to be kept
>   Done
>   Exit: found a peak that packs
> 
> -==
> 
> *** AND THEN ***
> --
> Advisory: The top solution from a TF rescoring did not pack
>

Re: [ccp4bb] doubt regarding MR search model

2017-09-18 Thread Andrew Leslie 
Regarding the warning message "The top solution from a TF rescoring did not 
pack”, I get this on all the PHASER jobs that I have run recently, but looking 
through the PHASER log file I cannot see any evidence for packing failure.

It may be that the failure is buried in an obscure place in the very long log 
file, but if I search for “pack” then I get the output summarised below, all of 
which, apart from the ADVISORY, suggests to me that there is no problem at all 
with the packing.

Perhaps someone on the PHASER team can cast light on this.

Andrew


Extracts from PHASER log file:


TRANSLATION FUNCTIONS
-

   Target Function: FAST LETF1
   Translation Packing Function applied: top peak will pack
   Translation Packing Cutoff: 50%
   Sampling:  1.82 Angstroms


===

PACKING FUNCTION


   There are 4 solutions to pack
   Packing analysis
   0%100%
   |=| DONE


   Packing Table
   -
   Solutions accepted if pairwise clashes less than 10 % of trace atoms
   #in  #out Clash-% Symm TF-SET  ROT TFpk#TFTFZSpaceGroup 
   1Top1  0.741  --   1 11325.94 26.03  P 1
   22 1.058  --   1 21293.29 24.34  P 1
   33 0.952  --   1 31245.70 21.88  P 1
   44 0.847  --   1 41211.49 20.11  P 1

   4 accepted of 4 solutions
  4 pack of 4 accepted solutions

==
---
TRANSLATION PACKING
---

   Translation Packing Cutoff: 50%
   All solutions have been packed

==
   Packing Fast Search Translations...
  9871 peaks
  500 peaks over 1049.74 checked for packing
  Translation peak 1 first to be kept
  Done


   New Top Packing Fast Translation Function FSS = 2181.37 (TFZ=46.3) at Trial 
#1


   Top Peaks Without Clustering
   Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
   There was 1 site over 67.5% of top
   1 peak selected
   The sites over 67.5% are:
   # Frac X Frac Y Frac ZFSS   Z-score
   1  0.719  0.122  0.890 2181.4 46.35

   Top 1 translations before clustering will be rescored
   Calculating Likelihood for TF SET #1 of 1 TRIAL #1 of 1
   0% 100%
   |==| DONE

   Packing LLG Translations: pass 1 of 11...
  1 peaks
  No peaks over 1878.46 - no packing check
   Packing LLG Translations: pass 2 of 11...
  1 peaks
  1 peaks over 1878.46 checked for packing
  Translation peak 1 first to be kept
  Done
  Exit: found a peak that packs

-==

*** AND THEN ***
--
Advisory: The top solution from a TF rescoring did not pack
--


-==
-

> On 18 Sep 2017, at 15:06, Eleanor Dodson  wrote:
> 
> You need to provide a bit more information.
> 
> First of all about the data processing..
> 
> Is the space group correct?
> ways of being misled are:
> Non-crystallographic translations with a shift of ~0.5 along an axis - say a. 
>  This will generate absences in the odd h 0 0 reflections and can make the 
> space group appear to be P 21 21 21 whilst it is really P 2 21 21..
> 
> Perfect twinning can have the same effect. In an orthorhombix space group 
> this can usually only occur if two axes have approximately the same length, 
> but the data processing stats can indicate if that is the case.
> 
> Then - re PHASER. The packing rejection criteria may be set too severely - 
> that seems the case for your solution.
> 
> Best check on any MR solution is: does it refine - give it 20 cycles of 
> mindless refinement and see if the R and FreeR go down.
> 
> Then look at the maps and see if there are obvious corrections to be made..
> 
> Eleanor
> 
> On 18 September 2017 at 14:59, Satvik Kumar  > wrote:
> Dear Crystallographers,
> 
> I am trying to solve a structure in the space group P212121. Based on 
> Matthews coefficient, there are 4 molecules in the asymmetric unit.
> 
> Based on my limited reading about using of Phaser, I understand that a single 
> chain should be used as search model even though many copies are present in 
> asymmetric unit. Am I correct?
> 
> So when I use a single chain as search model and ask Phaser to search for 4 
> molecules, Phaser identifies a single solution with a warning "The top 
> solution from a TF rescoring did not pack" and a warning "Search request 
> requires more scattering than defined in composition. Composition increased 
> to accommodate search components". But the final values reported "PAK=2 
> LLG=1065 TFZ==22.6" indicate that phas

Re: [ccp4bb] doubt regarding MR search model

2017-09-18 Thread Eleanor Dodson 
You need to provide a bit more information.

First of all about the data processing..

Is the space group correct?
ways of being misled are:
Non-crystallographic translations with a shift of ~0.5 along an axis - say
a.  This will generate absences in the odd h 0 0 reflections and can make
the space group appear to be P 21 21 21 whilst it is really P 2 21 21..

Perfect twinning can have the same effect. In an orthorhombix space group
this can usually only occur if two axes have approximately the same length,
but the data processing stats can indicate if that is the case.

Then - re PHASER. The packing rejection criteria may be set too severely -
that seems the case for your solution.

Best check on any MR solution is: does it refine - give it 20 cycles of
mindless refinement and see if the R and FreeR go down.

Then look at the maps and see if there are obvious corrections to be made..

Eleanor

On 18 September 2017 at 14:59, Satvik Kumar  wrote:

> Dear Crystallographers,
>
> I am trying to solve a structure in the space group P212121. Based on
> Matthews coefficient, there are 4 molecules in the asymmetric unit.
>
> Based on my limited reading about using of Phaser, I understand that a
> single chain should be used as search model even though many copies are
> present in asymmetric unit. Am I correct?
>
> So when I use a single chain as search model and ask Phaser to search for
> 4 molecules, Phaser identifies a single solution with a warning "The top
> solution from a TF rescoring did not pack" and a warning "Search request
> requires more scattering than defined in composition. Composition
> increased to accommodate search components". But the final values reported 
> "PAK=2
> LLG=1065 TFZ==22.6" indicate that phaser has solved the problem.
>
> Can anyone please explain the meaning of the warning.
>
> When I inspect the arrangement of the chains (attachment), I observe
> minimal contact between the chains and a large cavity in the center. Can a
> crystal form this way?
>
> I have also tried using the dimer as search model and asking phaser to
> search for 2 molecules. Even in this case, Phaser finds a single solution
> but the warning and the advisory still appear as before. The numbers
> reported reduce a bit to "PAK=1 LLG=722 TFZ==29.2".
>
> Please help me in understanding these results.
>
> Thanks,
> Satvik
>
>
>