Re: [ccp4bb] Phaser 2.8.3: Hendrickson-Lattman coefficients generated from dataset lacking anomalous signal

[Eleanor Dodson]

If I remember  for coefficients with FOM and a precise PHI calculated, A =
FOM*cos(phi) B = FOM*sin(phi) C=D=0

If you have a probability curve for PHI. 0 to 360  such as you get from
experimental phasing, A B C D mirror this bimodal curve better ..


On Fri, 9 Feb 2024 at 09:58, Nitin Kulhar <
9dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear sir
>
> Thank you for clearing that. I checked back to see that HLC/D are
> invariably 0 for all reflections, with the non-zero HLA/B supposedly having
> been originated from the probability distribution of phases *calculated*
> by phaser. Hopefully, I have not misunderstood it.
>
> Thanks and regards
> Nitin Kulhar
>
> On Thu, Feb 8, 2024 at 9:07 PM Randy John Read  wrote:
>
>> Hi,
>>
>> Hendrickson-Lattman coefficients are just a way of storing phase
>> probability information, and they can come from different sources including
>> atomic models. Phaser puts in HL coefficients because they could be handy
>> under some circumstances for combining the phase information from
>> experimental phasing. You might notice that only A and B are non-zero for
>> the molecular replacement HL coefficients. That’s because the phase
>> probability distribution is unimodal for calculated phases, whereas it’s
>> generally bimodal for experimental phases (thus requiring more
>> coefficients).
>>
>> Best wishes,
>>
>> Randy Read
>>
>> > On 8 Feb 2024, at 14:32, Nitin Kulhar <
>> 9dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote:
>> >
>> > Dear all
>> >
>> > Is anomalous diffraction necessary for determining experimental phases
>> and the Hendrickson-Lattman coefficients (HLA, HLB, HLC, and HLD)?
>> >
>> > MR solution from Phaser 2.8.3 (interfaced in ccp4 8.0.000 suite) seems
>> to be generating HLA/B/C/D coefficients from an x-ray diffraction dataset.
>> >
>> > Wavelength:
>> > 1.54179 Angstrom.
>> >
>> > Sample:
>> > •
>> > Protein-small molecule ligand complex crystal.
>> > • No anomalous scatterer in the protein, the ligand, or the
>> crystallization condition.
>> >
>> > Data reduction:
>> > Xtriage and aimless analyses did not indicate significant anomalous
>> signal.
>> >
>> > I would appreciate any help in understanding the reasons for these
>> observations.
>> >
>> > Thanks and regards
>> > Nitin Kulhar
>> > PhD student
>> > c/o Dr Rajakumara Eerappa
>> > Macromolecular Structural Biology Lab
>> > Department of Biotechnology
>> > Indian Institute of Technology Hyderabad
>> > Kandi, Sangareddy
>> > Telangana, India - 502284
>> >
>> > Disclaimer:- This footer text is to convey that this email is sent by
>> one of the users of IITH. So, do not mark it as SPAM.
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>> -
>> Randy J. Read
>> Department of Haematology, University of Cambridge
>> Cambridge Institute for Medical Research Tel: +44 1223 336500
>> The Keith Peters Building
>> Hills Road   E-mail:
>> rj...@cam.ac.uk
>> Cambridge CB2 0XY, U.K.
>> www-structmed.cimr.cam.ac.uk
>>
>>
> Disclaimer:- This footer text is to convey that this email is sent by one
> of the users of IITH. So, do not mark it as SPAM.
>
> --
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Re: [ccp4bb] Phaser 2.8.3: Hendrickson-Lattman coefficients generated from dataset lacking anomalous signal

[Nitin Kulhar]

Dear sir

Thank you for clearing that. I checked back to see that HLC/D are
invariably 0 for all reflections, with the non-zero HLA/B supposedly having
been originated from the probability distribution of phases *calculated* by
phaser. Hopefully, I have not misunderstood it.

Thanks and regards
Nitin Kulhar

On Thu, Feb 8, 2024 at 9:07 PM Randy John Read  wrote:

> Hi,
>
> Hendrickson-Lattman coefficients are just a way of storing phase
> probability information, and they can come from different sources including
> atomic models. Phaser puts in HL coefficients because they could be handy
> under some circumstances for combining the phase information from
> experimental phasing. You might notice that only A and B are non-zero for
> the molecular replacement HL coefficients. That’s because the phase
> probability distribution is unimodal for calculated phases, whereas it’s
> generally bimodal for experimental phases (thus requiring more
> coefficients).
>
> Best wishes,
>
> Randy Read
>
> > On 8 Feb 2024, at 14:32, Nitin Kulhar <
> 9dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote:
> >
> > Dear all
> >
> > Is anomalous diffraction necessary for determining experimental phases
> and the Hendrickson-Lattman coefficients (HLA, HLB, HLC, and HLD)?
> >
> > MR solution from Phaser 2.8.3 (interfaced in ccp4 8.0.000 suite) seems
> to be generating HLA/B/C/D coefficients from an x-ray diffraction dataset.
> >
> > Wavelength:
> > 1.54179 Angstrom.
> >
> > Sample:
> > •
> > Protein-small molecule ligand complex crystal.
> > • No anomalous scatterer in the protein, the ligand, or the
> crystallization condition.
> >
> > Data reduction:
> > Xtriage and aimless analyses did not indicate significant anomalous
> signal.
> >
> > I would appreciate any help in understanding the reasons for these
> observations.
> >
> > Thanks and regards
> > Nitin Kulhar
> > PhD student
> > c/o Dr Rajakumara Eerappa
> > Macromolecular Structural Biology Lab
> > Department of Biotechnology
> > Indian Institute of Technology Hyderabad
> > Kandi, Sangareddy
> > Telangana, India - 502284
> >
> > Disclaimer:- This footer text is to convey that this email is sent by
> one of the users of IITH. So, do not mark it as SPAM.
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> -
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: +44 1223 336500
> The Keith Peters Building
> Hills Road   E-mail:
> rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
>

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Re: [ccp4bb] Phaser 2.8.3: Hendrickson-Lattman coefficients generated from dataset lacking anomalous signal

[Randy John Read]

Hi,

Hendrickson-Lattman coefficients are just a way of storing phase probability 
information, and they can come from different sources including atomic models. 
Phaser puts in HL coefficients because they could be handy under some 
circumstances for combining the phase information from experimental phasing. 
You might notice that only A and B are non-zero for the molecular replacement 
HL coefficients. That’s because the phase probability distribution is unimodal 
for calculated phases, whereas it’s generally bimodal for experimental phases 
(thus requiring more coefficients).

Best wishes,

Randy Read

> On 8 Feb 2024, at 14:32, Nitin Kulhar 
> <9dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Dear all
> 
> Is anomalous diffraction necessary for determining experimental phases and 
> the Hendrickson-Lattman coefficients (HLA, HLB, HLC, and HLD)?
> 
> MR solution from Phaser 2.8.3 (interfaced in ccp4 8.0.000 suite) seems to be 
> generating HLA/B/C/D coefficients from an x-ray diffraction dataset.
> 
> Wavelength: 
> 1.54179 Angstrom. 
> 
> Sample: 
> • 
> Protein-small molecule ligand complex crystal. 
> • No anomalous scatterer in the protein, the ligand, or the 
> crystallization condition.
> 
> Data reduction:
> Xtriage and aimless analyses did not indicate significant anomalous signal. 
> 
> I would appreciate any help in understanding the reasons for these 
> observations.
> 
> Thanks and regards
> Nitin Kulhar
> PhD student
> c/o Dr Rajakumara Eerappa
> Macromolecular Structural Biology Lab
> Department of Biotechnology
> Indian Institute of Technology Hyderabad
> Kandi, Sangareddy
> Telangana, India - 502284
> 
> Disclaimer:- This footer text is to convey that this email is sent by one of 
> the users of IITH. So, do not mark it as SPAM. 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk




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[ccp4bb] Phaser 2.8.3: Hendrickson-Lattman coefficients generated from dataset lacking anomalous signal

[Nitin Kulhar]

Dear all

Is anomalous diffraction necessary for determining experimental phases and
the Hendrickson-Lattman coefficients (HLA, HLB, HLC, and HLD)?

MR solution from Phaser 2.8.3 (interfaced in ccp4 8.0.000 suite) seems to
be generating HLA/B/C/D coefficients from an x-ray diffraction dataset.

Wavelength:
1.54179 Angstrom.

Sample:

   1. Protein-small molecule ligand complex crystal.
   2. No anomalous scatterer in the protein, the ligand, or the
   crystallization condition.

Data reduction:
Xtriage and aimless analyses did not indicate significant anomalous signal.

I would appreciate any help in understanding the reasons for these
observations.

Thanks and regards
Nitin Kulhar
PhD student
c/o Dr Rajakumara Eerappa
Macromolecular Structural Biology Lab
Department of Biotechnology
Indian Institute of Technology Hyderabad
Kandi, Sangareddy
Telangana, India - 502284

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Re: [ccp4bb] phaser-MR warning

[Paul Emsley]

On 31/03/2021 04:37, rohit kumar wrote:
I tried to remove H atoms in pdbcur in ccp4 but still there are lots of HD and HH atoms present in the pdb. 
Could anyone please suggest how to fix this problem.


PDBCUR would want to use the element column in order to identify that the atom 
is a Hydrogen atom.
And that's what's missing. One wonders why.

You can do a grep:

$ egrep -v ' HD| HH..| HH. ' input.pdb > selected.pdb

Paul.



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Re: [ccp4bb] Phaser Warning Message

[Randy Read]

Thanks to Damian for the clear explanation!

Just a bit more background.  Airlie put this feature in because, with small 
fragments such as helices (which our collaborator Isabel Usón uses in 
ARCIMBOLDO), the initial translation function scores are often higher for 
trials where symmetry-related copies are superimposed, and better solutions 
were otherwise being excluded because they had much lower scores than these 
deceptive ones.  The advisory is printed out so that the user can be aware this 
is happening, in case what you need to do (as Damian says) is to go back and 
edit out a part of your model.

This case turns out to be interesting.  Before the structure has been solved, 
it’s not clear whether the space group is P6522 or its mirror image, P6122.  
Although P6122 is the answer, P6522 is tested first.  In the translation 
search, there will be peaks where part of the structure is right (the molecules 
related by the symmetry operators shared by the two space groups) so the 
likelihood score is much better than random, but the incorrect symmetry will 
lead to clashes.  The advisories come from the translation searches in P6522, 
and then much better scores without serious clashes are found in P6122.

Thanks for sharing the log file so we could see what is going on!

Best wishes,

Randy Read

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters 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 16 Jun 2020, at 22:40, Damian Ekiert  wrote:
> 
> Hi Silvia,
> 
> Looking at the end of the log file, it looks like you have a very clear 
> solution and are ready to go!
> 
> This message means that a better solution from the Fast Translation Function 
> was excluded because it failed the packing test (too many clashes with 
> neighboring molecules). Sometimes this will prevent you from getting a usable 
> solution altogether, and this message would clue you into that. In such a 
> situation, you could prune flexible/non-conserved loops from your protein and 
> try MR again with the truncated model.
> 
> But in this case, your still managed to get a very clear solution, so I think 
> you are ready to look at your maps and begin rebuilding and refinement.
> 
> Good luck!
> 
> Best,
> 
> Damian
> 
>> On Jun 16, 2020, at 4:47 PM, Napolitano Silvia 
>>  wrote:
>> 
>> 
>> Dear ccp44 Bulletin Board,
>> 
>> I am trying to solve a structure by molecular replacement.
>> I am doing that by using PhaserMR (simple one-component interface).
>> 
>> I tried out setting up different parameters (e.g.changing # of components, 
>> #search, different space group search settings...), no matter what I try I 
>> always get this warning message:
>> 
>> --
>> Advisory: The top solution from a FTF did not pack
>> --
>> 
>> --
>> Advisory: The top solution from a TF rescoring did not pack
>> 
>> (please, see log file attached).
>> 
>> What does this Warning mean? I tried to look it up online but, 
>> unfortunately, I could not find the answer I was looking for.
>> 
>> Please, let me know if you need more detailed information.
>> 
>> Many thanks in advance for your help and your time!
>> 
>> Best Regards
>> 
>> Silvia
>> 
>> Silvia Napolitano
>> ETH Zurich
>> Institute of Molecular Biology and Biophysics
>> Otto-Stern-Weg 5, HPK E14
>> CH–8093 Zurich
>> Phone: +41 44 6332482
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>> 
> 
> 
> 
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Re: [ccp4bb] Phaser Warning Message

[Damian Ekiert]

Hi Silvia,

Looking at the end of the log file, it looks like you have a very clear 
solution and are ready to go!

This message means that a better solution from the Fast Translation Function 
was excluded because it failed the packing test (too many clashes with 
neighboring molecules). Sometimes this will prevent you from getting a usable 
solution altogether, and this message would clue you into that. In such a 
situation, you could prune flexible/non-conserved loops from your protein and 
try MR again with the truncated model.

But in this case, your still managed to get a very clear solution, so I think 
you are ready to look at your maps and begin rebuilding and refinement.

Good luck!

Best,

Damian

> On Jun 16, 2020, at 4:47 PM, Napolitano Silvia 
>  wrote:
> 
>  
> Dear ccp44 Bulletin Board,
>  
> I am trying to solve a structure by molecular replacement.
> I am doing that by using PhaserMR (simple one-component interface).
>  
> I tried out setting up different parameters (e.g.changing # of components, 
> #search, different space group search settings...), no matter what I try I 
> always get this warning message:
>  
> --
> Advisory: The top solution from a FTF did not pack
> --
>  
> --
> Advisory: The top solution from a TF rescoring did not pack
>  
> (please, see log file attached).
>  
> What does this Warning mean? I tried to look it up online but, unfortunately, 
> I could not find the answer I was looking for.
>  
> Please, let me know if you need more detailed information.
>  
> Many thanks in advance for your help and your time!
>  
> Best Regards
>  
> Silvia
>  
> Silvia Napolitano
> ETH Zurich
> Institute of Molecular Biology and Biophysics
> Otto-Stern-Weg 5, HPK E14
> CH–8093 Zurich
> Phone: +41 44 6332482
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 



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Re: [ccp4bb] Phaser MR pairwise percent packing criterion

[Randy Read]

Hi,

The old approach of counting the number of clashes was changed to the 
percentage of trace atoms (typically CA atoms) involved in clashes largely 
because, as people like Eleanor pointed out to us, the number of clashes grows 
with the size of the problem and solutions can be rejected when the fraction of 
the structure involved in clashes is still very small.  The default now is to 
accept up to 10% of the trace atoms being involved in clashes.  So increasing 
that to a larger number should have the same basic effect as increasing the 
number of allowed clashes did in the old version.

If you want to get sophisticated, there's even another new feature, where you 
can use the ENSEMBLE…TRACE command to define a TRACE molecule.  That will be 
carried along with the actual search model and used to check for clashes.  This 
might be useful if, for instance, you think a domain might change  conformation 
slightly so you don't want it in the search model, but you want to exclude 
solutions that would create clashes with that domain.

Best wishes,

Randy Read

> On 17 Feb 2017, at 08:28, Xiao Lei  wrote:
> 
> Dear CCP4bb members,
> 
> I found in the newer CCP4 Phaser MR version (I use CCP4 7.0.0 in Win7), there 
> is no "allow maximal clash..." option anymore. There are only two options 
> "pairwise percent packing" and "accept all solutions".  I used to increase 
> the number in the "allow maximal clash" (let's say from 100 to 200) to do MR 
> and this works fine in a couple of cases.
> 
> With the new Phaser version, I could not do this anymore, can I understand 
> that I just need to increase the pairwise percent packing cutoff (let's say 
> from 5% to 10%) to loose the tight packing criteria and allow more clashes in 
> finding solutions? 
> 
> 

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

[ccp4bb] Phaser MR pairwise percent packing criterion

[Xiao Lei]

Dear CCP4bb members,

I found in the newer CCP4 Phaser MR version (I use CCP4 7.0.0 in Win7),
there is no "allow maximal clash..." option anymore. There are only two
options "pairwise percent packing" and "accept all solutions".  I used to
increase the number in the "allow maximal clash" (let's say from 100 to
200) to do MR and this works fine in a couple of cases.

With the new Phaser version, I could not do this anymore, can I understand
that I just need to increase the pairwise percent packing cutoff (let's say
from 5% to 10%) to loose the tight packing criteria and allow more clashes
in finding solutions?

Re: [ccp4bb] phaser

[Randy Read]

Hi,

The syntax of the PACK command has changed, but the commands generated by the 
GUI have also changed in synch, so this problem shouldn't normally arise.

Our best guess is that the user is attempting to rerun an old job, and ccp4i is 
getting confused when trying to interpret the saved old GUI variables in terms 
of the new possibilities.  Checking through the GUI for a PACK choice that has 
been toggled without a valid choice being made might fix it, or alternatively 
the user could set up the whole job from scratch.

If that doesn't explain the problem, please get in touch directly with us!

Best wishes,

Randy Read

> On 6 Jan 2017, at 14:01, Sidhu, Khushwant (Dr.)  
> wrote:
> 
> Dear all,
>  
> A user has upgraded to ccp4-7 on her Mac. Previously phaser was running fine.
> She is now getting the following error. Could somebody help ?
>  
> The error log is attached.
>  
> Regards
>  
> Sid
>  
>  
>  
> 
>  
> Dr Khushwant Sidhu
> Senior Experimental Officer / I. T. Professional
>  
> Department of Molecular and Cell Biology, 
> 1/61 Henry Wellcome Building , University of Leicester, 
> Lancaster Road, 
> Leicester,
> LE1 7RH
>  
> T: 0116 229 7237
> E: k.si...@le.ac.uk 
> 
> Elite without being elitist
> Follow us on Twitter  or visit our 
> Facebook  page
>  
>  
> <20_phaser_MR[2][3].log>

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

Re: [ccp4bb] Phaser: tNCS present but correction not applied

[Eleanor Dodson]

That is a very high nTCS vector (78% of the origin. Are you sure your unit
cell isny doubled
ie cell is not 94.2073 148.003 72.9967 90 97.6686 90

But
47.136 148 7390 98 90
What does pointless suggest for theSG

Eleanor



On 26 November 2016 at 18:56, KAUSHIK H.S. <
02b42c18251e-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear Dr. Read,
>
> For the first time, Phaser gave the following warning.
> XXX
> Warning: Input/Default tNCS NMOL (2) does not match suggested NMOL (4):
> Please check cell content analysis and tNCS to confirm NMOL
>
> Warning: tNCS is present but correction factors NOT applied
> XXX
>
> Hence, I set NMOL=4 (under other setting using the Phenix GUI of Phaser)
> following which, only the second Warning message was displayed.  The LLG
> and TFZ scores remained the same in both the cases.  The warnings remain
> the same when I try to place more protomers in the ASU.
>
> XXX
> Warning: tNCS is present but correction factors NOT applied
> XXX
>
>
> However, I found the following message from the log file:
> 
> Large non-origin Patterson peaks indicate that multiple tNCS vectors are
> present
>Please analyse peaks for NMOL multiplicity
>tNCS correction will NOT be applied
>   To activate tNCS correction, enter tNCS vector manually
> 
>
> I (think, I have) identified the t-vector (0.500 0.000 0.000) but, don't
> know what parameters of Phaser to tweak with.  Any suggestions or pointers
> to related papers could be very helpful.
>
> I have a similar problem with another dataset of a different protein which
> is nearly cylindrical.
>
> Thank,
> Kaushik
>
>
> On Saturday, 26 November 2016 11:46 PM, Randy Read 
> wrote:
>
>
> Hi,
>
> That message should mean that you didn't ask for a number of molecules
> divisible by the order of the tNCS. With that vector you need to search for
> an even number of copies.
>
> Let me know if that doesn't explain what you're saying.
>
> Best wishes,
> Randy Read
>
> 
> Randy J. Read
>
> On 25 Nov 2016, at 21:27, KAUSHIK H.S. <02b42c18251e-dmarc-
> requ...@jiscmail.ac.uk> wrote:
>
> Hello,
>
> I have a crystal in C2 spacegroup (94.2073 148.003 72.9967 90 97.6686 90)
> and Xtriage predicts 923 residues in ASU.  My protein could be anywhere
> between 95 to 110 residues long (assuming the terminals could be cleaved).
> Using a homolog, Phaser gives me a solution with LLG=1072 and TFZ=45.
> Molrep placed 4 protomers in the ASU however, the crystal packing is poor.
>
> I understand from Phaser that the tNCS is not accounted for (because the
> structure is linear?).  Is there a way the exact location of the tNCS
> related protomers be predicted using information from SfCheck and Xtriage?
>
> Xtriage information:
> Fraqc. coord. : 0.500 0.000 0.000
> Distance to origin: 47.104
> Height relative to origin: 79.688%
> p_value(height) : 5.283e-07
>
> SFCHECK:
> Pseudo-translation is detected: 62.6%
> Pseudo-translation vector: 0.500 0.000 0.000
>
> Sorry if my question is too naive.
>
> Thanks in advance,
> Kaushik Hatti,
> Molecular Biophysics Unit,
> Indian Institute of Science,
> India.
>
>
>
>

Re: [ccp4bb] Phaser: tNCS present but correction not applied

[KAUSHIK H.S.]

Dear Dr. Read,
For the first time, Phaser gave the following warning.XXXWarning: 
Input/Default tNCS NMOL (2) does not match suggested NMOL (4): Please check 
cell content analysis and tNCS to confirm NMOL
Warning: tNCS is present but correction factors NOT applied
XXX
Hence, I set NMOL=4 (under other setting using the Phenix GUI of Phaser) 
following which, only the second Warning message was displayed.  The LLG and 
TFZ scores remained the same in both the cases.  The warnings remain the same 
when I try to place more protomers in the ASU.
XXX Warning: tNCS is present but correction factors NOT appliedXXX

However, I found the following message from the log file:Large 
non-origin Patterson peaks indicate that multiple tNCS vectors are present   
Please analyse peaks for NMOL multiplicity   tNCS correction will NOT be 
applied      To activate tNCS correction, enter tNCS vector manually
I (think, I have) identified the t-vector (0.500 0.000 0.000) but, don't know 
what parameters of Phaser to tweak with.  Any suggestions or pointers to 
related papers could be very helpful.
I have a similar problem with another dataset of a different protein which is 
nearly cylindrical. 
Thank,Kaushik

On Saturday, 26 November 2016 11:46 PM, Randy Read  wrote:
 

 Hi,
That message should mean that you didn't ask for a number of molecules 
divisible by the order of the tNCS. With that vector you need to search for an 
even number of copies.
Let me know if that doesn't explain what you're saying. 
Best wishes,Randy Read 


Randy J. Read
On 25 Nov 2016, at 21:27, KAUSHIK H.S. 
<02b42c18251e-dmarc-requ...@jiscmail.ac.uk> wrote:


Hello,
I have a crystal in C2 spacegroup (94.2073 148.003 72.9967 90 97.6686 90) and 
Xtriage predicts 923 residues in ASU.  My protein could be anywhere between 95 
to 110 residues long (assuming the terminals could be cleaved).  Using a 
homolog, Phaser gives me a solution with LLG=1072 and TFZ=45.  Molrep placed 4 
protomers in the ASU however, the crystal packing is poor.
I understand from Phaser that the tNCS is not accounted for (because the 
structure is linear?).  Is there a way the exact location of the tNCS related 
protomers be predicted using information from SfCheck and Xtriage?  

Xtriage information:Fraqc. coord. : 0.500 0.000 0.000Distance to origin: 
47.104Height relative to origin: 79.688%p_value(height) : 5.283e-07
SFCHECK:
Pseudo-translation is detected: 62.6%Pseudo-translation vector: 0.500 0.000 
0.000
Sorry if my question is too naive.
Thanks in advance,Kaushik Hatti,Molecular Biophysics Unit,Indian Institute of 
Science,India.




   

Re: [ccp4bb] Phaser: tNCS present but correction not applied

[Randy Read]

Hi,

That message should mean that you didn't ask for a number of molecules 
divisible by the order of the tNCS. With that vector you need to search for an 
even number of copies.

Let me know if that doesn't explain what you're saying. 

Best wishes,
Randy Read 


Randy J. Read

> On 25 Nov 2016, at 21:27, KAUSHIK H.S. 
> <02b42c18251e-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hello,
> 
> I have a crystal in C2 spacegroup (94.2073 148.003 72.9967 90 97.6686 90) and 
> Xtriage predicts 923 residues in ASU.  My protein could be anywhere between 
> 95 to 110 residues long (assuming the terminals could be cleaved).  Using a 
> homolog, Phaser gives me a solution with LLG=1072 and TFZ=45.  Molrep placed 
> 4 protomers in the ASU however, the crystal packing is poor.
> 
> I understand from Phaser that the tNCS is not accounted for (because the 
> structure is linear?).  Is there a way the exact location of the tNCS related 
> protomers be predicted using information from SfCheck and Xtriage?  
> 
> Xtriage information:
> Fraqc. coord. : 0.500 0.000 0.000
> Distance to origin: 47.104
> Height relative to origin: 79.688%
> p_value(height) : 5.283e-07
> 
> SFCHECK:
> Pseudo-translation is detected: 62.6%
> Pseudo-translation vector: 0.500 0.000 0.000
> 
> Sorry if my question is too naive.
> 
> Thanks in advance,
> Kaushik Hatti,
> Molecular Biophysics Unit,
> Indian Institute of Science,
> India.
> 

[ccp4bb] Phaser: tNCS present but correction not applied

[KAUSHIK H.S.]

Hello,
I have a crystal in C2 spacegroup (94.2073 148.003 72.9967 90 97.6686 90) and 
Xtriage predicts 923 residues in ASU.  My protein could be anywhere between 95 
to 110 residues long (assuming the terminals could be cleaved).  Using a 
homolog, Phaser gives me a solution with LLG=1072 and TFZ=45.  Molrep placed 4 
protomers in the ASU however, the crystal packing is poor.
I understand from Phaser that the tNCS is not accounted for (because the 
structure is linear?).  Is there a way the exact location of the tNCS related 
protomers be predicted using information from SfCheck and Xtriage?  

Xtriage information:Fraqc. coord. : 0.500 0.000 0.000Distance to origin: 
47.104Height relative to origin: 79.688%p_value(height) : 5.283e-07
SFCHECK:
Pseudo-translation is detected: 62.6%Pseudo-translation vector: 0.500 0.000 
0.000
Sorry if my question is too naive.
Thanks in advance,Kaushik Hatti,Molecular Biophysics Unit,Indian Institute of 
Science,India.

[ccp4bb] Phaser solution and solvent content for arp warp

[xaravich ivan]

Hi everyone,
I think I have finally got a solution in Phaser (screen shot attached) as
the TFZ  is 10.
However the solution PDB has 30 molecules in it as the search model was an
NMR solution.
As I have 0.944 Angs resolution data pretty complete, I thought of building
the initial model in ArpWarp.
I prepared a new PDB file form the Phaser solution output with only one
molecule instead of 30. Prepared the sequence file in pir format for the
target. Now the wilson plot says B-factor of 3.66 and solvent content 0.98
even if I cut off the low resolution data to 8.0 from 20.0 and increase the
high resolution to 1.0.
Initially when I calculated the mathews coefficient it showed the best
estimate to be 2 molecules in the assymmetric unit.
Am I missing something again?

Thanks in advance,
Ivan

Re: [ccp4bb] Phaser solution and solvent content for arp warp

[Keller, Jacob]

Just throw your phaser-placed model into Buccaneer

JPK

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of xaravich 
ivan
Sent: Monday, June 29, 2015 3:10 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Phaser solution and solvent content for arp warp

Hi everyone,
I think I have finally got a solution in Phaser (screen shot attached) as the 
TFZ  is 10.
However the solution PDB has 30 molecules in it as the search model was an NMR 
solution.
As I have 0.944 Angs resolution data pretty complete, I thought of building the 
initial model in ArpWarp.
I prepared a new PDB file form the Phaser solution output with only one 
molecule instead of 30. Prepared the sequence file in pir format for the 
target. Now the wilson plot says B-factor of 3.66 and solvent content 0.98 even 
if I cut off the low resolution data to 8.0 from 20.0 and increase the high 
resolution to 1.0.
Initially when I calculated the mathews coefficient it showed the best estimate 
to be 2 molecules in the assymmetric unit.
Am I missing something again?

Thanks in advance,
Ivan

Re: [ccp4bb] Phaser solution and solvent content for arp warp

[Roger Rowlett]

I think I would be tempted to chainsaw one of the ensemble chains of 
2IT8 (they look very similar except for side-chain disposition) and use 
1 or 2 of these as search models in a Phaser run. If this works, you 
should see good Z-values and the final result inspected in Coot should 
show good molecular packing with clear solvent channels and no isolated 
molecules. Electron density should look reasonable, and if there are any 
known non-protein features (like metal ions) they should clearly show up 
in difference density.


If the initial Phaser solution looks OK in terms of packing, I would be 
tempted to take the phased generated and, using the sequence of your 
protein, subject it to auto-building with Parrot and Buccanner, using 
2-fold NCS (if you do in fact have 2 molecules in the ASU). With any 
luck, you should be able to auto-build 90% of your model. This approach 
worked for us for a medium resolution problem with 8-fold symmetry for a 
really marginal search model.


___
Roger S. Rowlett
Gordon  Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu

On 6/29/2015 3:10 PM, xaravich ivan wrote:

Hi everyone,
I think I have finally got a solution in Phaser (screen shot attached) 
as the TFZ  is 10.
However the solution PDB has 30 molecules in it as the search model 
was an NMR solution.
As I have 0.944 Angs resolution data pretty complete, I thought of 
building the initial model in ArpWarp.
I prepared a new PDB file form the Phaser solution output with only 
one molecule instead of 30. Prepared the sequence file in pir format 
for the target. Now the wilson plot says B-factor of 3.66 and solvent 
content 0.98 even if I cut off the low resolution data to 8.0 from 
20.0 and increase the high resolution to 1.0.
Initially when I calculated the mathews coefficient it showed the best 
estimate to be 2 molecules in the assymmetric unit.

Am I missing something again?

Thanks in advance,
Ivan

Re: [ccp4bb] Phaser going into infinite loop in Ample

[Dale Tronrud]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

   Thanks for all the help!

   We will restart the job with the KILL option as Jens suggested.

   We will also send a copy of the Phaser log file to Randy.  This is
not a case of Phaser simply trying harder - it is doing the same
search over and over again.  After four days the log file is getting
pretty long.  I may have to use DropBox.

   We considered trying ARCIMBOLDO but the resolution of the data did
not reach the 2.1 A limit usually suggested for that program.  If we
get AMPLE running, and it fails, we will give ARCIMBOLDO a try.

Dale Tronrud
Sarah Clark

On 4/22/2015 2:06 AM, Thomas, Jens wrote:
 Dear Dale,
 
 This is a known issue with AMPLE and will be fixed with the next
 release.
 
 In the meantime you can tell AMPLE to pass the KILL option that
 Randy mentions to PHASER, by adding the following arguments to your
 script:
 
 -mr_keys PKEY KILL TIME 360
 
 this will kill PHASER after 360 minutes (6 hours), which we've
 found if normally enough, although pick whatever time works for
 you,
 
 I should also point out that I think George is doing a disservice
 to SHELXE. In our last paper looking at coiled-coils, we saw
 successes at resolutions much lower than 2.1, in one case, AMPLE
 was able to solve a structure with a resolution of 2.9A:
 
 http://dx.doi.org/10.1107/S2052252515002080
 
 If you have any issues getting the KILL command to work, please
 feel free to contact me off-list.
 
 Best wishes,
 
 Jens
 
  From: CCP4 bulletin board
 [CCP4BB@JISCMAIL.AC.UK] on behalf of Randy Read [rj...@cam.ac.uk] 
 Sent: 22 April 2015 09:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re:
 [ccp4bb] Phaser going into infinite loop in Ample
 
 Hi Dale,
 
 It must actually be AMPLE deciding how many copies to search for.
 Phaser will give you some information about how consistent the
 specified composition is with the Matthews volume, but it just
 searches for the number of copies that it's instructed to look for.
 We haven't put the intelligence into it to correlate the model(s)
 with the composition information and try out different
 possibilities.  At the moment, we're leaving that level of analysis
 to pipelines like MRage.
 
 We're well aware of the tension between looking hard enough to find
 a solution in a difficult case and not throwing good CPU cycles
 after bad when it's hopeless.  We're gradually introducing new
 features to make these decisions better, but we do tend to prefer
 wasting CPU time to missing solutions.  However, we've introduced a
 couple of ways to limit the amount of time that Phaser spends
 pursuing very difficult or hopeless solutions, partly for the
 benefit of people such as the developers of Arcimboldo, AMPLE and
 the wide-search molecular replacement pipeline.  One is the KILL
 command, which is a rather blunt instrument saying to give up if a
 solution isn't found in a certain length of time.  In AMPLE, if you
 set quick mode, then the KILL time is set to 15 minutes.  Another
 option (which I don't think AMPLE uses) is the PURGE command, where
 you can say (for instance) that Phaser should pursue a maximum of
 25 partial solutions when adding the next component.
 
 If you're seeing an infinite loop, it would be handy if you could
 send me a copy of the logfile showing what is going on.  There have
 been some bugs leading to such infinite loops under some
 circumstances, and if you're running into one of those there's a
 good chance that it has been fixed in a recent nightly build of
 Phaser available through Phenix.  You can instruct CCP4 to use the
 Phaser executable from Phenix, and I think this should work fine in
 AMPLE, though I haven't tested it — I don't think any relevant
 syntax has changed.  It's been a while since we've had a new stable
 release of Phaser in either CCP4 or Phenix, so we're aiming to get
 one out in the not too distant future.
 
 All the best,
 
 Randy
 
 On 22 Apr 2015, at 05:56, Dale Tronrud de...@daletronrud.com
 wrote:
 
 
 We are having a problem with AMPLE and hope someone can help.
 
 The protein is about 70 amino acids long and we suspect it forms a 
 coiled-coil.  Our previous attempts at molecular replacement have 
 failed so we hoped that AMPLE, with its ability to generate a
 variety of potential models, would do the trick.
 
 Our problem is that all of our CPU cores are consumed by Phaser 
 jobs that are not making progress.  With this protein Phaser
 decides that it will look for 11 copies in the asymmetric unit.
 For a few of the possible ensembles it fails to find even one copy
 and gives up. That's fine with us.  For other ensembles it finds a
 handful of possible first positions, goes on to look for a second
 and fails, then goes back to try to place a second copy again.  We
 presume that the intent is to lower the acceptance criteria in the
 second pass, but in actuality Phaser simply repeats the same search
 that failed before and fails again

Re: [ccp4bb] Phaser going into infinite loop in Ample

[Randy Read]

Hi Dale,

It must actually be AMPLE deciding how many copies to search for.  Phaser will 
give you some information about how consistent the specified composition is 
with the Matthews volume, but it just searches for the number of copies that 
it's instructed to look for.  We haven't put the intelligence into it to 
correlate the model(s) with the composition information and try out different 
possibilities.  At the moment, we're leaving that level of analysis to 
pipelines like MRage.

We're well aware of the tension between looking hard enough to find a solution 
in a difficult case and not throwing good CPU cycles after bad when it's 
hopeless.  We're gradually introducing new features to make these decisions 
better, but we do tend to prefer wasting CPU time to missing solutions.  
However, we've introduced a couple of ways to limit the amount of time that 
Phaser spends pursuing very difficult or hopeless solutions, partly for the 
benefit of people such as the developers of Arcimboldo, AMPLE and the 
wide-search molecular replacement pipeline.  One is the KILL command, which is 
a rather blunt instrument saying to give up if a solution isn't found in a 
certain length of time.  In AMPLE, if you set quick mode, then the KILL time is 
set to 15 minutes.  Another option (which I don't think AMPLE uses) is the 
PURGE command, where you can say (for instance) that Phaser should pursue a 
maximum of 25 partial solutions when adding the next component.

If you're seeing an infinite loop, it would be handy if you could send me a 
copy of the logfile showing what is going on.  There have been some bugs 
leading to such infinite loops under some circumstances, and if you're running 
into one of those there's a good chance that it has been fixed in a recent 
nightly build of Phaser available through Phenix.  You can instruct CCP4 to use 
the Phaser executable from Phenix, and I think this should work fine in AMPLE, 
though I haven't tested it — I don't think any relevant syntax has changed.  
It's been a while since we've had a new stable release of Phaser in either CCP4 
or Phenix, so we're aiming to get one out in the not too distant future.

All the best,

Randy

 On 22 Apr 2015, at 05:56, Dale Tronrud de...@daletronrud.com wrote:
 
 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1
 
 
   We are having a problem with AMPLE and hope someone can help.
 
   The protein is about 70 amino acids long and we suspect it forms a
 coiled-coil.  Our previous attempts at molecular replacement have
 failed so we hoped that AMPLE, with its ability to generate a variety
 of potential models, would do the trick.
 
   Our problem is that all of our CPU cores are consumed by Phaser
 jobs that are not making progress.  With this protein Phaser decides
 that it will look for 11 copies in the asymmetric unit.  For a few of
 the possible ensembles it fails to find even one copy and gives up.
 That's fine with us.  For other ensembles it finds a handful of
 possible first positions, goes on to look for a second and fails, then
 goes back to try to place a second copy again.  We presume that the
 intent is to lower the acceptance criteria in the second pass, but in
 actuality Phaser simply repeats the same search that failed before and
 fails again.  The leads to an infinite loop.
 
   Once all the cores are occupied in this futile endeavor AMPLE makes
 no further progress.
 
   How can we get Phaser to either try harder to place a molecule or
 to give up?
 
   We are using CCP4 6.5.008 and the copy of Phaser that came with it.
 We used CCP4i to create a script which we modified slightly and ran
 using the at command.  The command is:
 
 /usr/local/ccp4-6.5/bin/ccp4-python -u /usr/local/ccp4-6.5/bin/ample
 - -mtz /user/sarah/xray/1Apr_Athena/SD6004_2_001_mergedunique14.mtz
 - -fasta /user/sarah/xray/1Apr_Athena/swaseq.fa -mr_sequence
 /user/sarah/xray/1Apr_Athena/swaseq.fa -nmodels 500 -name MVD0
 - -run_dir /home/sarah/AMPLE -nproc 6 -make_models True -rosetta_dir
 /usr/local/rosetta-3.5 -frags_3mers
 /user/sarah/xray/1Apr_Athena/aat000_03_05.200_v1_3 -frags_9mers
 /user/sarah/xray/1Apr_Athena/aat000_09_05.200_v1_3 -make_frags False
 - -F F -SIGF SIGF -FREE FreeR_flag  -early_terminate True   -use_shelxe
 True -shelx_cycles 15 -use_arpwarp False
 
 Any help is appreciated,
 Dale Tronrud
 Sarah Clark
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--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

Re: [ccp4bb] Phaser going into infinite loop in Ample

[George Sheldrick]

Dear Dale,

Isabel Uson's ARCIMBOLDO-LITE works well for coiled coils and has the 
same resolution
requirements (2.1A or better) as AMPLE because both use SHELXE to expand 
the solution.
It also employs PHASER to place a small fragment but it is often 
sufficient to let it search for

just two or three copies in the asymmetric unit.

Best wishes, George


On 04/22/2015 06:56 AM, Dale Tronrud wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1


We are having a problem with AMPLE and hope someone can help.

The protein is about 70 amino acids long and we suspect it forms a
coiled-coil.  Our previous attempts at molecular replacement have
failed so we hoped that AMPLE, with its ability to generate a variety
of potential models, would do the trick.

Our problem is that all of our CPU cores are consumed by Phaser
jobs that are not making progress.  With this protein Phaser decides
that it will look for 11 copies in the asymmetric unit.  For a few of
the possible ensembles it fails to find even one copy and gives up.
That's fine with us.  For other ensembles it finds a handful of
possible first positions, goes on to look for a second and fails, then
goes back to try to place a second copy again.  We presume that the
intent is to lower the acceptance criteria in the second pass, but in
actuality Phaser simply repeats the same search that failed before and
fails again.  The leads to an infinite loop.

Once all the cores are occupied in this futile endeavor AMPLE makes
no further progress.

How can we get Phaser to either try harder to place a molecule or
to give up?

We are using CCP4 6.5.008 and the copy of Phaser that came with it.
  We used CCP4i to create a script which we modified slightly and ran
using the at command.  The command is:

/usr/local/ccp4-6.5/bin/ccp4-python -u /usr/local/ccp4-6.5/bin/ample
- -mtz /user/sarah/xray/1Apr_Athena/SD6004_2_001_mergedunique14.mtz
- -fasta /user/sarah/xray/1Apr_Athena/swaseq.fa -mr_sequence
/user/sarah/xray/1Apr_Athena/swaseq.fa -nmodels 500 -name MVD0
- -run_dir /home/sarah/AMPLE -nproc 6 -make_models True -rosetta_dir
/usr/local/rosetta-3.5 -frags_3mers
/user/sarah/xray/1Apr_Athena/aat000_03_05.200_v1_3 -frags_9mers
/user/sarah/xray/1Apr_Athena/aat000_09_05.200_v1_3 -make_frags False
- -F F -SIGF SIGF -FREE FreeR_flag  -early_terminate True   -use_shelxe
True -shelx_cycles 15 -use_arpwarp False

Any help is appreciated,
Dale Tronrud
Sarah Clark
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--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

Re: [ccp4bb] Phaser going into infinite loop in Ample

[Claudia Millán Nebot]

Dear Dale,

as George points out, you may be interested in trying ARCIMBOLDO, as it has
been successfully applied to coiled coil proteins recently, as in the case
of
Franke et al (2014)  Open Biology, 4. p. 130172 or  Sammito et al (2013)
Nature Methods 10: 1099-1101 . Different models can be searched for,
starting from single helices with or without sidechains, going to
precomputed libraries of helices in parallel or antiparallel configurations.

If you need help or support to use it, please feel free to ask any question.
Best wishes,

Claudia



Claudia Millán

2015-04-22 6:56 GMT+02:00 Dale Tronrud de...@daletronrud.com:

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1


We are having a problem with AMPLE and hope someone can help.

The protein is about 70 amino acids long and we suspect it forms a
 coiled-coil.  Our previous attempts at molecular replacement have
 failed so we hoped that AMPLE, with its ability to generate a variety
 of potential models, would do the trick.

Our problem is that all of our CPU cores are consumed by Phaser
 jobs that are not making progress.  With this protein Phaser decides
 that it will look for 11 copies in the asymmetric unit.  For a few of
 the possible ensembles it fails to find even one copy and gives up.
 That's fine with us.  For other ensembles it finds a handful of
 possible first positions, goes on to look for a second and fails, then
 goes back to try to place a second copy again.  We presume that the
 intent is to lower the acceptance criteria in the second pass, but in
 actuality Phaser simply repeats the same search that failed before and
 fails again.  The leads to an infinite loop.

Once all the cores are occupied in this futile endeavor AMPLE makes
 no further progress.

How can we get Phaser to either try harder to place a molecule or
 to give up?

We are using CCP4 6.5.008 and the copy of Phaser that came with it.
  We used CCP4i to create a script which we modified slightly and ran
 using the at command.  The command is:

 /usr/local/ccp4-6.5/bin/ccp4-python -u /usr/local/ccp4-6.5/bin/ample
 - -mtz /user/sarah/xray/1Apr_Athena/SD6004_2_001_mergedunique14.mtz
 - -fasta /user/sarah/xray/1Apr_Athena/swaseq.fa -mr_sequence
 /user/sarah/xray/1Apr_Athena/swaseq.fa -nmodels 500 -name MVD0
 - -run_dir /home/sarah/AMPLE -nproc 6 -make_models True -rosetta_dir
 /usr/local/rosetta-3.5 -frags_3mers
 /user/sarah/xray/1Apr_Athena/aat000_03_05.200_v1_3 -frags_9mers
 /user/sarah/xray/1Apr_Athena/aat000_09_05.200_v1_3 -make_frags False
 - -F F -SIGF SIGF -FREE FreeR_flag  -early_terminate True   -use_shelxe
 True -shelx_cycles 15 -use_arpwarp False

 Any help is appreciated,
 Dale Tronrud
 Sarah Clark
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 =A/Sj
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Re: [ccp4bb] Phaser going into infinite loop in Ample

[Thomas, Jens]

Dear Dale,

This is a known issue with AMPLE and will be fixed with the next release.

In the meantime you can tell AMPLE to pass the KILL option that Randy mentions 
to PHASER, by adding the following arguments to your script:

-mr_keys PKEY KILL TIME 360

this will kill PHASER after 360 minutes (6 hours), which we've found if 
normally enough, although pick whatever time works for you,

I should also point out that I think George is doing a disservice to SHELXE. In 
our last paper looking at coiled-coils, we saw successes at resolutions much 
lower than 2.1, in one case, AMPLE was able to solve a structure with a 
resolution of 2.9A:

http://dx.doi.org/10.1107/S2052252515002080

If you have any issues getting the KILL command to work, please feel free to 
contact me off-list.

Best wishes,

Jens


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Randy Read 
[rj...@cam.ac.uk]
Sent: 22 April 2015 09:04
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Phaser going into infinite loop in Ample

Hi Dale,

It must actually be AMPLE deciding how many copies to search for.  Phaser will 
give you some information about how consistent the specified composition is 
with the Matthews volume, but it just searches for the number of copies that 
it's instructed to look for.  We haven't put the intelligence into it to 
correlate the model(s) with the composition information and try out different 
possibilities.  At the moment, we're leaving that level of analysis to 
pipelines like MRage.

We're well aware of the tension between looking hard enough to find a solution 
in a difficult case and not throwing good CPU cycles after bad when it's 
hopeless.  We're gradually introducing new features to make these decisions 
better, but we do tend to prefer wasting CPU time to missing solutions.  
However, we've introduced a couple of ways to limit the amount of time that 
Phaser spends pursuing very difficult or hopeless solutions, partly for the 
benefit of people such as the developers of Arcimboldo, AMPLE and the 
wide-search molecular replacement pipeline.  One is the KILL command, which is 
a rather blunt instrument saying to give up if a solution isn't found in a 
certain length of time.  In AMPLE, if you set quick mode, then the KILL time is 
set to 15 minutes.  Another option (which I don't think AMPLE uses) is the 
PURGE command, where you can say (for instance) that Phaser should pursue a 
maximum of 25 partial solutions when adding the next component.

If you're seeing an infinite loop, it would be handy if you could send me a 
copy of the logfile showing what is going on.  There have been some bugs 
leading to such infinite loops under some circumstances, and if you're running 
into one of those there's a good chance that it has been fixed in a recent 
nightly build of Phaser available through Phenix.  You can instruct CCP4 to use 
the Phaser executable from Phenix, and I think this should work fine in AMPLE, 
though I haven't tested it — I don't think any relevant syntax has changed.  
It's been a while since we've had a new stable release of Phaser in either CCP4 
or Phenix, so we're aiming to get one out in the not too distant future.

All the best,

Randy

 On 22 Apr 2015, at 05:56, Dale Tronrud de...@daletronrud.com wrote:

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1


   We are having a problem with AMPLE and hope someone can help.

   The protein is about 70 amino acids long and we suspect it forms a
 coiled-coil.  Our previous attempts at molecular replacement have
 failed so we hoped that AMPLE, with its ability to generate a variety
 of potential models, would do the trick.

   Our problem is that all of our CPU cores are consumed by Phaser
 jobs that are not making progress.  With this protein Phaser decides
 that it will look for 11 copies in the asymmetric unit.  For a few of
 the possible ensembles it fails to find even one copy and gives up.
 That's fine with us.  For other ensembles it finds a handful of
 possible first positions, goes on to look for a second and fails, then
 goes back to try to place a second copy again.  We presume that the
 intent is to lower the acceptance criteria in the second pass, but in
 actuality Phaser simply repeats the same search that failed before and
 fails again.  The leads to an infinite loop.

   Once all the cores are occupied in this futile endeavor AMPLE makes
 no further progress.

   How can we get Phaser to either try harder to place a molecule or
 to give up?

   We are using CCP4 6.5.008 and the copy of Phaser that came with it.
 We used CCP4i to create a script which we modified slightly and ran
 using the at command.  The command is:

 /usr/local/ccp4-6.5/bin/ccp4-python -u /usr/local/ccp4-6.5/bin/ample
 - -mtz /user/sarah/xray/1Apr_Athena/SD6004_2_001_mergedunique14.mtz
 - -fasta /user/sarah/xray/1Apr_Athena/swaseq.fa -mr_sequence
 /user/sarah/xray/1Apr_Athena/swaseq.fa -nmodels 500 -name MVD0

[ccp4bb] Phaser going into infinite loop in Ample

[Dale Tronrud]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1


   We are having a problem with AMPLE and hope someone can help.

   The protein is about 70 amino acids long and we suspect it forms a
coiled-coil.  Our previous attempts at molecular replacement have
failed so we hoped that AMPLE, with its ability to generate a variety
of potential models, would do the trick.

   Our problem is that all of our CPU cores are consumed by Phaser
jobs that are not making progress.  With this protein Phaser decides
that it will look for 11 copies in the asymmetric unit.  For a few of
the possible ensembles it fails to find even one copy and gives up.
That's fine with us.  For other ensembles it finds a handful of
possible first positions, goes on to look for a second and fails, then
goes back to try to place a second copy again.  We presume that the
intent is to lower the acceptance criteria in the second pass, but in
actuality Phaser simply repeats the same search that failed before and
fails again.  The leads to an infinite loop.

   Once all the cores are occupied in this futile endeavor AMPLE makes
no further progress.

   How can we get Phaser to either try harder to place a molecule or
to give up?

   We are using CCP4 6.5.008 and the copy of Phaser that came with it.
 We used CCP4i to create a script which we modified slightly and ran
using the at command.  The command is:

/usr/local/ccp4-6.5/bin/ccp4-python -u /usr/local/ccp4-6.5/bin/ample
- -mtz /user/sarah/xray/1Apr_Athena/SD6004_2_001_mergedunique14.mtz
- -fasta /user/sarah/xray/1Apr_Athena/swaseq.fa -mr_sequence
/user/sarah/xray/1Apr_Athena/swaseq.fa -nmodels 500 -name MVD0
- -run_dir /home/sarah/AMPLE -nproc 6 -make_models True -rosetta_dir
/usr/local/rosetta-3.5 -frags_3mers
/user/sarah/xray/1Apr_Athena/aat000_03_05.200_v1_3 -frags_9mers
/user/sarah/xray/1Apr_Athena/aat000_09_05.200_v1_3 -make_frags False
- -F F -SIGF SIGF -FREE FreeR_flag  -early_terminate True   -use_shelxe
True -shelx_cycles 15 -use_arpwarp False

Any help is appreciated,
Dale Tronrud
Sarah Clark
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Re: [ccp4bb] PHASER MR solution

[Randy Read]

Hi all,

Actually, what I think has happened here is that Phaser has limited the 
resolution to what it estimated was needed to get a clear enough solution, and 
then the final refinement was carried out with all the data.  The 
signal-to-noise is lower with limited data, but it’s a price that seems worth 
paying to get the answer more quickly.  The final refined LLG of 1848 is a very 
large number, and the TFZ-equivalent calculation indicates that, if the 
translation search had been carried out with the final refined orientation 
using all the data, the TFZ would have been a very respectable 30.2.  That’s 
probably a better number to look at now, with the new adaptive Phaser searches.

Of course, I agree completely that you would also like to see that the correct 
space group gave a much higher score with the same data than the alternative 
space groups!  Phaser chose a single solution, so it was probably at least 
reasonably clear.

We’re stlll working on how to give the clearest possible indication at the end 
of a run as to whether you should be confident that it is correct.

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 28 Jan 2015, at 19:33, Matthew Franklin mfrank...@nysbc.org wrote:

 Hi Jeorge -
 
 Something seems to have changed for the worse in this MR run.  In your 
 earlier posting, where you failed to find a solution in P222, your log file 
 had solutions with RFZ=23.4, generally a clear indication of a correct 
 rotation function solution.  (You didn't include this log file as text, so I 
 can't extract the relevant lines to show you.)  But in this run, your log 
 file shows a solution with RFZ=5.7, which is much more marginal.  The space 
 group choice for the translation function shouldn't affect the results of the 
 rotation function.  What else did you vary - is the search model different?
 
 In addition to what Roger suggested, other indications that you have the 
 right solution come from the translation function tables.  You should have a 
 very clear distinction between the correct solution and incorrect solutions, 
 like this:
 
Fast Translation Function Table: Space Group C 1 2 1

#SET #TRIAL  Top(Z)Second(Z) Third(Z)Ensemble
   1  1  4328.56 (29.62)-  - -  -3gi8_fab
   1  2  4294.35 (26.16)-  - -  -3gi8_fab
   1  3  4252.29 (27.13)-  - -  -3gi8_fab
   1  4  3746.99 (13.34)  3725.62 (12.73)-  -3gi8_fab
   1  5  3467.72 ( 5.02)  3467.43 ( 5.02)  3464.58 ( 4.94)   3gi8_fab
   1  6  3545.59 ( 6.93)  3482.22 ( 5.27)-  -3gi8_fab
 
 Trials 1-3 are correct, while trials 5-6 are incorrect.  (Trial 4 is probably 
 also correct, but wasn't tested further by Phaser.)
 
 You also want to check that the packing test did not throw out one of these 
 high-scoring translation solutions (e.g. your RFZ=23.4 solution).  If that 
 happened, this could mean you need to trim away some loops in your search 
 model.
 
 Good luck,
 
 Matt
 
 
 
 On 1/28/15 12:25 PM, jeorgemarley thomas wrote:
 Hi, all
 
 As per the suggestions, I hv done with the phaser MR and the solution has 
 come with screw axes P 21 21 21. here I am attaching the output text from Mr 
 and sol file. So Now should I go ahead with this? Please suggest. 
 
 Thank you very much in advance !
 
 On Tue, Jan 27, 2015 at 9:33 PM, jeorgemarley thomas kirtswab...@gmail.com 
 wrote:
 Thank you so much to all for your kind concern.
 
 
 
 Jeorge
 
 On Mon, Jan 26, 2015 at 5:55 PM, Kay Diederichs 
 kay.diederi...@uni-konstanz.de wrote:
 Dear Jeorge,
 
 you'll find some information about this in 
 http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination
  . A practical and easy way is described in 
 http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Pointless
 
 HTH,
 
 Kay
 
 On Mon, 26 Jan 2015 11:24:27 +0100, Tim Gruene t...@shelx.uni-ac.gwdg.de 
 wrote:
 
 Dear Jeorge,
 
 XDS make no claim to determine the SPACE GROUP but rather the LAUE
 GROUP, as only the latter is taken into account during data integration.
 
 This is definitely so during the indexing step (IDXREF.LP), but even in
 CORRECT, when systematic absences are sometimes indicated, XDS does not
 really choose the space group.
 
 Best,
 Tim
 
 On 01/26/2015 05:46 AM, jeorgemarley thomas wrote:
  Hello Dr. Randy
  Here is the IDXREF.LP I got in which, on the basis of quality of fit, I
  went for this space group well I would also try 

Re: [ccp4bb] PHASER MR solution

[Roger Rowlett]

The Z-values may be marginal, but of course you should inspect the 
solution in Coot to see if the electron density makes sense, and the 
packing of the protein molecules in the unit cell (look at symmetry 
mates) is sensible. If this passes the sniff test, then you should clean 
up your model (make it consistent with the target protein) and try to 
refine it. If your target and model are really different in terms of 
gaps, insertions, etc., and your electron density is good, this would be 
a good opportunity to do some auto-building with Buccaneer based on your 
initial phase solution, for example, to get to a better starting point 
for refinement. If you can't refine the MR solution and drive R and 
Rfree down significantly, you may still have some problems. With 70% 
sequence identity, I would expect your model to be pretty close to your 
target, and autobuilding may not be necessary to get to a good starting 
point, although this can often save you some time.


___
Roger S. Rowlett
Gordon  Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu

On 1/28/2015 12:25 PM, jeorgemarley thomas wrote:

Hi, all

As per the suggestions, I hv done with the phaser MR and the solution 
has come with screw axes P 21 21 21. here I am attaching the output 
text from Mr and sol file. So Now should I go ahead with this? Please 
suggest.


Thank you very much in advance !

On Tue, Jan 27, 2015 at 9:33 PM, jeorgemarley thomas 
kirtswab...@gmail.com mailto:kirtswab...@gmail.com wrote:


Thank you so much to all for your kind concern.



Jeorge

On Mon, Jan 26, 2015 at 5:55 PM, Kay Diederichs
kay.diederi...@uni-konstanz.de
mailto:kay.diederi...@uni-konstanz.de wrote:

Dear Jeorge,

you'll find some information about this in

http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination
. A practical and easy way is described in
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Pointless

HTH,

Kay

On Mon, 26 Jan 2015 11:24:27 +0100, Tim Gruene
t...@shelx.uni-ac.gwdg.de mailto:t...@shelx.uni-ac.gwdg.de wrote:

Dear Jeorge,

XDS make no claim to determine the SPACE GROUP but rather the
LAUE
GROUP, as only the latter is taken into account during data
integration.

This is definitely so during the indexing step (IDXREF.LP),
but even in
CORRECT, when systematic absences are sometimes indicated,
XDS does not
really choose the space group.

Best,
Tim

On 01/26/2015 05:46 AM, jeorgemarley thomas wrote:
 Hello Dr. Randy
 Here is the IDXREF.LP I got in which, on the basis of
quality of fit, I
 went for this space group well I would also try for the
other screw axes.
 So should I Integrate the data from beginning with all
possible screw axes
 of orthogonal space group?  I am attaching the IDXREF.LP
screen shot here.

 Jeorge

 On Sun, Jan 25, 2015 at 5:00 PM, Roger Rowlett
rrowl...@colgate.edu mailto:rrowl...@colgate.edu wrote:

 Did you search all 8 possibilities of screw axes, e.g.
P2221, P21212,
 P212121, etc?

 Roger Rowlett
 On Jan 25, 2015 4:50 AM, jeorgemarley thomas
kirtswab...@gmail.com mailto:kirtswab...@gmail.com
 wrote:

 Hi, I have processed the data using XDS and space group
found to be P 2 2
 2 (16) and I used the phaser MR for first phase
determination. The model I
 have used has has more than 70 % sequence identity, when
I run the phaser I
 got the message which I have attached here. And only sum.
file I got as an
 output. Does any one have suggestion what should I do ? I
would highly
 appreciate your kind suggestions. Thank you in advance.





--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

Re: [ccp4bb] PHASER MR solution

[Matthew Franklin]

Hi Jeorge -

Something seems to have changed for the worse in this MR run.  In your 
earlier posting, where you failed to find a solution in P222, your log 
file had solutions with RFZ=23.4, generally a clear indication of a 
correct rotation function solution.  (You didn't include this log file 
as text, so I can't extract the relevant lines to show you.)  But in 
this run, your log file shows a solution with RFZ=5.7, which is much 
more marginal.  The space group choice for the translation function 
shouldn't affect the results of the rotation function.  What else did 
you vary - is the search model different?


In addition to what Roger suggested, other indications that you have the 
right solution come from the translation function tables.  You should 
have a very clear distinction between the correct solution and incorrect 
solutions, like this:



   Fast Translation Function Table: Space Group C 1 2 1
   
   #SET #TRIAL  Top(Z)Second(Z) Third(Z)Ensemble
  1  1  4328.56 (29.62)-  - -  -3gi8_fab
  1  2  4294.35 (26.16)-  - -  -3gi8_fab
  1  3  4252.29 (27.13)-  - -  -3gi8_fab
  1  4  3746.99 (13.34)  3725.62 (12.73) -  -3gi8_fab
  1  5  3467.72 ( 5.02)  3467.43 ( 5.02) 3464.58 ( 4.94)   
3gi8_fab

  1  6  3545.59 ( 6.93)  3482.22 ( 5.27) -  -3gi8_fab


Trials 1-3 are correct, while trials 5-6 are incorrect.  (Trial 4 is 
probably also correct, but wasn't tested further by Phaser.)


You also want to check that the packing test did not throw out one of 
these high-scoring translation solutions (e.g. your RFZ=23.4 solution).  
If that happened, this could mean you need to trim away some loops in 
your search model.


Good luck,

Matt



On 1/28/15 12:25 PM, jeorgemarley thomas wrote:

Hi, all

As per the suggestions, I hv done with the phaser MR and the solution 
has come with screw axes P 21 21 21. here I am attaching the output 
text from Mr and sol file. So Now should I go ahead with this? Please 
suggest.


Thank you very much in advance !

On Tue, Jan 27, 2015 at 9:33 PM, jeorgemarley thomas 
kirtswab...@gmail.com mailto:kirtswab...@gmail.com wrote:


Thank you so much to all for your kind concern.



Jeorge

On Mon, Jan 26, 2015 at 5:55 PM, Kay Diederichs
kay.diederi...@uni-konstanz.de
mailto:kay.diederi...@uni-konstanz.de wrote:

Dear Jeorge,

you'll find some information about this in

http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination
. A practical and easy way is described in
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Pointless

HTH,

Kay

On Mon, 26 Jan 2015 11:24:27 +0100, Tim Gruene
t...@shelx.uni-ac.gwdg.de mailto:t...@shelx.uni-ac.gwdg.de wrote:

Dear Jeorge,

XDS make no claim to determine the SPACE GROUP but rather the
LAUE
GROUP, as only the latter is taken into account during data
integration.

This is definitely so during the indexing step (IDXREF.LP),
but even in
CORRECT, when systematic absences are sometimes indicated,
XDS does not
really choose the space group.

Best,
Tim

On 01/26/2015 05:46 AM, jeorgemarley thomas wrote:
 Hello Dr. Randy
 Here is the IDXREF.LP I got in which, on the basis of
quality of fit, I
 went for this space group well I would also try for the
other screw axes.
 So should I Integrate the data from beginning with all
possible screw axes
 of orthogonal space group?  I am attaching the IDXREF.LP
screen shot here.

 Jeorge

 On Sun, Jan 25, 2015 at 5:00 PM, Roger Rowlett
rrowl...@colgate.edu mailto:rrowl...@colgate.edu wrote:

 Did you search all 8 possibilities of screw axes, e.g.
P2221, P21212,
 P212121, etc?

 Roger Rowlett
 On Jan 25, 2015 4:50 AM, jeorgemarley thomas
kirtswab...@gmail.com mailto:kirtswab...@gmail.com
 wrote:

 Hi, I have processed the data using XDS and space group
found to be P 2 2
 2 (16) and I used the phaser MR for first phase
determination. The model I
 have used has has more than 70 % sequence identity, when
I run the phaser I
 got the message which I have attached here. And only sum.
file I got as an
 output. Does any one have suggestion what should I do ? I
would highly
 appreciate your kind suggestions. Thank you in advance.





--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 

Re: [ccp4bb] PHASER MR solution

[jeorgemarley thomas]

Thank you so much to all for your kind concern.



Jeorge

On Mon, Jan 26, 2015 at 5:55 PM, Kay Diederichs 
kay.diederi...@uni-konstanz.de wrote:

 Dear Jeorge,

 you'll find some information about this in
 http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination
 . A practical and easy way is described in
 http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Pointless

 HTH,

 Kay

 On Mon, 26 Jan 2015 11:24:27 +0100, Tim Gruene t...@shelx.uni-ac.gwdg.de
 wrote:

 Dear Jeorge,
 
 XDS make no claim to determine the SPACE GROUP but rather the LAUE
 GROUP, as only the latter is taken into account during data integration.
 
 This is definitely so during the indexing step (IDXREF.LP), but even in
 CORRECT, when systematic absences are sometimes indicated, XDS does not
 really choose the space group.
 
 Best,
 Tim
 
 On 01/26/2015 05:46 AM, jeorgemarley thomas wrote:
  Hello Dr. Randy
  Here is the IDXREF.LP I got in which, on the basis of quality of fit, I
  went for this space group well I would also try for the other screw
 axes.
  So should I Integrate the data from beginning with all possible screw
 axes
  of orthogonal space group?  I am attaching the IDXREF.LP screen shot
 here.
 
  Jeorge
 
  On Sun, Jan 25, 2015 at 5:00 PM, Roger Rowlett rrowl...@colgate.edu
 wrote:
 
  Did you search all 8 possibilities of screw axes, e.g. P2221, P21212,
  P212121, etc?
 
  Roger Rowlett
  On Jan 25, 2015 4:50 AM, jeorgemarley thomas kirtswab...@gmail.com
  wrote:
 
  Hi, I have processed the data using XDS and space group found to be P
 2 2
  2 (16) and I used the phaser MR for first phase determination. The
 model I
  have used has has more than 70 % sequence identity, when I run the
 phaser I
  got the message which I have attached here. And only sum. file I got
 as an
  output. Does any one have suggestion what should I do ? I would highly
  appreciate your kind suggestions. Thank you in advance.
 
 
 
 
 
 --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 
 

Re: [ccp4bb] PHASER MR solution

[Kay Diederichs]

Dear Jeorge,

you'll find some information about this in 
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination
 . A practical and easy way is described in 
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Pointless 

HTH,

Kay

On Mon, 26 Jan 2015 11:24:27 +0100, Tim Gruene t...@shelx.uni-ac.gwdg.de 
wrote:

Dear Jeorge,

XDS make no claim to determine the SPACE GROUP but rather the LAUE
GROUP, as only the latter is taken into account during data integration.

This is definitely so during the indexing step (IDXREF.LP), but even in
CORRECT, when systematic absences are sometimes indicated, XDS does not
really choose the space group.

Best,
Tim

On 01/26/2015 05:46 AM, jeorgemarley thomas wrote:
 Hello Dr. Randy
 Here is the IDXREF.LP I got in which, on the basis of quality of fit, I
 went for this space group well I would also try for the other screw axes.
 So should I Integrate the data from beginning with all possible screw axes
 of orthogonal space group?  I am attaching the IDXREF.LP screen shot here.
 
 Jeorge
 
 On Sun, Jan 25, 2015 at 5:00 PM, Roger Rowlett rrowl...@colgate.edu wrote:
 
 Did you search all 8 possibilities of screw axes, e.g. P2221, P21212,
 P212121, etc?

 Roger Rowlett
 On Jan 25, 2015 4:50 AM, jeorgemarley thomas kirtswab...@gmail.com
 wrote:

 Hi, I have processed the data using XDS and space group found to be P 2 2
 2 (16) and I used the phaser MR for first phase determination. The model I
 have used has has more than 70 % sequence identity, when I run the phaser I
 got the message which I have attached here. And only sum. file I got as an
 output. Does any one have suggestion what should I do ? I would highly
 appreciate your kind suggestions. Thank you in advance.



 

-- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

Re: [ccp4bb] PHASER MR solution

[Tim Gruene]

Dear Jeorge,

XDS make no claim to determine the SPACE GROUP but rather the LAUE
GROUP, as only the latter is taken into account during data integration.

This is definitely so during the indexing step (IDXREF.LP), but even in
CORRECT, when systematic absences are sometimes indicated, XDS does not
really choose the space group.

Best,
Tim

On 01/26/2015 05:46 AM, jeorgemarley thomas wrote:
 Hello Dr. Randy
 Here is the IDXREF.LP I got in which, on the basis of quality of fit, I
 went for this space group well I would also try for the other screw axes.
 So should I Integrate the data from beginning with all possible screw axes
 of orthogonal space group?  I am attaching the IDXREF.LP screen shot here.
 
 Jeorge
 
 On Sun, Jan 25, 2015 at 5:00 PM, Roger Rowlett rrowl...@colgate.edu wrote:
 
 Did you search all 8 possibilities of screw axes, e.g. P2221, P21212,
 P212121, etc?

 Roger Rowlett
 On Jan 25, 2015 4:50 AM, jeorgemarley thomas kirtswab...@gmail.com
 wrote:

 Hi, I have processed the data using XDS and space group found to be P 2 2
 2 (16) and I used the phaser MR for first phase determination. The model I
 have used has has more than 70 % sequence identity, when I run the phaser I
 got the message which I have attached here. And only sum. file I got as an
 output. Does any one have suggestion what should I do ? I would highly
 appreciate your kind suggestions. Thank you in advance.



 

-- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A



signature.asc
Description: OpenPGP digital signature

Re: [ccp4bb] PHASER MR solution

[Randy Read]

Dear Jeorge,

I can’t see anything in that output saying whether the systematic absences that 
would allow you to detect screw axes were covered in your data collection.

In any case, it’s not necessary to reintegrate.  All that happens when going 
from P222 to any one of the other 7 possible orthorhombic space groups is that 
some of the reflections will become systematically absent so they will be 
discarded, but Phaser will do that internally when testing all the space groups.

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 26 Jan 2015, at 04:46, jeorgemarley thomas kirtswab...@gmail.com wrote:

 Hello Dr. Randy 
 Here is the IDXREF.LP I got in which, on the basis of quality of fit, I went 
 for this space group well I would also try for the other screw axes. So 
 should I Integrate the data from beginning with all possible screw axes of 
 orthogonal space group?  I am attaching the IDXREF.LP screen shot here.
 
 Jeorge
 
 On Sun, Jan 25, 2015 at 5:00 PM, Roger Rowlett rrowl...@colgate.edu wrote:
 Did you search all 8 possibilities of screw axes, e.g. P2221, P21212, 
 P212121, etc?
 
 Roger Rowlett
 
 On Jan 25, 2015 4:50 AM, jeorgemarley thomas kirtswab...@gmail.com wrote:
 Hi, I have processed the data using XDS and space group found to be P 2 2 2 
 (16) and I used the phaser MR for first phase determination. The model I have 
 used has has more than 70 % sequence identity, when I run the phaser I got 
 the message which I have attached here. And only sum. file I got as an 
 output. Does any one have suggestion what should I do ? I would highly 
 appreciate your kind suggestions. Thank you in advance. 
 
 
 
 IDXREF.PNGSpaceG.PNG

[ccp4bb] PHASER warning

[rohit kumar]

Dear all,

i am solving a structure of 2.5 A resolution by PHASER but every time i got
this following warning.

$TEXT:Warning: $$ Baubles Markup $$

-

Large non-origin Patterson peak indicates that translational NCS is present:

correction factors applied

-

$$

$TEXT:Warning: $$ Baubles Markup $$

-

Solutions with Z-scores greater than 49.2 (the threshold indicating a definite

solution) were rejected for failing packing test

#1 TFZ=65.6 PAK=42

#2 TFZ=65.5 PAK=68

-

however every time PHASER run successfully and it give a output PDB as
a solution. is it a right solution or not?  or To get the right
solution what should i do?


if i used accept all the solution in expert parameter, i also got the
solution but which does not follow the Packing test.


Can anyone suggest...


-- 
WITH REGARDS
Rohit Kumar Singh
Lab. no. 430,
P.I. Dr. S. Gourinath,
School of Life Sciences,
Jawaharlal Nehru University
New Delhi -110067

Re: [ccp4bb] PHASER warning

[Rebuffet Etienne]

Dear Rohit,

Are you sure about your space group? I think you should look at this first

Hope it helps.

Etienne

Etienne Rebuffet, PhD
Tel: +334 86 97 73 34

Laboratory of 'integrative Structural  Chemical Biology (iSCB)'
Cancer Research Center of Marseille (CRCM)
CNRS UMR 7258; INSERM U 1068; Université Aix-Marseille
Institut Paoli Calmettes
27 Boulevard Leï Roure BP30059
13273 Marseille Cedex 9
France

Le 28/11/2014 14:36, rohit kumar a écrit :

Dear all,

i am solving a structure of 2.5 A resolution by PHASER but every time i
got this following warning.

$TEXT:Warning: $$ Baubles Markup $$

-

Large non-origin Patterson peak indicates that translational NCS is present:

correction factors applied

-

$$

$TEXT:Warning: $$ Baubles Markup $$

-

Solutions with Z-scores greater than 49.2 (the threshold indicating a definite

solution) were rejected for failing packing test

#1 TFZ=65.6 PAK=42

#2 TFZ=65.5 PAK=68

-

however every time PHASER run successfully and it give a output PDB as a 
solution.is it a right solution or not?   or To get the right solution what 
should i do?


if i used accept all the solution in expert parameter, i also got the solution 
but which does not follow the Packing test.


Can anyone suggest...


--
WITH REGARDS
Rohit Kumar Singh
Lab. no. 430,
P.I. Dr. S. Gourinath,
School of Life Sciences,
Jawaharlal Nehru University
New Delhi -110067

Re: [ccp4bb] Phaser question, twinning, DIALS, suggestions welcome

[Randy Read]

Hi Jurgen,

You could send me a logfile off-list, and maybe I would spot something in there.

We’ve put some effort into putting more intelligence into the Phaser search, so 
that it adapts to the initial perceived difficulty of the problem in setting 
the initial parameters, and then adapts to indicators of success or failure 
during the search.  Much of the time this works very well, but there’s 
obviously room for improvement.  For one thing, it appears that we’re 
frequently too optimistic about how good the model will be and how easy the 
search will be.

One question: when you say that you cut at 2.5A for MR, do you do that by 
setting the resolution within the Phaser run, or do you have an MTZ file with 
only data to 2.5A?  If the former, then you’re over-riding some of Phaser’s 
automation, which will choose the initial resolution limit based on the 
perceived difficulty of the problem (a function of model completeness, expected 
RMS error of the model, and the number of reflections to different resolution 
limits).  It’s this initial automated choice that can go wrong if we’re too 
optimistic, because then a clear solution isn’t found, and then Phaser repeats 
the search with data to the full resolution, which can take longer than just 
choosing an intermediate resolution from the start.

Anyway, if the problem is expected to be easy but turns out to be difficult, 
this implies that some of the information used to decide it should be easy is 
wrong or too optimistic.  One top possibility is that the model is not as good 
as expected, e.g. because of conformational changes.  If there’s a potential 
hinge-bending motion, then you’re usually better off searching with separate 
domains.  If the change is something that can’t be described with rigid-body 
motions, then it would be better to increase the expected RMS error from what 
Phaser deduces from the sequence identity.  Increasing the RMSD by 10-20% would 
be a good first bet in such a case.

The other top possibility is that the space group is wrong.  Is there any 
ambiguity in the space group?  In particular, do any of the twinning tests 
indicate that the data may be twinned (which can lead to choosing too high 
symmetry)?

Best wishes,

Randy

On 1 Oct 2014, at 03:02, Jurgen Bosch jbos...@jhu.edu wrote:

 Dear BB, or in particular Phaser developers :-)
 
 This must be part of British humor right (or was that the Canadian influence 
 Randy) ?
 
 eLLG indicates that placement of ensemble ensemble_1 will be straightforward
The data are sufficient to exceed the eLLG target
 
 The search space is finite 143 x 143 x 80 Å with 3 or 4 molecules per asu, 
 but Phaser has been burning CPU cycles quite a bit, we are approaching 24h by 
 now. Data extends to 1.7 Å - for MR we cut at 2.5 Å.
 
 I can hear Garib, yes, Molrep was done in few minutes but I’m not super 
 convinced about the solution either. Same with BALBES and MrBump (which took 
 a few more minutes, actually also days for MrBump)
 
 The space group appears to be P63 22 as judged by XDS, pointless, xtriage, 
 however the crystals are split (at least in some areas it’s visible) but I 
 thought XDS would take care of these “aliens” and eliminate them mostly. My 
 graduate student, Lauren, found a nifty program called DIALS that we wish to 
 explore further to rescue the “nice” data we have and hopefully solve the 
 structure.
 
 Lower symmetry space groups were tried down to P21 with increasing number of 
 molecules per asu and applying twin laws if necessary. The minor problem with 
 the twins is how do I really know that it is a higher symmetry space group 
 and not a 50% twin in a lower symmetry ? Rwork/Rfree in this particular case 
 do not seem to help at all for distinguishing between the solutions. Maps 
 looks sort of right but R-factors are not reflecting what you see on the 
 screen.
 
 We appreciate any suggestions and ideas what else we could do. 
 
 Thanks,
 
 Jürgen
 
 ..
 Jürgen Bosch
 Johns Hopkins University
 Bloomberg School of Public Health
 Department of Biochemistry  Molecular Biology
 Johns Hopkins Malaria Research Institute
 615 North Wolfe Street, W8708
 Baltimore, MD 21205
 Office: +1-410-614-4742
 Lab:  +1-410-614-4894
 Fax:  +1-410-955-2926
 http://lupo.jhsph.edu
 

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

Re: [ccp4bb] Phaser question, twinning, DIALS, suggestions welcome

[Randy Read]

Hi again,

I should have mentioned that, if you have a good enough model, it’s often 
possible to solve the structure in P1.  The molecular replacement solution will 
settle on one of the twin domains (or you may end up with more than one 
solution, related by the twin law(s)).  Then the symmetry of the solution will 
tell you the true symmetry of the crystal.  Otherwise, you’ll have to test all 
the subgroups, and there will be a lot of those for P6322, especially if you’re 
not sure about screw axes.

But the true point group symmetry will only be lower than the symmetry in which 
the data merge if there’s twinning, which is why I’m wondering whether there 
are indications of twinning.  It probably bears repeating that, if you test 
data merged in too low symmetry, the twinning tests that depend on twin laws 
can be misleading, because they look for reflections that are similar over a 
possible twin law.  You need to have independent evidence from tests that do 
not depend on twin laws (i.e. statistical tests such as the moment tests or the 
L-test) that the data are perturbed in a way that implies twinning.

Randy

On 1 Oct 2014, at 03:02, Jurgen Bosch jbos...@jhu.edu wrote:

 Dear BB, or in particular Phaser developers :-)
 
 This must be part of British humor right (or was that the Canadian influence 
 Randy) ?
 
 eLLG indicates that placement of ensemble ensemble_1 will be straightforward
The data are sufficient to exceed the eLLG target
 
 The search space is finite 143 x 143 x 80 Å with 3 or 4 molecules per asu, 
 but Phaser has been burning CPU cycles quite a bit, we are approaching 24h by 
 now. Data extends to 1.7 Å - for MR we cut at 2.5 Å.
 
 I can hear Garib, yes, Molrep was done in few minutes but I’m not super 
 convinced about the solution either. Same with BALBES and MrBump (which took 
 a few more minutes, actually also days for MrBump)
 
 The space group appears to be P63 22 as judged by XDS, pointless, xtriage, 
 however the crystals are split (at least in some areas it’s visible) but I 
 thought XDS would take care of these “aliens” and eliminate them mostly. My 
 graduate student, Lauren, found a nifty program called DIALS that we wish to 
 explore further to rescue the “nice” data we have and hopefully solve the 
 structure.
 
 Lower symmetry space groups were tried down to P21 with increasing number of 
 molecules per asu and applying twin laws if necessary. The minor problem with 
 the twins is how do I really know that it is a higher symmetry space group 
 and not a 50% twin in a lower symmetry ? Rwork/Rfree in this particular case 
 do not seem to help at all for distinguishing between the solutions. Maps 
 looks sort of right but R-factors are not reflecting what you see on the 
 screen.
 
 We appreciate any suggestions and ideas what else we could do. 
 
 Thanks,
 
 Jürgen
 
 ..
 Jürgen Bosch
 Johns Hopkins University
 Bloomberg School of Public Health
 Department of Biochemistry  Molecular Biology
 Johns Hopkins Malaria Research Institute
 615 North Wolfe Street, W8708
 Baltimore, MD 21205
 Office: +1-410-614-4742
 Lab:  +1-410-614-4894
 Fax:  +1-410-955-2926
 http://lupo.jhsph.edu
 

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

Re: [ccp4bb] Phaser question, twinning, DIALS, suggestions welcome

[Graeme Winter]

Dear Jurgen,

Thanks for your interest in DIALS - we are working hard at the moment on
testing the software and finding bugs (and fixing them!) and I would say
right now it's not quite ready for the general user, but we do plan to make
an alpha release of the software before the end of the year. When we're
ready, we'll send an email out to the CCP4 BB of course.

In the meantime some more information may be found at:

http://dials.sourceforge.net/

Best wishes Graeme, and the DIALS development team


On 1 October 2014 03:02, Jurgen Bosch jbos...@jhu.edu wrote:

  Dear BB, or in particular Phaser developers :-)

  This must be part of British humor right (or was that the Canadian
 influence Randy) ?

  eLLG indicates that placement of ensemble ensemble_1 will be
 straightforward
The data are sufficient to exceed the eLLG target

  The search space is finite 143 x 143 x 80 Å with 3 or 4 molecules per
 asu, but Phaser has been burning CPU cycles quite a bit, we are approaching
 24h by now. Data extends to 1.7 Å - for MR we cut at 2.5 Å.

  I can hear Garib, yes, Molrep was done in few minutes but I’m not super
 convinced about the solution either. Same with BALBES and MrBump (which
 took a few more minutes, actually also days for MrBump)

  The space group appears to be P63 22 as judged by XDS, pointless,
 xtriage, however the crystals are split (at least in some areas it’s
 visible) but I thought XDS would take care of these “aliens” and eliminate
 them mostly. My graduate student, Lauren, found a nifty program called
 DIALS that we wish to explore further to rescue the “nice” data we have and
 hopefully solve the structure.

  Lower symmetry space groups were tried down to P21 with increasing
 number of molecules per asu and applying twin laws if necessary. The minor
 problem with the twins is how do I really know that it is a higher symmetry
 space group and not a 50% twin in a lower symmetry ? Rwork/Rfree in this
 particular case do not seem to help at all for distinguishing between the
 solutions. Maps looks sort of right but R-factors are not reflecting what
 you see on the screen.

  We appreciate any suggestions and ideas what else we could do.

  Thanks,

  Jürgen

  ..
 Jürgen Bosch
 Johns Hopkins University
 Bloomberg School of Public Health
 Department of Biochemistry  Molecular Biology
 Johns Hopkins Malaria Research Institute
 615 North Wolfe Street, W8708
 Baltimore, MD 21205
 Office: +1-410-614-4742
 Lab:  +1-410-614-4894
 Fax:  +1-410-955-2926
 http://lupo.jhsph.edu

Re: [ccp4bb] Phaser question, twinning, DIALS, suggestions welcome

[Jurgen Bosch]

Thanks Randy,

so from your reply it seems that cutoff is differently treated. And if I 
interpret your email correctly it is better to provide Phaser with a truncated 
versus a full data set. I tried both cases, but I had assumed that if you 
restrict the resolution within Phaser it would be the same as if you give 
Phaser to begin with a truncated dataset.
Perhaps it would be a good idea in th automatic routine to first check if the 
user wants to truncate the data and then run the automatic scoring analysis 
with that value ?

Jürgen

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742tel:%2B1-410-614-4742
Lab:  +1-410-614-4894tel:%2B1-410-614-4894
Fax:  +1-410-955-2926tel:%2B1-410-955-2926
http://lupo.jhsph.edu

On Oct 1, 2014, at 5:15 AM, Randy Read 
rj...@cam.ac.ukmailto:rj...@cam.ac.uk wrote:

Hi Jurgen,

You could send me a logfile off-list, and maybe I would spot something in there.

We’ve put some effort into putting more intelligence into the Phaser search, so 
that it adapts to the initial perceived difficulty of the problem in setting 
the initial parameters, and then adapts to indicators of success or failure 
during the search.  Much of the time this works very well, but there’s 
obviously room for improvement.  For one thing, it appears that we’re 
frequently too optimistic about how good the model will be and how easy the 
search will be.

One question: when you say that you cut at 2.5A for MR, do you do that by 
setting the resolution within the Phaser run, or do you have an MTZ file with 
only data to 2.5A?  If the former, then you’re over-riding some of Phaser’s 
automation, which will choose the initial resolution limit based on the 
perceived difficulty of the problem (a function of model completeness, expected 
RMS error of the model, and the number of reflections to different resolution 
limits).  It’s this initial automated choice that can go wrong if we’re too 
optimistic, because then a clear solution isn’t found, and then Phaser repeats 
the search with data to the full resolution, which can take longer than just 
choosing an intermediate resolution from the start.

Anyway, if the problem is expected to be easy but turns out to be difficult, 
this implies that some of the information used to decide it should be easy is 
wrong or too optimistic.  One top possibility is that the model is not as good 
as expected, e.g. because of conformational changes.  If there’s a potential 
hinge-bending motion, then you’re usually better off searching with separate 
domains.  If the change is something that can’t be described with rigid-body 
motions, then it would be better to increase the expected RMS error from what 
Phaser deduces from the sequence identity.  Increasing the RMSD by 10-20% would 
be a good first bet in such a case.

The other top possibility is that the space group is wrong.  Is there any 
ambiguity in the space group?  In particular, do any of the twinning tests 
indicate that the data may be twinned (which can lead to choosing too high 
symmetry)?

Best wishes,

Randy

On 1 Oct 2014, at 03:02, Jurgen Bosch jbos...@jhu.edumailto:jbos...@jhu.edu 
wrote:

Dear BB, or in particular Phaser developers :-)

This must be part of British humor right (or was that the Canadian influence 
Randy) ?

eLLG indicates that placement of ensemble ensemble_1 will be straightforward
   The data are sufficient to exceed the eLLG target

The search space is finite 143 x 143 x 80 Å with 3 or 4 molecules per asu, but 
Phaser has been burning CPU cycles quite a bit, we are approaching 24h by now. 
Data extends to 1.7 Å - for MR we cut at 2.5 Å.

I can hear Garib, yes, Molrep was done in few minutes but I’m not super 
convinced about the solution either. Same with BALBES and MrBump (which took a 
few more minutes, actually also days for MrBump)

The space group appears to be P63 22 as judged by XDS, pointless, xtriage, 
however the crystals are split (at least in some areas it’s visible) but I 
thought XDS would take care of these “aliens” and eliminate them mostly. My 
graduate student, Lauren, found a nifty program called DIALS that we wish to 
explore further to rescue the “nice” data we have and hopefully solve the 
structure.

Lower symmetry space groups were tried down to P21 with increasing number of 
molecules per asu and applying twin laws if necessary. The minor problem with 
the twins is how do I really know that it is a higher symmetry space group and 
not a 50% twin in a lower symmetry ? Rwork/Rfree in this particular case do not 
seem to help at all for distinguishing between the solutions. Maps looks sort 
of right but R-factors are not reflecting what you see on the screen.

We appreciate any suggestions and ideas what else we could do.

Thanks,

Jürgen

[ccp4bb] Phaser question, twinning, DIALS, suggestions welcome

[Jurgen Bosch]

Dear BB, or in particular Phaser developers :-)

This must be part of British humor right (or was that the Canadian influence 
Randy) ?

eLLG indicates that placement of ensemble ensemble_1 will be straightforward
   The data are sufficient to exceed the eLLG target

The search space is finite 143 x 143 x 80 Å with 3 or 4 molecules per asu, but 
Phaser has been burning CPU cycles quite a bit, we are approaching 24h by now. 
Data extends to 1.7 Å - for MR we cut at 2.5 Å.

I can hear Garib, yes, Molrep was done in few minutes but I’m not super 
convinced about the solution either. Same with BALBES and MrBump (which took a 
few more minutes, actually also days for MrBump)

The space group appears to be P63 22 as judged by XDS, pointless, xtriage, 
however the crystals are split (at least in some areas it’s visible) but I 
thought XDS would take care of these “aliens” and eliminate them mostly. My 
graduate student, Lauren, found a nifty program called DIALS that we wish to 
explore further to rescue the “nice” data we have and hopefully solve the 
structure.

Lower symmetry space groups were tried down to P21 with increasing number of 
molecules per asu and applying twin laws if necessary. The minor problem with 
the twins is how do I really know that it is a higher symmetry space group and 
not a 50% twin in a lower symmetry ? Rwork/Rfree in this particular case do not 
seem to help at all for distinguishing between the solutions. Maps looks sort 
of right but R-factors are not reflecting what you see on the screen.

We appreciate any suggestions and ideas what else we could do.

Thanks,

Jürgen

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742tel:%2B1-410-614-4742
Lab:  +1-410-614-4894tel:%2B1-410-614-4894
Fax:  +1-410-955-2926tel:%2B1-410-955-2926
http://lupo.jhsph.edu

Re: [ccp4bb] Phaser MR problem

[Randy Read]

Just to add to what Herman said:

The statistics are good for placing the domain represented by ensemble 1 
(TFZ=14.3) and the first copy of the domain represented by ensemble 2 
(TFZ=11.9), but not for the two possible solutions for placing the second copy 
of ensemble 2 (TFZs of 4.5 and 4.7).  So it’s possible that only the placement 
of the first two components is correct.  If you turn on symmetry in coot, do 
those two domains come together to form a sensible whole protein?  If so, you 
could try using that composite model to look for more copies of the whole 
protein (keeping in mind Herman’s point about the possible numbers of copies).

That said, it’s going to be a challenge to finish up the structure rebuilding 
and refinement when you have limited resolution and relatively low sequence 
identity starting models.  With 3-fold or greater NCS, averaging would help a 
great deal (2-fold helps somewhat but is less powerful); otherwise, you’re 
likely to need some additional phase information.

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 19 Sep 2014, at 10:33, Veerendra KUMAR (IMCB) 
veerend...@imcb.a-star.edu.sg wrote:

 Dear CCP4 members,
 
 Recently I have collected native data at 3.3 A resolution. The structure of 
 the protein should have two domains. The structure of c terminal domain from 
 homologous (30 seq similarity) is known. I took n terminal domain from 
 another homologous protein. I ran the phaser using these two ensembles and 
 got the following solutions.
 #   [No title given]
 SOLU SET RFZ=3.9 TFZ=14.3 PAK=4 LLG=144 TFZ==10.5 RFZ=2.4 TFZ=11.9 PAK=9 
 LLG=259 TFZ==7.0 RFZ=4.0 TFZ=4.5 PAK=24 LLG=207 TFZ==7.4
 SOLU SPAC I 41 3 2
 SOLU 6DIM ENSE ensemble1 EULER 43.364 14.638 271.356 FRAC 0.81509 0.22245 
 0.92422 BFAC -7.23070
 SOLU 6DIM ENSE ensemble2 EULER 173.495 55.758 234.557 FRAC 1.25797 -0.71934 
 0.10135 BFAC 1.81823
 SOLU 6DIM ENSE ensemble2 EULER 351.235 68.606 254.802 FRAC 0.64931 0.81795 
 0.27592 BFAC 5.82534
 SOLU ENSE ensemble1 VRMS 1.157
 SOLU ENSE ensemble2 VRMS 1.540
 SOLU SET RFZ=3.9 TFZ=14.3 PAK=4 LLG=144 TFZ==10.5 RFZ=2.4 TFZ=11.9 PAK=9 
 LLG=259 TFZ==7.0 RFZ=2.7 TFZ=4.7 PAK=19 LLG=202
 SOLU SPAC I 41 3 2
 SOLU 6DIM ENSE ensemble1 EULER 43.364 14.638 271.356 FRAC 0.81509 0.22245 
 0.92422 BFAC -7.23070
 SOLU 6DIM ENSE ensemble2 EULER 173.495 55.758 234.557 FRAC 1.25797 -0.71934 
 0.10135 BFAC 1.81823
 SOLU 6DIM ENSE ensemble2 EULER 41.452 118.850 315.630 FRAC 0.61025 0.05816 
 1.60902 BFAC 5.47988
 SOLU ENSE ensemble1 VRMS 1.157
 SOLU ENSE ensemble2 VRMS 1.540
 
 The TFZ score 14.3 suggests a solution. Then I did refinement using Ploy Ala 
 phaser model. The R values are 0.590/0.62. I use the map to build the model 
 in Buccaneer but it did not build anything.
 
 Is the pahser solution correct? Why are the R values so high despite the good 
 TFZ score? Any suggestions are greatly appreciated.
 
 Thank you
 
 Veerendra
 
 
 
 Note: This message may contain confidential information. If this Email/Fax 
 has been sent to you by mistake, please notify the sender and delete it 
 immediately. Thank you.

Re: [ccp4bb] Phaser MR problem

[Mark van Raaij]

Or perhaps there is only 1 copy and more solvent than you expect? This is not 
that uncommon.

On 20 Sep 2014 12:09, Randy Read rj...@cam.ac.uk wrote:

 Just to add to what Herman said: 

 The statistics are good for placing the domain represented by ensemble 1 
 (TFZ=14.3) and the first copy of the domain represented by ensemble 2 
 (TFZ=11.9), but not for the two possible solutions for placing the second 
 copy of ensemble 2 (TFZs of 4.5 and 4.7).  So it’s possible that only the 
 placement of the first two components is correct.  If you turn on symmetry in 
 coot, do those two domains come together to form a sensible whole protein?  
 If so, you could try using that composite model to look for more copies of 
 the whole protein (keeping in mind Herman’s point about the possible numbers 
 of copies). 

 That said, it’s going to be a challenge to finish up the structure rebuilding 
 and refinement when you have limited resolution and relatively low sequence 
 identity starting models.  With 3-fold or greater NCS, averaging would help a 
 great deal (2-fold helps somewhat but is less powerful); otherwise, you’re 
 likely to need some additional phase information. 

 Best wishes, 

 Randy Read 

 - 
 Randy J. Read 
 Department of Haematology, University of Cambridge 
 Cambridge Institute for Medical Research    Tel: +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 19 Sep 2014, at 10:33, Veerendra KUMAR (IMCB) 
 veerend...@imcb.a-star.edu.sg wrote: 

  Dear CCP4 members, 
  
  Recently I have collected native data at 3.3 A resolution. The structure of 
  the protein should have two domains. The structure of c terminal domain 
  from homologous (30 seq similarity) is known. I took n terminal domain from 
  another homologous protein. I ran the phaser using these two ensembles and 
  got the following solutions. 
  #   [No title given] 
  SOLU SET RFZ=3.9 TFZ=14.3 PAK=4 LLG=144 TFZ==10.5 RFZ=2.4 TFZ=11.9 PAK=9 
  LLG=259 TFZ==7.0 RFZ=4.0 TFZ=4.5 PAK=24 LLG=207 TFZ==7.4 
  SOLU SPAC I 41 3 2 
  SOLU 6DIM ENSE ensemble1 EULER 43.364 14.638 271.356 FRAC 0.81509 0.22245 
  0.92422 BFAC -7.23070 
  SOLU 6DIM ENSE ensemble2 EULER 173.495 55.758 234.557 FRAC 1.25797 -0.71934 
  0.10135 BFAC 1.81823 
  SOLU 6DIM ENSE ensemble2 EULER 351.235 68.606 254.802 FRAC 0.64931 0.81795 
  0.27592 BFAC 5.82534 
  SOLU ENSE ensemble1 VRMS 1.157 
  SOLU ENSE ensemble2 VRMS 1.540 
  SOLU SET RFZ=3.9 TFZ=14.3 PAK=4 LLG=144 TFZ==10.5 RFZ=2.4 TFZ=11.9 PAK=9 
  LLG=259 TFZ==7.0 RFZ=2.7 TFZ=4.7 PAK=19 LLG=202 
  SOLU SPAC I 41 3 2 
  SOLU 6DIM ENSE ensemble1 EULER 43.364 14.638 271.356 FRAC 0.81509 0.22245 
  0.92422 BFAC -7.23070 
  SOLU 6DIM ENSE ensemble2 EULER 173.495 55.758 234.557 FRAC 1.25797 -0.71934 
  0.10135 BFAC 1.81823 
  SOLU 6DIM ENSE ensemble2 EULER 41.452 118.850 315.630 FRAC 0.61025 0.05816 
  1.60902 BFAC 5.47988 
  SOLU ENSE ensemble1 VRMS 1.157 
  SOLU ENSE ensemble2 VRMS 1.540 
  
  The TFZ score 14.3 suggests a solution. Then I did refinement using Ploy 
  Ala phaser model. The R values are 0.590/0.62. I use the map to build the 
  model in Buccaneer but it did not build anything. 
  
  Is the pahser solution correct? Why are the R values so high despite the 
  good TFZ score? Any suggestions are greatly appreciated. 
  
  Thank you 
  
  Veerendra 
  
  
  
  Note: This message may contain confidential information. If this Email/Fax 
  has been sent to you by mistake, please notify the sender and delete it 
  immediately. Thank you. 

[ccp4bb] Phaser MR problem

[Veerendra KUMAR (IMCB)]

Dear CCP4 members,

Recently I have collected native data at 3.3 A resolution. The structure of the 
protein should have two domains. The structure of c terminal domain from 
homologous (30 seq similarity) is known. I took n terminal domain from another 
homologous protein. I ran the phaser using these two ensembles and got the 
following solutions.
#   [No title given]
SOLU SET RFZ=3.9 TFZ=14.3 PAK=4 LLG=144 TFZ==10.5 RFZ=2.4 TFZ=11.9 PAK=9 
LLG=259 TFZ==7.0 RFZ=4.0 TFZ=4.5 PAK=24 LLG=207 TFZ==7.4
SOLU SPAC I 41 3 2
SOLU 6DIM ENSE ensemble1 EULER 43.364 14.638 271.356 FRAC 0.81509 0.22245 
0.92422 BFAC -7.23070
SOLU 6DIM ENSE ensemble2 EULER 173.495 55.758 234.557 FRAC 1.25797 -0.71934 
0.10135 BFAC 1.81823
SOLU 6DIM ENSE ensemble2 EULER 351.235 68.606 254.802 FRAC 0.64931 0.81795 
0.27592 BFAC 5.82534
SOLU ENSE ensemble1 VRMS 1.157
SOLU ENSE ensemble2 VRMS 1.540
SOLU SET RFZ=3.9 TFZ=14.3 PAK=4 LLG=144 TFZ==10.5 RFZ=2.4 TFZ=11.9 PAK=9 
LLG=259 TFZ==7.0 RFZ=2.7 TFZ=4.7 PAK=19 LLG=202
SOLU SPAC I 41 3 2
SOLU 6DIM ENSE ensemble1 EULER 43.364 14.638 271.356 FRAC 0.81509 0.22245 
0.92422 BFAC -7.23070
SOLU 6DIM ENSE ensemble2 EULER 173.495 55.758 234.557 FRAC 1.25797 -0.71934 
0.10135 BFAC 1.81823
SOLU 6DIM ENSE ensemble2 EULER 41.452 118.850 315.630 FRAC 0.61025 0.05816 
1.60902 BFAC 5.47988
SOLU ENSE ensemble1 VRMS 1.157
SOLU ENSE ensemble2 VRMS 1.540

The TFZ score 14.3 suggests a solution. Then I did refinement using Ploy Ala 
phaser model. The R values are 0.590/0.62. I use the map to build the model in 
Buccaneer but it did not build anything.

Is the pahser solution correct? Why are the R values so high despite the good 
TFZ score? Any suggestions are greatly appreciated.

Thank you

Veerendra



Note: This message may contain confidential information. If this Email/Fax has 
been sent to you by mistake, please notify the sender and delete it 
immediately. Thank you.

[ccp4bb] Fwd: [ccp4bb] phaser issue MR

[Almudena Ponce Salvatierra]

Dear all,

thank you for your suggestions, I finally fix the problem as follows. I'll
write a summary here for future reference.

1) Phaser run 1#

- I provide different ensembles
- I get a solution in which some of them have been placed

2) Phaser run 2# ERROR

- I provide the ensembles that were not placed in the previous run and
REMOVE THE ONES THAT HAD BEEN PLACED
- I provide the .sol file
- The program gives the error I sent yesterday

3) Phaser run 3# it works again

Since you said what happened was that Phaser was not finding something and
the .sol file contained information about the ensembles that I removed...

- I provided again all the ensembles I gave in run 1#
- I provide de .sol file (I understand it will fix the solution of the
ensembles from run 1#)
- It runs

So, this was my fix :-) I hear many times the sentence fix a solution,
but then whenever I asked someone (before yesterday), each person refers to
it in an ambiguous way! some say you need to provide phaser with the pdb
from the solution you want to fix, some say that you need to provide the
.sol file from what you want to fix and then provide only one new ensemble
at the time... maybe it would be useful to have some script/example online
of the command line itself, so that one knows what to input exactly. Maybe
each one's way of explaining the same thing can lead to misunderstandings
at the end.

Best wishes,

Have a nice day.

Almudena


-- Forwarded message --
From: Almudena Ponce Salvatierra maps.fa...@gmail.com
Date: 2014-06-03 9:49 GMT+02:00
Subject: Re: [ccp4bb] phaser issue MR
To: Airlie McCoy ajm...@cam.ac.uk


Dear Airlie,

don't worry, actually it was you who gave me the clue when you told me what
the error was standing for. I will try to be a clear as possible:

1) Phaser run 1#

- I provide different ensembles
- I get a solution in which some of them have been placed

2) Phaser run 2# ERROR

- I provide the ensembles that were not placed in the previous run and
REMOVE THE ONES THAT HAD BEEN PLACED
- I provide the .sol file
- The program gives the error I sent yesterday

3) Phaser run 3# it works again

Since you said what happened was that Phaser was not finding something and
the .sol file contained information about the ensembles that I removed...

- I provided again all the ensembles I gave in run 1#
- I provide de .sol file (I understand it will fix the solution of the
ensembles from run 1#)
- It runs

So, this was my fix :-) I hear many times the sentence fix a solution,
but then whenever I asked someone (before yesterday), each person refers to
it in an ambiguous way! some say you need to provide phaser with the pdb
from the solution you want to fix, some say that you need to provide the
.sol file from what you want to fix and then provide only one new ensemble
at the time... maybe it would be useful to have some script/example online
of the command line itself, so that one knows what to input exactly. Maybe
each one's way of explaining the same thing can lead to misunderstandings
at the end.

I have another question, if you don't mind. How good does the TFZ score get
in one of this iterative Molecular replacement routines? I am now above 5
(5.4) which I know is unlikely but I need to take into account that I
start with fragments that maybe are not exactly as they are in the
structure (I mean in reality) and also that the model is incomplete,
meaning that even though I have now most of it places there are still some
regions that are not connected, some others with empty electron density...
What would you recommend in this case?

I also have the following warinings:

- Best model and data are insufficient to reach half expected LLG target:
placement of one/first ensemble will be very difficult.

- Search request requires more scattering than defined in composition.
Composition increased to accomodate search components.

Thank you very much for your time and consideration.

Best wishes,

Almudena.



2014-06-02 22:33 GMT+02:00 Airlie McCoy ajm...@cam.ac.uk:

Hi Almundena, Apologies, I had not had a chance to look at it... what was
 your fix? Airlie


 On Jun 2 2014, Almudena Ponce Salvatierra wrote:

  Dear Airlie,

 I already solved the problem.

 Thank you very much anyway.

 Best wishes,

 Almudena


 2014-06-02 15:43 GMT+02:00 Almudena Ponce Salvatierra 
 maps.fa...@gmail.com
 :

  Sorry, Airlie, the input is this one,

 ENTER KEYWORD INPUT FROM FILE OR FROM STANDARD INPUT


 $TEXT:Script: $$ Baubles Markup $$

 #---PHASER COMMAND SCRIPT GENERATED BY CCP4I---

 TITLE start

 MODE MR_AUTO

 ROOT /data/almudena/ccp4/iterativeMR/may_attempt/epmrsol/epmr_24

  #---DEFINE DATA---

 HKLIN /data/almudena/ccp4/iterativeMR/epmr/forccp4_itMR.mtz

 LABIN  F=FP SIGF=SIGFP

 SGALTERNATIVE SELECT HAND

 #---DEFINE ENSEMBLES---

 ENSEMBLE loop 

 PDB 
 /data/almudena/ccp4/iterativeMR/epmr/epmr_start_6bp/4ntloop-coot-0.pdb
 

  IDENT 99.0

 ENSEMBLE 6bp 

 PDB 

   /data/almudena/ccp4/iterativeMR/epmr

Re: [ccp4bb] [ccp4bb] phaser issue MR

[Randy Read]

Dear Almudena,

We actually have a tutorial that goes through the process of defining a 
solution step by step: 
http://www.phaser.cimr.cam.ac.uk/index.php/MR_using_keyword_input.

The .sol file is a small text file that just contains the description of how a 
defined ensemble should be rotated and translated.  If you look at that file, 
you’ll see that it doesn’t contain the ENSEMBLE definitions, so those still 
have to be provided in the script that refers to the .sol file.

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 3 Jun 2014, at 09:55, Almudena Ponce Salvatierra maps.fa...@gmail.com 
wrote:

 Dear all, 
 
 thank you for your suggestions, I finally fix the problem as follows. I'll 
 write a summary here for future reference. 
 
 1) Phaser run 1# 
 
 - I provide different ensembles
 - I get a solution in which some of them have been placed
 
 2) Phaser run 2# ERROR
 
 - I provide the ensembles that were not placed in the previous run and REMOVE 
 THE ONES THAT HAD BEEN PLACED
 - I provide the .sol file
 - The program gives the error I sent yesterday
 
 3) Phaser run 3# it works again
 
 Since you said what happened was that Phaser was not finding something and 
 the .sol file contained information about the ensembles that I removed...
 
 - I provided again all the ensembles I gave in run 1#
 - I provide de .sol file (I understand it will fix the solution of the 
 ensembles from run 1#)
 - It runs
 
 So, this was my fix :-) I hear many times the sentence fix a solution, but 
 then whenever I asked someone (before yesterday), each person refers to it in 
 an ambiguous way! some say you need to provide phaser with the pdb from the 
 solution you want to fix, some say that you need to provide the .sol file 
 from what you want to fix and then provide only one new ensemble at the 
 time... maybe it would be useful to have some script/example online of the 
 command line itself, so that one knows what to input exactly. Maybe each 
 one's way of explaining the same thing can lead to misunderstandings at the 
 end.
 
 Best wishes, 
 
 Have a nice day.
 
 Almudena
 
 
 -- Forwarded message --
 From: Almudena Ponce Salvatierra maps.fa...@gmail.com
 Date: 2014-06-03 9:49 GMT+02:00
 Subject: Re: [ccp4bb] phaser issue MR
 To: Airlie McCoy ajm...@cam.ac.uk
 
 
 Dear Airlie, 
 
 don't worry, actually it was you who gave me the clue when you told me what 
 the error was standing for. I will try to be a clear as possible:
 
 1) Phaser run 1# 
 
 - I provide different ensembles
 - I get a solution in which some of them have been placed
 
 2) Phaser run 2# ERROR
 
 - I provide the ensembles that were not placed in the previous run and REMOVE 
 THE ONES THAT HAD BEEN PLACED
 - I provide the .sol file
 - The program gives the error I sent yesterday
 
 3) Phaser run 3# it works again
 
 Since you said what happened was that Phaser was not finding something and 
 the .sol file contained information about the ensembles that I removed...
 
 - I provided again all the ensembles I gave in run 1#
 - I provide de .sol file (I understand it will fix the solution of the 
 ensembles from run 1#)
 - It runs
 
 So, this was my fix :-) I hear many times the sentence fix a solution, but 
 then whenever I asked someone (before yesterday), each person refers to it in 
 an ambiguous way! some say you need to provide phaser with the pdb from the 
 solution you want to fix, some say that you need to provide the .sol file 
 from what you want to fix and then provide only one new ensemble at the 
 time... maybe it would be useful to have some script/example online of the 
 command line itself, so that one knows what to input exactly. Maybe each 
 one's way of explaining the same thing can lead to misunderstandings at the 
 end.
 
 I have another question, if you don't mind. How good does the TFZ score get 
 in one of this iterative Molecular replacement routines? I am now above 5 
 (5.4) which I know is unlikely but I need to take into account that I start 
 with fragments that maybe are not exactly as they are in the structure (I 
 mean in reality) and also that the model is incomplete, meaning that even 
 though I have now most of it places there are still some regions that are not 
 connected, some others with empty electron density... What would you 
 recommend in this case? 
 
 I also have the following warinings:
 
 - Best model and data are insufficient to reach half expected LLG target: 
 placement of one/first ensemble will be very difficult. 
 
 - Search request requires more scattering than defined in composition. 
 Composition increased

[ccp4bb] phaser issue MR

[Almudena Ponce Salvatierra]

Dear all,

I am using Phaser for Molecular replacement. After Phaser places part of
the structure, I would like to run it again, giving this time as search
ensembles new pieces of structure. I thought what I had to do was simply to
put in know solution the .sol file coming out from the previous Phaser
run. However when I do so I get the following message:

UNHANDLED ERROR: Program internal error in source file data_pdb.cc (line
144)

*** Consistency check (M  MOLECULE.size()) failed. ***

Please email this log file with some supporting information and/or data to

cimr-pha...@lists.cam.ac.uk


Could anybody please tell me how to proceed? Maybe there is some option I
am not using or some addtional data I need to provide the program... I
don't know.

Any suggestions are welcome!

Thanks a lot in advance!

Best wishes,

Almu

-- 
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany

[ccp4bb] Phaser segmentation fault (core dump)

[de Waal, Parker]

Hello Everyone,

I'm trying to using Phaser to perform molecular replacement, however each time 
I run my input script Phaser ends with a segmentation fault. Here is the error 
phaser0.inp: line 29:  1414 Segmentation fault  (core dumped) phaser  
EOF

My input script can be found here: 
https://gist.github.com/anonymous/2b474f501e1ad694be47

If anyone can provide any input I would be greatly appreciative.

Best,
Parker

[ccp4bb] AW: [ccp4bb] Phaser output problem

[Herman . Schreuder]

Looks like you need to search for more molecules.
Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Amanda 
Blythe
Gesendet: Montag, 16. Dezember 2013 11:46
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Phaser output problem

I am trying to solve a structure by molecular replacement using Phaser.  The 
pdb fits the density really well but the output shows strange crystal packing. 
I've attached an image, does anyone know what is causing this?

[cid:image001.jpg@01CEFA56.DCDA5270]

Amanda
PhD student

Laboratory 4.26, Bayliss Building

School of Chemistry and Biochemistry
M313
The University of Western Australia
35 Stirling Highway
Crawley WA 6009
Australia

T (+61 8) 6488 3163
E lewis...@student.uwa.edu.aumailto:lewis...@student.uwa.edu.au

inline: image001.jpg

Re: [ccp4bb] AW: [ccp4bb] Phaser output problem

[Eleanor Dodson]

Things to check - number of molecules to search for.
You can use Matthewscoeff to get a suggestion - MOLREP does it
autromatically .

Space group - has Phaser chosen as best SG an alternative to that in your
header?

Eleanor


On 16 December 2013 11:03, herman.schreu...@sanofi.com wrote:

  Looks like you need to search for more molecules.

 Best,

 Herman



 *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
 *Amanda Blythe
 *Gesendet:* Montag, 16. Dezember 2013 11:46
 *An:* CCP4BB@JISCMAIL.AC.UK
 *Betreff:* [ccp4bb] Phaser output problem



 I am trying to solve a structure by molecular replacement using Phaser.
  The pdb fits the density really well but the output shows strange crystal
 packing. I've attached an image, does anyone know what is causing this?





 Amanda

 PhD student

 Laboratory 4.26, Bayliss Building

 School of Chemistry and Biochemistry
 M313
 The University of Western Australia
 35 Stirling Highway
 Crawley WA 6009
 Australia

 *T* (+61 8) 6488 3163

 *E* lewis...@student.uwa.edu.au



image001.jpg

Re: [ccp4bb] Phaser question

[Randy Read]

Just to follow up on this:

The enormous increase between the TFZ= and TFZ== numbers is surprising, so I 
focused on that in my original answer to Fred's question.  However, if anyone 
wants to know the difference between these, it's documented on this web page: 
http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#Annotation.

Best wishes,

Randy Read

On 5 Dec 2013, at 08:36, vellieux frederic.velli...@ibs.fr wrote:

 Hiyya all,
 
 I have a question about the latest Phaser output, concerning TFZ = and TFZ == 
 .
 
 I do not know how to interpret outputs of the type
 
 TFZ = 5.2 TFZ == 54.1;
 TFZ = 5.8 TFZ == 63.0;
 TFZ = 6.4 TFZ == 19.7 (these are real TFZ figures coming from Phaser log 
 files).
 
 I used to analyse the Phaser output using TFZ, when only a single number was 
 given. Now with two figures to consider, I do not know what to think of it 
 any more.
 
 Any ideas out there ?
 
 And best wishes for an enjoyable end-of-the-year season (be it in the cold or 
 in the sun depending on which side of the planet you sit).
 
 Fred.
 
 -- 
 Fred. Vellieux (B.Sc., Ph.D., hdr)
 
 IBS2 / ELMA
 Campus EPN
 6 rue Jules Horowitz
 F-38042 Grenoble
 Tel: +33 457428605
 (Fax: +33 438785494)

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

[ccp4bb] Phaser question

[vellieux]

Hiyya all,

I have a question about the latest Phaser output, concerning TFZ = and 
TFZ == .


I do not know how to interpret outputs of the type

TFZ = 5.2 TFZ == 54.1;
TFZ = 5.8 TFZ == 63.0;
TFZ = 6.4 TFZ == 19.7 (these are real TFZ figures coming from Phaser log 
files).


I used to analyse the Phaser output using TFZ, when only a single number 
was given. Now with two figures to consider, I do not know what to think 
of it any more.


Any ideas out there ?

And best wishes for an enjoyable end-of-the-year season (be it in the 
cold or in the sun depending on which side of the planet you sit).


Fred.

--
Fred. Vellieux (B.Sc., Ph.D., hdr)

IBS2 / ELMA
Campus EPN
6 rue Jules Horowitz
F-38042 Grenoble
Tel: +33 457428605
(Fax: +33 438785494)

Re: [ccp4bb] Phaser question

[Randy Read]

Hi Fred,

Send me the logfiles (off-line), because this shouldn't be happening and I'd 
like to have a look.  That said, we've been seeing some similar problems in 
certain circumstances, i.e. B-factor refinement refines to significant negative 
B-factor values, and data at high resolution have very low signal-to-noise.  If 
those are the circumstances, we're currently working on a fix and maybe we can 
get you to test it on your data once it's implemented.

All the best,

Randy

On 5 Dec 2013, at 08:36, vellieux frederic.velli...@ibs.fr wrote:

 Hiyya all,
 
 I have a question about the latest Phaser output, concerning TFZ = and TFZ == 
 .
 
 I do not know how to interpret outputs of the type
 
 TFZ = 5.2 TFZ == 54.1;
 TFZ = 5.8 TFZ == 63.0;
 TFZ = 6.4 TFZ == 19.7 (these are real TFZ figures coming from Phaser log 
 files).
 
 I used to analyse the Phaser output using TFZ, when only a single number was 
 given. Now with two figures to consider, I do not know what to think of it 
 any more.
 
 Any ideas out there ?
 
 And best wishes for an enjoyable end-of-the-year season (be it in the cold or 
 in the sun depending on which side of the planet you sit).
 
 Fred.
 
 -- 
 Fred. Vellieux (B.Sc., Ph.D., hdr)
 
 IBS2 / ELMA
 Campus EPN
 6 rue Jules Horowitz
 F-38042 Grenoble
 Tel: +33 457428605
 (Fax: +33 438785494)

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

[ccp4bb] Phaser output in QtRView under Windows XP

[Derek Logan]

Hi,

I need (reluctantly!) to install CCP4 on 20 fairly ancient Windows XP machines 
for a course. I have installed CCP4 on a central server with network-mounted 
drive and applied all the updates. CCP4 is then runnable on the individual 
computers. However when I run a Phaser job the output in QtRView ouptut does 
not look the same as it does when I run the same job on my Mac. All the graphs 
are missing and the only sections displayed are Input Files and Output 
Files. I don't have the same problem for Refmac, where the graphs display 
correctly. I also tested running the Phaser job directly on the server (which 
has Windows Server 2003 R2) and the output is also lacking the graphs. I was 
wondering if this was a known issue. I haven't found anything on the Web.

Thanks
Derek

Derek Logan tel: +46 46 222 1443
Associate Professor mob: +46 76 8585 707
Dept. of Biochemistry and Structural Biology  
www.cmps.lu.sehttp://www.cmps.lu.se
Centre for Molecular Protein Science   
www.maxlab.lu.se/node/307http://www.maxlab.lu.se/node/307
Lund University, Box 124, 221 00 Lund, Sweden

[ccp4bb] Phaser gives error in 6.4.0 version

[S. Karthikeyan]

 

Dear All, 

Installed the CCP4 6.4.0 version recently on CentoS 5. When I try to run
phaser I get the following error. Apparently I can reproduce the error
for different reflection file. This happens after getting the rotation,
translation and packing function. Any suggestions to this problem is
highly appreciated. 

--

REFINEMENT

--

 Protocol cycle #1 of 1

 Refinement protocol for this macrocycle:

 ROTATION : REFINE

 TRANSLATION : REFINE

 BFACTOR : REFINE

 MODEL VRMS : FIX

 MAP CELL SCALE: FIX

 LAST ONLY : FALSE

 There are 2 solutions to refine

 Spreading calculation onto 2 threads.

 Refining solutions

 0% 100%


|***

* Information from CCP4Interface script

***

The program run with command:
/home/programs/linux/ccp4/ccp4-6.4.0/bin/phaser 

has failed with error message

terminate called after throwing an instance of 'cctbx::error'

 what(): cctbx Error: Lattice type not specified.

***

Thanking you 

With regards 

-Karthik 

-- 
*
Dr.Karthikeyan Subramanian, Ph.D
Scientist, Protein Crystallography Lab
Institute of Microbial Technology 
Council of Scientific and Industrial Research (CSIR)
Sector 39-A, Chandigarh - 160036, INDIA
email:skart...@imtech.res.in, skarthi...@gmail.com
Phone: +91-172-6665193 Fax: +91-172-2690585 
*
 

Re: [ccp4bb] phaser 2.5.2 in ccp4 6.3.0 does not output Hendrickson Lattman coefficients

[Randy Read]

Dear Petr,

Presumably you're just talking about Phaser for molecular replacement, because 
Phaser still produces HL coefficients for SAD phasing.

There were two major reasons we made this change.  First, the presence of HL 
coefficients can fool some programs into thinking that you have experimental 
phase information that is independent of your model, which is not true for 
phases from molecular replacement.  Second, for unimodal sources of phase 
information like model phases, the HL coefficients are redundant and can be 
generated from the phase and FOM, e.g. by using the HLCONV command in sftools.

We could easily put this option back in, controlled for instance by setting the 
VERBOSE flag, if there were a compelling reason.  No-one else has complained 
since we made this change a year ago, but maybe they have been suffering in 
silence!  Could you let us know why you find this feature extremely useful?

Best wishes,

Randy Read
 
On 2 Jul 2013, at 18:41, Petr Leiman petr.lei...@epfl.ch wrote:

 I have just found out that phaser v. 2.5.2 in ccp4 6.3.0-021 does not 
 output columns with HL coefficients. I cannot find a combination of 
 buttons in CCP4i GUI to enable this extremely useful feature. This is 
 the first time I tried phaser in the latest CCP4 release and I am 
 shocked this problem has not been discovered and fixed already. If there 
 is a reason to this new output column behavior, it would be very useful 
 to hear this reason.
 
 Sincerely,
 
 Petr
 
 -- 
 Petr Leiman
 EPFL
 BSP 415
 CH-1015 Lausanne
 Switzerand
 Office: +41 21 69 30 441
 Mobile: +41 79 538 7647
 Fax: +41 21 69 30 422

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

Re: [ccp4bb] phaser 2.5.2 in ccp4 6.3.0 does not output Hendrickson Lattman coefficients

[Petr Leiman]

Dear Randy,

Thank you for your quick response. Obviously, you have given this a lot 
of thought.

I would like to have the HL coefficients in the phaser output file for 
downstream compatibility with density modification programs such as 
resolve.

Thank you,

Petr

On 07/03/2013 10:46 AM, Randy Read wrote:
 Dear Petr,

 Presumably you're just talking about Phaser for molecular replacement, 
 because Phaser still produces HL coefficients for SAD phasing.

 There were two major reasons we made this change.  First, the presence of HL 
 coefficients can fool some programs into thinking that you have experimental 
 phase information that is independent of your model, which is not true for 
 phases from molecular replacement.  Second, for unimodal sources of phase 
 information like model phases, the HL coefficients are redundant and can be 
 generated from the phase and FOM, e.g. by using the HLCONV command in sftools.

 We could easily put this option back in, controlled for instance by setting 
 the VERBOSE flag, if there were a compelling reason.  No-one else has 
 complained since we made this change a year ago, but maybe they have been 
 suffering in silence!  Could you let us know why you find this feature 
 extremely useful?

 Best wishes,

 Randy Read
   
 On 2 Jul 2013, at 18:41, Petr Leiman petr.lei...@epfl.ch wrote:

 I have just found out that phaser v. 2.5.2 in ccp4 6.3.0-021 does not
 output columns with HL coefficients. I cannot find a combination of
 buttons in CCP4i GUI to enable this extremely useful feature. This is
 the first time I tried phaser in the latest CCP4 release and I am
 shocked this problem has not been discovered and fixed already. If there
 is a reason to this new output column behavior, it would be very useful
 to hear this reason.

 Sincerely,

 Petr

 -- 
 Petr Leiman
 EPFL
 BSP 415
 CH-1015 Lausanne
 Switzerand
 Office: +41 21 69 30 441
 Mobile: +41 79 538 7647
 Fax: +41 21 69 30 422
 --
 Randy J. Read
 Department of Haematology, University of Cambridge
 Cambridge Institute for Medical Research  Tel: + 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

[ccp4bb] phaser 2.5.2 in ccp4 6.3.0 does not output Hendrickson Lattman coefficients

[Petr Leiman]

I have just found out that phaser v. 2.5.2 in ccp4 6.3.0-021 does not 
output columns with HL coefficients. I cannot find a combination of 
buttons in CCP4i GUI to enable this extremely useful feature. This is 
the first time I tried phaser in the latest CCP4 release and I am 
shocked this problem has not been discovered and fixed already. If there 
is a reason to this new output column behavior, it would be very useful 
to hear this reason.

Sincerely,

Petr

-- 
Petr Leiman
EPFL
BSP 415
CH-1015 Lausanne
Switzerand
Office: +41 21 69 30 441
Mobile: +41 79 538 7647
Fax: +41 21 69 30 422

Re: [ccp4bb] Phaser MR with partial solution, 8 molecules/ASU

[Eleanor Dodson]

On the whole it is good practice to refine the 7 molecules you have - correct 
sequence etc etc, all with NCS restraints a 3A, then if you like use one of 
your improved molecules as the search model. But don't you have some NC 
symmetry such as dimers or tetramers - if so take one of the complete units and 
fit over the partner of the missing molecule - it is very probable then that 
you have positioned the lost one.
Or if you want to be completely automated - use the dimer/tetramer whatever as 
the search model..
  Eleanor
MOLREP is good at this - 


On 30 Oct 2012, at 14:53, Mark J van Raaij wrote:

 if you are sure about it's position, why not put the 8th molecule by hand?
 why believe what a program does more than you can see by eye?
 (this is nothing against Phaser, it is a great program)
 
 Mark J van Raaij
 Laboratorio M-4
 Dpto de Estructura de Macromoleculas
 Centro Nacional de Biotecnologia - CSIC
 c/Darwin 3
 E-28049 Madrid, Spain
 tel. (+34) 91 585 4616
 http://www.cnb.csic.es/~mjvanraaij
 
 
 
 On 30 Oct 2012, at 15:44, Jacob Wong wrote:
 
 Dear all, I have this (3.0 A) structure that has 8 molecules per ASU - 
 Phaser was able to find 7 molecules correctly, but not the last one, as 
 indicated by the .sol file (TFZ=5.1) below and the resultant density map. I 
 tried to delete the entry of the last molecule and give the truncated .sol 
 file for another round of MR but Phaser returned with the same solution that 
 has the 8th molecule misplaced. I am tempted to place the 8th molecule by 
 hand but before that would like to learn from you a better way of handling 
 it. One thing I could think of is to refine/rebuild the partial structure 
 with the 7 molecules so as to resolve any potential packing clashes due to 
 model/structure variations and then let Phaser find/position the 8th one for 
 me, but it appears that Phaser doesn't accept .pdb file for a MR with 
 partial solution routine? Thank you, Jacob 
 
 #   [No title given] 
 SPACEGROUP P 21 21 21
 SOLU SET RFZ=3.7 TFZ=8.2 PAK=0 LLG=78 RFZ=3.7 TFZ=16.0 PAK=0 LLG=248 
 TFZ==17.2 RFZ=3.7 TFZ=17.8 PAK=0 LLG=463 TFZ==19.7 RFZ=2.9 TFZ=23.0 PAK=0 
 LLG=765 TFZ==23.2 RFZ=2.8 TFZ=28.6 PAK=0 LLG=1201 TFZ==30.0 RFZ=3.9 TFZ=23.1 
 PAK=0 LLG=1537 TFZ==24.3 RFZ=2.6 TFZ=19.5 PAK=1 LLG=2096 TFZ==32.1 RFZ=3.0 
 TFZ=5.1 PAK=1 LLG=1945 TFZ==7.0
 SOLU 6DIM ENSE ensemble1 EULER 333.533 143.979 14.880 FRAC -0.30547 0.22985 
 -0.12420 BFAC 0.0
 SOLU 6DIM ENSE ensemble1 EULER 287.095 31.031 200.132 FRAC -0.01202 0.48107 
 -0.12591 BFAC 0.0
 SOLU 6DIM ENSE ensemble1 EULER 220.563 33.756 203.275 FRAC -0.33196 0.18927 
 -0.27514 BFAC 0.0
 SOLU 6DIM ENSE ensemble1 EULER 125.978 23.511 167.527 FRAC 0.36411 -0.45096 
 -0.17121 BFAC 0.0
 SOLU 6DIM ENSE ensemble1 EULER 148.925 162.593 356.498 FRAC -0.41711 
 -0.09462 -0.07282 BFAC 0.0
 SOLU 6DIM ENSE ensemble1 EULER 323.033 34.903 192.073 FRAC -0.53201 -0.04754 
 -0.02533 BFAC 0.0
 SOLU 6DIM ENSE ensemble1 EULER 113.904 157.019 345.596 FRAC 0.09892 -0.60041 
 -0.17986 BFAC 0.0
 SOLU 6DIM ENSE ensemble1 EULER 79.967 95.631 1.727 FRAC -0.41239 0.07915 
 -0.05760 BFAC 0.0

Re: [ccp4bb] Phaser MR with partial solution, 8 molecules/ASU

[Mark J van Raaij]

if you are sure about it's position, why not put the 8th molecule by hand?
why believe what a program does more than you can see by eye?
(this is nothing against Phaser, it is a great program)

Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij



On 30 Oct 2012, at 15:44, Jacob Wong wrote:

 Dear all, I have this (3.0 A) structure that has 8 molecules per ASU - Phaser 
 was able to find 7 molecules correctly, but not the last one, as indicated by 
 the .sol file (TFZ=5.1) below and the resultant density map. I tried to 
 delete the entry of the last molecule and give the truncated .sol file for 
 another round of MR but Phaser returned with the same solution that has the 
 8th molecule misplaced. I am tempted to place the 8th molecule by hand but 
 before that would like to learn from you a better way of handling it. One 
 thing I could think of is to refine/rebuild the partial structure with the 7 
 molecules so as to resolve any potential packing clashes due to 
 model/structure variations and then let Phaser find/position the 8th one for 
 me, but it appears that Phaser doesn't accept .pdb file for a MR with 
 partial solution routine? Thank you, Jacob 
 
 #   [No title given] 
 SPACEGROUP P 21 21 21
 SOLU SET RFZ=3.7 TFZ=8.2 PAK=0 LLG=78 RFZ=3.7 TFZ=16.0 PAK=0 LLG=248 
 TFZ==17.2 RFZ=3.7 TFZ=17.8 PAK=0 LLG=463 TFZ==19.7 RFZ=2.9 TFZ=23.0 PAK=0 
 LLG=765 TFZ==23.2 RFZ=2.8 TFZ=28.6 PAK=0 LLG=1201 TFZ==30.0 RFZ=3.9 TFZ=23.1 
 PAK=0 LLG=1537 TFZ==24.3 RFZ=2.6 TFZ=19.5 PAK=1 LLG=2096 TFZ==32.1 RFZ=3.0 
 TFZ=5.1 PAK=1 LLG=1945 TFZ==7.0
 SOLU 6DIM ENSE ensemble1 EULER 333.533 143.979 14.880 FRAC -0.30547 0.22985 
 -0.12420 BFAC 0.0
 SOLU 6DIM ENSE ensemble1 EULER 287.095 31.031 200.132 FRAC -0.01202 0.48107 
 -0.12591 BFAC 0.0
 SOLU 6DIM ENSE ensemble1 EULER 220.563 33.756 203.275 FRAC -0.33196 0.18927 
 -0.27514 BFAC 0.0
 SOLU 6DIM ENSE ensemble1 EULER 125.978 23.511 167.527 FRAC 0.36411 -0.45096 
 -0.17121 BFAC 0.0
 SOLU 6DIM ENSE ensemble1 EULER 148.925 162.593 356.498 FRAC -0.41711 -0.09462 
 -0.07282 BFAC 0.0
 SOLU 6DIM ENSE ensemble1 EULER 323.033 34.903 192.073 FRAC -0.53201 -0.04754 
 -0.02533 BFAC 0.0
 SOLU 6DIM ENSE ensemble1 EULER 113.904 157.019 345.596 FRAC 0.09892 -0.60041 
 -0.17986 BFAC 0.0
 SOLU 6DIM ENSE ensemble1 EULER 79.967 95.631 1.727 FRAC -0.41239 0.07915 
 -0.05760 BFAC 0.0

[ccp4bb] Phaser and space groups

[Jan Abendroth]

Hi all,
we have been running into a space group issue when we start phaser (2.5.1) 
through ccp4i since the installation of ccp4-6.3.0:

We typically scale data in the point group and then let Phaser go through 
various space groups. Even though the corresponding line appears in the input 
file
SGALTERNATIVE SELECT LIST
SGALTERNATIVE TEST P41
rotation and translation function would only run in the space group provided by 
the mtz file. Obviously it does not matter for the rotation function.

As a work around one can edit the input file (run view com file), by replacing 
the two lines mentioned above with 
SPACEGROUP P41
This is a bit inconvenient though.

Any ideas what is going wrong with the standard way?

Cheers,
Jan
--
Jan Abendroth
Emerald BioStructures
Seattle / Bainbridge Island WA, USA
home: Jan.Abendroth_at_gmail.com
work: JAbendroth_at_embios.com
http://www.emeraldbiostructures.com

Re: [ccp4bb] Phaser and space groups

[Randy Read]

Hi,

As of last week, this is a known bug (defined as one where I got around to 
adding it to the list on our Phaser Wiki).  It has been fixed in the latest 
nightly builds of Phenix, and a new executable will be released through CCP4 in 
a few weeks, coordinated with the next stable release of Phenix.

It only happens under very specific circumstances, i.e. when you say 
SGALTERNATIVE SELECT LIST and then give a list with only one element.  We 
didn't think this would happen much because we thought that, if people know 
which space group they should be using, they will put the correct space group 
in the MTZ file.  If you don't know the correct space group, it's pretty easy 
to list all of the possibilities in one job and then you don't run into this 
bug.  The new version of Phaser is more clever than the old one about choosing 
the correct space group (it used to make such decisions prematurely, but now 
waits until the choice is unambiguous), so there shouldn't be a real incentive 
to submitting separate jobs for the possible space groups.

Thanks for reporting it, and sorry for the trouble!

Randy Read

On 20 Aug 2012, at 16:06, Jan Abendroth wrote:

 Hi all,
 we have been running into a space group issue when we start phaser (2.5.1) 
 through ccp4i since the installation of ccp4-6.3.0:
 
 We typically scale data in the point group and then let Phaser go through 
 various space groups. Even though the corresponding line appears in the input 
 file
   SGALTERNATIVE SELECT LIST
   SGALTERNATIVE TEST P41
 rotation and translation function would only run in the space group provided 
 by the mtz file. Obviously it does not matter for the rotation function.
 
 As a work around one can edit the input file (run view com file), by 
 replacing the two lines mentioned above with 
   SPACEGROUP P41
 This is a bit inconvenient though.
 
 Any ideas what is going wrong with the standard way?
 
 Cheers,
 Jan
 --
 Jan Abendroth
 Emerald BioStructures
 Seattle / Bainbridge Island WA, USA
 home: Jan.Abendroth_at_gmail.com
 work: JAbendroth_at_embios.com
 http://www.emeraldbiostructures.com

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

Re: [ccp4bb] phaser with MR------search ensemble

[Eleanor Dodson]

The ensemble should be a set of coordinates
 Eleanor
On 15 Aug 2012, at 04:42, 李华 wrote:

 Dear ccp4er,
  I try to use Phaser MR to solve a structure. A mtz file from oasis was 
 used as a ensemble. All of the parameters containing protein MW, nucleic acid 
 MW, extent of X, Y, Z and center of X, Y, Z and RMS error were assigned. 
 However, when I ran phaser mr, the program complain that NOT SET: search 
 ensemble. Does anybody has any advice about this? 
  Thanks very much!
  Hua

Re: [ccp4bb] phaser with MR------search ensemble

[Randy Read]

No, it's possible also to specify a model in the form of the molecular 
transform in an MTZ file, derived either from coordinates or a density map.

I see that I failed to Reply all in my earlier reply to this email, which was 
the following:

=
Does the MTZ file from oasis contain electron density for another crystal form 
of the same protein (or a close relative)?  If so, I presume you've made sure 
to cut out the density corresponding to one molecule and place it in a large 
unit cell.

Assuming that's right, the error message you got arises when you haven't told 
the ccp4i GUI for Phaser which ensemble you want to search for.  Even if you've 
only defined one ensemble, you have to specify that that's the one you want to 
search for.  This is in a pulldown in the Search Parameters pane labelled 
Perform search using.  I've just tested with the new CCP4 6.3.0 release, and 
this works for me.

Good luck!

Randy Read
=
On 15 Aug 2012, at 10:07, Eleanor Dodson wrote:

 The ensemble should be a set of coordinates
  Eleanor
 On 15 Aug 2012, at 04:42, 李华 wrote:
 
 Dear ccp4er,
  I try to use Phaser MR to solve a structure. A mtz file from oasis was 
 used as a ensemble. All of the parameters containing protein MW, nucleic 
 acid MW, extent of X, Y, Z and center of X, Y, Z and RMS error were 
 assigned. However, when I ran phaser mr, the program complain that NOT SET: 
 search ensemble. Does anybody has any advice about this? 
  Thanks very much!
  Hua
 

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

[ccp4bb] 答复: [ccp4bb] phaser with MR------search ensemble

[张涛]

Hi Hua,

 

   I am so curious why you used an mtz file from OASIS as ensemble. OASIS
has ability to complete the model, position and orientation of which have
been determined correctly. And PHASER is a quite excellent program to fix MR
model. So I think a normal procedure is PHASER - OASIS, but not OASIS -
PHASER. Or do you have some special idea？

 

   Zhang, Tao 

 

 

发件人: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] 代表 李华
发送时间: 2012年8月15日 11:42
收件人: CCP4BB@JISCMAIL.AC.UK
主题: [ccp4bb] phaser with MR--search ensemble

 

Dear ccp4er,
 I try to use Phaser MR to solve a structure. A mtz file from oasis was
used as a ensemble. All of the parameters containing protein MW, nucleic
acid MW, extent of X, Y, Z and center of X, Y, Z and RMS error were
assigned. However, when I ran phaser mr, the program complain that NOT SET:
search ensemble. Does anybody has any advice about this? 
 Thanks very much!
 Hua

[ccp4bb] phaser with MR------search ensemble

[李华]

Dear ccp4er,
 I try to use Phaser MR to solve a structure. A mtz file from oasis was 
used as a ensemble. All of the parameters containing protein MW, nucleic acid 
MW, extent of X, Y, Z and center of X, Y, Z and RMS error were assigned. 
However, when I ran phaser mr, the program complain that NOT SET: search 
ensemble. Does anybody has any advice about this? 
 Thanks very much!
 Hua
  

Re: [ccp4bb] Phaser Fatal runtime error.

[Stephen Carr]

Dear all,

Thanks for the many of responses, the data from Crysalis is scaled, but 
unmerged so needed to be fed through scala/truncate before running Phaser.  
Phaser is now running with no problems and I am looking at some nice maps.

Bestr wishes and thanks again for your help,

Steve


Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

From: Roger Rowlett [rrowl...@colgate.edu]
Sent: 27 June 2012 13:07
To: Carr, Stephen (MRC,RAL,RCAH)
Cc: ccp4bb
Subject: Re: [ccp4bb] Phaser Fatal runtime error.


We have an in-house Agilent (Oxford) system and routinely use data with CCP4. 
You will need to run sortmtz, scala (w/constant scale), and truncate to prep 
the data properly. This can be done via batch file or GUI.You may also have to 
reset/reassign the space group for some space groups due to an apparent bug in 
the CrysalisPro MTZ conversion routine. You can find details at 
capsicum.colgate.edu/chwikihttp://capsicum.colgate.edu/chwiki in our 
crystallography pages.

Roger Rowlett

On Jun 26, 2012 1:34 PM, lt;Stephen Carrgt; 
stephen.c...@rc-harwell.ac.ukmailto:stephen.c...@rc-harwell.ac.uk wrote:
Dear CCP4bb

I have collected a data-set using the supernova x-ray generator from Agilent 
and taken the mtz file generated by the data processing software in crysalis 
pro forward for structure solution.  The data collection was straight forward 
and the software seemingly processed the data successfully - space-group P2221, 
overall Rmerge 9%, I/sigmaI 11, redundancy 4.5 etc.  Truncate converted the 
intensities to structure factors with no problems, but when I tried to use the 
data for molecular replacement with Phaser it produced the following error:

FATAL RUNTIME ERROR: Reflections are not a unique set by symmetry

I'm not sure how to proceed from here as other programs in the suite do not 
seem to detect this problem.  Also when this error has been mentioned in the 
past on the bb it was with a data set collected on a Bruker home source and the 
data processed with Denzo/scalepack, and the suggested solution was to use the 
Bruker software to process the data.

I am currently attempting to reprocess the data with mosflm, but that is likely 
to be the subject of another post!

Any suggestions will be gratefully received.

Best wishes,

Steve

Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.ukmailto:stephen.c...@rc-harwell.ac.uk
tel 01235 567717

Re: [ccp4bb] Phaser Fatal runtime error.

[Jan Dohnalek]

Data from Crysalis in mtz format are not merged I think - you have to go
through the scale and merge step in Scala first ...

Jan Dohnalek


On Tue, Jun 26, 2012 at 11:21 PM, Steiner, Roberto 
roberto.stei...@kcl.ac.uk wrote:

 Don't know where the exact problem is. However, it is definitely possible
 to use a Crysalis-Scala-Truncate-Phaser pipeline without runtime errors. I
 have done a few times.
 I am sure you will be able to get help from Agilent people. If not, feel
 free to get back to me.

 Best
 Roberto


 On 26 Jun 2012, at 18:34, Stephen Carr wrote:

  Dear CCP4bb
 
  I have collected a data-set using the supernova x-ray generator from
 Agilent and taken the mtz file generated by the data processing software in
 crysalis pro forward for structure solution.  The data collection was
 straight forward and the software seemingly processed the data successfully
 - space-group P2221, overall Rmerge 9%, I/sigmaI 11, redundancy 4.5 etc.
  Truncate converted the intensities to structure factors with no problems,
 but when I tried to use the data for molecular replacement with Phaser it
 produced the following error:
 
  FATAL RUNTIME ERROR: Reflections are not a unique set by symmetry
 
  I'm not sure how to proceed from here as other programs in the suite do
 not seem to detect this problem.  Also when this error has been mentioned
 in the past on the bb it was with a data set collected on a Bruker home
 source and the data processed with Denzo/scalepack, and the suggested
 solution was to use the Bruker software to process the data.
 
  I am currently attempting to reprocess the data with mosflm, but that is
 likely to be the subject of another post!
 
  Any suggestions will be gratefully received.
 
  Best wishes,
 
  Steve
 
  Dr Stephen Carr
  Research Complex at Harwell (RCaH)
  Rutherford Appleton Laboratory
  Harwell Oxford
  Didcot
  Oxon OX11 0FA
  United Kingdom
  Email stephen.c...@rc-harwell.ac.uk
  tel 01235 567717

 Roberto Steiner, PhD
 Group Leader
 Randall Division of Cell and Molecular Biophysics
 King's College London

 Room 3.10A
 New Hunt's House
 Guy's Campus
 SE1 1UL, London, UK
 Tel 0044-20-78488216
 Fax 0044-20-78486435
 roberto.stei...@kcl.ac.uk




-- 
Jan Dohnalek, Ph.D
Institute of Macromolecular Chemistry
Academy of Sciences of the Czech Republic
Heyrovskeho nam. 2
16206 Praha 6
Czech Republic

Tel: +420 296 809 340
Fax: +420 296 809 410

Re: [ccp4bb] Phaser Fatal runtime error.

[Tadeusz Skarzynski]

Dear Steve,

The mtz file produced by the current version of CrysAlisPro is scaled but 
unmerged and requires SCALA to produce the merged data set. The new version of 
CrysAlisPro (currently under testing) will generate the merged mtz file as well.

With regards,

Tadeusz
Agilent Technologies


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jan 
Dohnalek
Sent: 27 June 2012 07:30
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Phaser Fatal runtime error.

Data from Crysalis in mtz format are not merged I think - you have to go 
through the scale and merge step in Scala first ...

Jan Dohnalek

On Tue, Jun 26, 2012 at 11:21 PM, Steiner, Roberto 
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk wrote:
Don't know where the exact problem is. However, it is definitely possible to 
use a Crysalis-Scala-Truncate-Phaser pipeline without runtime errors. I have 
done a few times.
I am sure you will be able to get help from Agilent people. If not, feel free 
to get back to me.

Best
Roberto


On 26 Jun 2012, at 18:34, Stephen Carr wrote:

 Dear CCP4bb

 I have collected a data-set using the supernova x-ray generator from Agilent 
 and taken the mtz file generated by the data processing software in crysalis 
 pro forward for structure solution.  The data collection was straight forward 
 and the software seemingly processed the data successfully - space-group 
 P2221, overall Rmerge 9%, I/sigmaI 11, redundancy 4.5 etc.  Truncate 
 converted the intensities to structure factors with no problems, but when I 
 tried to use the data for molecular replacement with Phaser it produced the 
 following error:

 FATAL RUNTIME ERROR: Reflections are not a unique set by symmetry

 I'm not sure how to proceed from here as other programs in the suite do not 
 seem to detect this problem.  Also when this error has been mentioned in the 
 past on the bb it was with a data set collected on a Bruker home source and 
 the data processed with Denzo/scalepack, and the suggested solution was to 
 use the Bruker software to process the data.

 I am currently attempting to reprocess the data with mosflm, but that is 
 likely to be the subject of another post!

 Any suggestions will be gratefully received.

 Best wishes,

 Steve

 Dr Stephen Carr
 Research Complex at Harwell (RCaH)
 Rutherford Appleton Laboratory
 Harwell Oxford
 Didcot
 Oxon OX11 0FA
 United Kingdom
 Email stephen.c...@rc-harwell.ac.ukmailto:stephen.c...@rc-harwell.ac.uk
 tel 01235 567717
Roberto Steiner, PhD
Group Leader
Randall Division of Cell and Molecular Biophysics
King's College London

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk



--
Jan Dohnalek, Ph.D
Institute of Macromolecular Chemistry
Academy of Sciences of the Czech Republic
Heyrovskeho nam. 2
16206 Praha 6
Czech Republic

Tel: +420 296 809 340
Fax: +420 296 809 410

Re: [ccp4bb] Phaser Fatal runtime error.

[Eleanor Dodson]

I suspect you didn't request the FreeR assignment on the TRUNCATE interface? 
This calls amongst other programs, CAD and CAD makes sure that the reflection 
list is unique and that it is in a standard asymmetric unit.  Most people do it 
by default so don't hit these problems...
I suggest you just run CAD (on the reflection utilities) and select - input all 
observations , then try again with the output mtz. All that will have happened 
is that the reflections are now assigned to a standard asymmetric unit and 
sorted. 
Eleanor
On 26 Jun 2012, at 22:21, Steiner, Roberto wrote:

 Don't know where the exact problem is. However, it is definitely possible to 
 use a Crysalis-Scala-Truncate-Phaser pipeline without runtime errors. I have 
 done a few times.
 I am sure you will be able to get help from Agilent people. If not, feel free 
 to get back to me.
 
 Best
 Roberto
 
 
 On 26 Jun 2012, at 18:34, Stephen Carr wrote:
 
 Dear CCP4bb
 
 I have collected a data-set using the supernova x-ray generator from Agilent 
 and taken the mtz file generated by the data processing software in crysalis 
 pro forward for structure solution.  The data collection was straight 
 forward and the software seemingly processed the data successfully - 
 space-group P2221, overall Rmerge 9%, I/sigmaI 11, redundancy 4.5 etc.  
 Truncate converted the intensities to structure factors with no problems, 
 but when I tried to use the data for molecular replacement with Phaser it 
 produced the following error:
 
 FATAL RUNTIME ERROR: Reflections are not a unique set by symmetry
 
 I'm not sure how to proceed from here as other programs in the suite do not 
 seem to detect this problem.  Also when this error has been mentioned in the 
 past on the bb it was with a data set collected on a Bruker home source and 
 the data processed with Denzo/scalepack, and the suggested solution was to 
 use the Bruker software to process the data.
 
 I am currently attempting to reprocess the data with mosflm, but that is 
 likely to be the subject of another post!
 
 Any suggestions will be gratefully received.
 
 Best wishes,
 
 Steve
 
 Dr Stephen Carr
 Research Complex at Harwell (RCaH)
 Rutherford Appleton Laboratory
 Harwell Oxford
 Didcot
 Oxon OX11 0FA
 United Kingdom
 Email stephen.c...@rc-harwell.ac.uk
 tel 01235 567717
 
 Roberto Steiner, PhD
 Group Leader
 Randall Division of Cell and Molecular Biophysics 
 King's College London
 
 Room 3.10A 
 New Hunt's House 
 Guy's Campus
 SE1 1UL, London, UK
 Tel 0044-20-78488216
 Fax 0044-20-78486435
 roberto.stei...@kcl.ac.uk

Re: [ccp4bb] Phaser Fatal runtime error.

[Airlie McCoy]

Just to be clear, Phaser does not require the reflections to be in a 
standard asymmetric unit, only that they are unique (as the error message 
thrown says).


Airlie

On Jun 27 2012, Eleanor Dodson wrote:

I suspect you didn't request the FreeR assignment on the TRUNCATE 
interface? This calls amongst other programs, CAD and CAD makes sure that 
the reflection list is unique and that it is in a standard asymmetric 
unit. Most people do it by default so don't hit these problems... I 
suggest you just run CAD (on the reflection utilities) and select - input 
all observations , then try again with the output mtz. All that will have 
happened is that the reflections are now assigned to a standard 
asymmetric unit and sorted. Eleanor On 26 Jun 2012, at 22:21, Steiner, 
Roberto wrote:


Don't know where the exact problem is. However, it is definitely 
possible to use a Crysalis-Scala-Truncate-Phaser pipeline without 
runtime errors. I have done a few times. I am sure you will be able to 
get help from Agilent people. If not, feel free to get back to me.


Best
Roberto


On 26 Jun 2012, at 18:34, Stephen Carr wrote:


Dear CCP4bb

I have collected a data-set using the supernova x-ray generator from 
Agilent and taken the mtz file generated by the data processing 
software in crysalis pro forward for structure solution. The data 
collection was straight forward and the software seemingly processed 
the data successfully - space-group P2221, overall Rmerge 9%, I/sigmaI 
11, redundancy 4.5 etc. Truncate converted the intensities to structure 
factors with no problems, but when I tried to use the data for 
molecular replacement with Phaser it produced the following error:


FATAL RUNTIME ERROR: Reflections are not a unique set by symmetry

I'm not sure how to proceed from here as other programs in the suite 
do not seem to detect this problem. Also when this error has been 
mentioned in the past on the bb it was with a data set collected on a 
Bruker home source and the data processed with Denzo/scalepack, and the 
suggested solution was to use the Bruker software to process the data.


I am currently attempting to reprocess the data with mosflm, but that 
is likely to be the subject of another post!


Any suggestions will be gratefully received.

Best wishes,

Steve

Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717


Roberto Steiner, PhD
Group Leader
Randall Division of Cell and Molecular Biophysics 
King's College London


Room 3.10A 
New Hunt's House 
Guy's Campus

SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.uk

Re: [ccp4bb] Phaser Fatal runtime error.

[Roger Rowlett]

We have an in-house Agilent (Oxford) system and routinely use data with
CCP4. You will need to run sortmtz, scala (w/constant scale), and truncate
to prep the data properly. This can be done via batch file or GUI.You may
also have to reset/reassign the space group for some space groups due to an
apparent bug in the CrysalisPro MTZ conversion routine. You can find
details at capsicum.colgate.edu/chwiki in our crystallography pages.

Roger Rowlett
On Jun 26, 2012 1:34 PM, lt;Stephen Carrgt; 
stephen.c...@rc-harwell.ac.uk wrote:

 Dear CCP4bb

 I have collected a data-set using the supernova x-ray generator from
 Agilent and taken the mtz file generated by the data processing software in
 crysalis pro forward for structure solution.  The data collection was
 straight forward and the software seemingly processed the data successfully
 - space-group P2221, overall Rmerge 9%, I/sigmaI 11, redundancy 4.5 etc.
  Truncate converted the intensities to structure factors with no problems,
 but when I tried to use the data for molecular replacement with Phaser it
 produced the following error:

 FATAL RUNTIME ERROR: Reflections are not a unique set by symmetry

 I'm not sure how to proceed from here as other programs in the suite do
 not seem to detect this problem.  Also when this error has been mentioned
 in the past on the bb it was with a data set collected on a Bruker home
 source and the data processed with Denzo/scalepack, and the suggested
 solution was to use the Bruker software to process the data.

 I am currently attempting to reprocess the data with mosflm, but that is
 likely to be the subject of another post!

 Any suggestions will be gratefully received.

 Best wishes,

 Steve

 Dr Stephen Carr
 Research Complex at Harwell (RCaH)
 Rutherford Appleton Laboratory
 Harwell Oxford
 Didcot
 Oxon OX11 0FA
 United Kingdom
 Email stephen.c...@rc-harwell.ac.uk
 tel 01235 567717

[ccp4bb] Phaser Fatal runtime error.

[Stephen Carr]

Dear CCP4bb

I have collected a data-set using the supernova x-ray generator from Agilent 
and taken the mtz file generated by the data processing software in crysalis 
pro forward for structure solution.  The data collection was straight forward 
and the software seemingly processed the data successfully - space-group P2221, 
overall Rmerge 9%, I/sigmaI 11, redundancy 4.5 etc.  Truncate converted the 
intensities to structure factors with no problems, but when I tried to use the 
data for molecular replacement with Phaser it produced the following error:

FATAL RUNTIME ERROR: Reflections are not a unique set by symmetry

I'm not sure how to proceed from here as other programs in the suite do not 
seem to detect this problem.  Also when this error has been mentioned in the 
past on the bb it was with a data set collected on a Bruker home source and the 
data processed with Denzo/scalepack, and the suggested solution was to use the 
Bruker software to process the data.

I am currently attempting to reprocess the data with mosflm, but that is likely 
to be the subject of another post!

Any suggestions will be gratefully received.

Best wishes,

Steve

Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

Re: [ccp4bb] Phaser Fatal runtime error.

[Steiner, Roberto]

Don't know where the exact problem is. However, it is definitely possible to 
use a Crysalis-Scala-Truncate-Phaser pipeline without runtime errors. I have 
done a few times.
I am sure you will be able to get help from Agilent people. If not, feel free 
to get back to me.

Best
Roberto


On 26 Jun 2012, at 18:34, Stephen Carr wrote:

 Dear CCP4bb
 
 I have collected a data-set using the supernova x-ray generator from Agilent 
 and taken the mtz file generated by the data processing software in crysalis 
 pro forward for structure solution.  The data collection was straight forward 
 and the software seemingly processed the data successfully - space-group 
 P2221, overall Rmerge 9%, I/sigmaI 11, redundancy 4.5 etc.  Truncate 
 converted the intensities to structure factors with no problems, but when I 
 tried to use the data for molecular replacement with Phaser it produced the 
 following error:
 
 FATAL RUNTIME ERROR: Reflections are not a unique set by symmetry
 
 I'm not sure how to proceed from here as other programs in the suite do not 
 seem to detect this problem.  Also when this error has been mentioned in the 
 past on the bb it was with a data set collected on a Bruker home source and 
 the data processed with Denzo/scalepack, and the suggested solution was to 
 use the Bruker software to process the data.
 
 I am currently attempting to reprocess the data with mosflm, but that is 
 likely to be the subject of another post!
 
 Any suggestions will be gratefully received.
 
 Best wishes,
 
 Steve
 
 Dr Stephen Carr
 Research Complex at Harwell (RCaH)
 Rutherford Appleton Laboratory
 Harwell Oxford
 Didcot
 Oxon OX11 0FA
 United Kingdom
 Email stephen.c...@rc-harwell.ac.uk
 tel 01235 567717

Roberto Steiner, PhD
Group Leader
Randall Division of Cell and Molecular Biophysics 
King's College London

Room 3.10A 
New Hunt's House 
Guy's Campus
SE1 1UL, London, UK
Tel 0044-20-78488216
Fax 0044-20-78486435
roberto.stei...@kcl.ac.uk

[ccp4bb] Phaser - changing number of clashes parameter

[Santarsiero, Bernard D.]

The new CCP4I interface for PHASER removed the menu item where you could
change the number of clashes. It's not set as a default to 5% of the
number of C-alpha atoms. Where is the default file?

I found the phaser_MR.def file in share/ccp4i/tasks, and changed the
parameter value, but it still used the default of 5%.

Thanks,

Bernie
-- 
Bernard D. Santarsiero
Research Professor
Center for Pharmaceutical Biotechnology and the
 Department of Medicinal Chemistry and Pharmacognosy
Center for Structural Biology
Center for Clinical and Translational Science
University of Illinois at Chicago
MC870  3070MBRB  900 South Ashland Avenue
Chicago, IL 60607-7173  USA
(312) 413-0339 (office)
(312) 413-9303 (FAX)
http://www.uic.edu/labs/bds

Re: [ccp4bb] Phaser - changing number of clashes parameter

[Roger Rowlett]

If you install the .tcl update from the CCP4 site, you will find the clash
menu setting under advanced options, IIRC.

Roger Rowlett
On Jun 20, 2012 6:08 PM, Santarsiero, Bernard D. b...@uic.edu wrote:

 The new CCP4I interface for PHASER removed the menu item where you could
 change the number of clashes. It's not set as a default to 5% of the
 number of C-alpha atoms. Where is the default file?

 I found the phaser_MR.def file in share/ccp4i/tasks, and changed the
 parameter value, but it still used the default of 5%.

 Thanks,

 Bernie
 --
 Bernard D. Santarsiero
 Research Professor
 Center for Pharmaceutical Biotechnology and the
  Department of Medicinal Chemistry and Pharmacognosy
 Center for Structural Biology
 Center for Clinical and Translational Science
 University of Illinois at Chicago
 MC870  3070MBRB  900 South Ashland Avenue
 Chicago, IL 60607-7173  USA
 (312) 413-0339 (office)
 (312) 413-9303 (FAX)
 http://www.uic.edu/labs/bds

Re: [ccp4bb] phaser: high z score but no sol

[Herman . Schreuder]

Hi Lisa,
 
Why are you so sure there are 4 molecules in the ASU? There may only be
3 and forcing a fourth molecule is causing lots of clashes. In a similar
case, I have seen phaser put two molecules right on top of each other
when I forced it to search for too many molecules. 
 
In your case I would look at the solution (crystal packing) in coot and
see whether the clashes are due to some loops (or domains) which may
move upon ligand binding, or whether one of the molecules is at a
completely wrong position and if you get a good crystal packing (crystal
contacts in all directions) with fewer molecules. You can also start
refinement with fewer molecules and see if additional density for
missing molecule(s) appears.
 
Good luck!
Herman




From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of LISA
Sent: Thursday, April 19, 2012 8:20 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] phaser: high z score but no sol


Hi all,

I am trying to solve one structure by molecular replacement with
phaser in CCP4. This  a complex of a multi-domain domains with small
ligand. I have structues of this protein in apo state and with other
similar ligand.  The space group of this crystal is P21. This crystal
should have 4 molecules in ASU.  I used the full protein as model but
did get any sol and LLG is below zero. Then each domain were used as the
search models in phaser with rotation and tranlsation. I can the get
high z score (20), and LLG is raising. It looks like I get the right
sol, but it  have more 50 clashes.  Why phaser give wrong sol with so
high z socre? Can anyone give me some suggestion to solve my strucutes?
Thank you.
Best

Lisa

Re: [ccp4bb] phaser: high z score but no sol

[Bosch, Juergen]

Would the self rotation map make sense with 4 molecules ?
Jürgen

Sent from my iPad

On Apr 20, 2012, at 2:55, 
herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.com 
herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.com wrote:

Hi Lisa,

Why are you so sure there are 4 molecules in the ASU? There may only be 3 and 
forcing a fourth molecule is causing lots of clashes. In a similar case, I have 
seen phaser put two molecules right on top of each other when I forced it to 
search for too many molecules.

In your case I would look at the solution (crystal packing) in coot and see 
whether the clashes are due to some loops (or domains) which may move upon 
ligand binding, or whether one of the molecules is at a completely wrong 
position and if you get a good crystal packing (crystal contacts in all 
directions) with fewer molecules. You can also start refinement with fewer 
molecules and see if additional density for missing molecule(s) appears.

Good luck!
Herman


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of LISA
Sent: Thursday, April 19, 2012 8:20 AM
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] phaser: high z score but no sol

Hi all,

I am trying to solve one structure by molecular replacement with phaser in 
CCP4. This  a complex of a multi-domain domains with small ligand. I have 
structues of this protein in apo state and with other similar ligand.  The 
space group of this crystal is P21. This crystal should have 4 molecules in 
ASU.  I used the full protein as model but did get any sol and LLG is below 
zero. Then each domain were used as the search models in phaser with rotation 
and tranlsation. I can the get high z score (20), and LLG is raising. It looks 
like I get the right sol, but it  have more 50 clashes.  Why phaser give wrong 
sol with so high z socre? Can anyone give me some suggestion to solve my 
strucutes? Thank you.
Best

Lisa

Re: [ccp4bb] phaser: high z score but no sol

[Francis E Reyes]

P21.. You sure about this space group?  (very high confidences for space group 
and laue group in pointless?)



F

On Apr 19, 2012, at 12:20 AM, LISA wrote:

 Hi all,
 
 I am trying to solve one structure by molecular replacement with phaser in 
 CCP4. This  a complex of a multi-domain domains with small ligand. I have 
 structues of this protein in apo state and with other similar ligand.  The 
 space group of this crystal is P21. This crystal should have 4 molecules in 
 ASU.  I used the full protein as model but did get any sol and LLG is below 
 zero. Then each domain were used as the search models in phaser with rotation 
 and tranlsation. I can the get high z score (20), and LLG is raising. It 
 looks like I get the right sol, but it  have more 50 clashes.  Why phaser 
 give wrong sol with so high z socre? Can anyone give me some suggestion to 
 solve my strucutes? Thank you.
 Best
 
 Lisa

[ccp4bb] phaser: high z score but no sol

[LISA]

Hi all,

I am trying to solve one structure by molecular replacement with phaser in
CCP4. This  a complex of a multi-domain domains with small ligand. I have
structues of this protein in apo state and with other similar ligand.  The
space group of this crystal is P21. This crystal should have 4 molecules in
ASU.  I used the full protein as model but did get any sol and LLG is below
zero. Then each domain were used as the search models in phaser with
rotation and tranlsation. I can the get high z score (20), and LLG is
raising. It looks like I get the right sol, but it  have more 50 clashes.
Why phaser give wrong sol with so high z socre? Can anyone give me some
suggestion to solve my strucutes? Thank you.
Best

Lisa

Re: [ccp4bb] phaser: high z score but no sol

[Vellieux Frederic]

Hi,

If you have the correct solution, clashes may be due to loops. It may be 
an idea to clip these off for the molecular replacement calculations 
(loops might be shorter in the structure-to-be-solved than in the search 
model, they may have different conformations in the 
structure-to-be-solved than in the search model, a common property of 
loops is that they sometimes have different conformations).


You didn't provide much information about what was precisely done wrt 
molecular replacement calculations, I notice... So what I write is just 
guesswork.


If you have little experience with molecular replacement, it may be a 
good idea to get advice from a colleague who has plenty and can sit next 
to you and guide you through the process (again, this is guesswork).


HTH,

Fred.

LISA wrote:

Hi all,

I am trying to solve one structure by molecular replacement with 
phaser in CCP4. This  a complex of a multi-domain domains with small 
ligand. I have structues of this protein in apo state and with other 
similar ligand.  The space group of this crystal is P21. This crystal 
should have 4 molecules in ASU.  I used the full protein as model but 
did get any sol and LLG is below zero. Then each domain were used as 
the search models in phaser with rotation and tranlsation. I can the 
get high z score (20), and LLG is raising. It looks like I get the 
right sol, but it  have more 50 clashes.  Why phaser give wrong sol 
with so high z socre? Can anyone give me some suggestion to solve my 
strucutes? Thank you.

Best

Lisa

Re: [ccp4bb] phaser: high z score but no sol

[Randy Read]

Hi,

My first guess would be that this crystal possesses translational NCS, and that 
you're using the old (distributed with current old CCP4) version of Phaser 
that can't handle tNCS.  You can tell if this is the case by looking at whether 
there's a large off-origin peak in the native Patterson map.  If so, then you 
should try Molrep from the current CCP4 or a newer version of Phaser (recent 
Phenix release, or upcoming CCP4 release).

Regards,

Randy Read

On 19 Apr 2012, at 07:20, LISA wrote:

 Hi all,
 
 I am trying to solve one structure by molecular replacement with phaser in 
 CCP4. This  a complex of a multi-domain domains with small ligand. I have 
 structues of this protein in apo state and with other similar ligand.  The 
 space group of this crystal is P21. This crystal should have 4 molecules in 
 ASU.  I used the full protein as model but did get any sol and LLG is below 
 zero. Then each domain were used as the search models in phaser with rotation 
 and tranlsation. I can the get high z score (20), and LLG is raising. It 
 looks like I get the right sol, but it  have more 50 clashes.  Why phaser 
 give wrong sol with so high z socre? Can anyone give me some suggestion to 
 solve my strucutes? Thank you.
 Best
 
 Lisa

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

Re: [ccp4bb] phaser: high z score but no sol

[Ed Pozharski]

As Randy pointed out, you should check Patterson map for off-origin
peaks.  There is also a small chance that you actually have P2 -
systematic absences may result from tNCS nearly colinear with
crystallographic axis.

On Thu, 2012-04-19 at 14:20 +0800, LISA wrote:
 Hi all,
 
 I am trying to solve one structure by molecular replacement with
 phaser in CCP4. This  a complex of a multi-domain domains with small
 ligand. I have structues of this protein in apo state and with other
 similar ligand.  The space group of this crystal is P21. This crystal
 should have 4 molecules in ASU.  I used the full protein as model but
 did get any sol and LLG is below zero. Then each domain were used as
 the search models in phaser with rotation and tranlsation. I can the
 get high z score (20), and LLG is raising. It looks like I get the
 right sol, but it  have more 50 clashes.  Why phaser give wrong sol
 with so high z socre? Can anyone give me some suggestion to solve my
 strucutes? Thank you.
 Best
 
 Lisa

-- 
I'd jump in myself, if I weren't so good at whistling.
   Julian, King of Lemurs

Re: [ccp4bb] Phaser problem child killed: segmentation violation in phaser

[Randy Read]

This was resolved offline.  It turns out that there's an obscure bug in Phaser 
triggered if you search for the same model twice as an alternative for itself 
(e.g. SEARCH ENSEMBLE ensemble1 OR ENSEMBLE ensemble1 NUM 1).  When the input 
was fixed (SEARCH ENSEMBLE ensemble1 NUM 1), Phaser didn't crash any more, 
but unfortunately, it didn't solve the structure either.

The bug is fixed now for future versions of Phaser.

Best wishes,

Randy Read

On 29 Nov 2011, at 10:11, Sita Ram Meena wrote:

  Hi CCP4 community. 
 
 While running the Phaser in the CCP4 GUI, It was terminated and giving the 
 error message.
 
 #CCP4I TERMINATION STATUS 0 child killed: segmentation violation   
  
 #CCP4I VERSION CCP4Interface 2.0.6
 
 CCP4 Version ccp4-6.1.13
 
 
 Thanks in advance.
 
 
 Sita Ram

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

[ccp4bb] Phaser problem child killed: segmentation violation in phaser

[Sita Ram Meena]

 Hi CCP4 community.

While running the Phaser in the CCP4 GUI, It was terminated and giving the
error message.

#CCP4I TERMINATION STATUS 0 child killed: segmentation violation

#CCP4I VERSION CCP4Interface 2.0.6

CCP4 Version ccp4-6.1.13


Thanks in advance.


Sita Ram

Re: [ccp4bb] phaser openmp

[Randy Read]

Thanks for pointing out that link.  The graph makes the point I was going to 
mention, i.e. that you notice a big difference in using up to about 4 
processors for typical jobs, but after that point the non-parallelisable parts 
of the code start to dominate and there's less improvement.  This is very 
useful if you have one MR job to run on a typical modern workstation (2-8 
cores), but if you have several separate jobs to run then you're better off 
submitting them simultaneously, each using a subset of the available cores.  Of 
course, that assumes you have enough memory for several simultaneous separate 
jobs!

Regards,

Randy Read

On 9 Nov 2011, at 07:21, Ed Pozharski wrote:

 See page 3 of this
 
 http://www-structmed.cimr.cam.ac.uk/phaser/ccp4-sw2011.pdf
 
 
 
 On Wed, 2011-11-09 at 09:22 +0900, Francois Berenger wrote:
 Hello,
 
 How faster is the OpenMP version of Phaser
 versus number of cores used?
 
 In the past I have been quite badly surprised by
 the no-acceleration I gained when using OpenMP
 with some of my programs... :(
 
 Regards,
 F.
 
 On 11/09/2011 02:59 AM, Dr G. Bunkoczi wrote:
 Hi Ed,
 
 in the CCP4 distribution, openmp is not enabled by default, and there
 seems to be no easy way to enable it (i.e. by setting a flag at the
 configure stage).
 
 On the other hand, you can easily create a separate build for phaser
 that is openmp enabled and use phaser from there. To do this, create a
 new folder, say phaser-build, cd into it, and issue the following
 commands (this assumes you are using bash):
 
 $ python $CCP4/lib/cctbx/cctbx_sources/cctbx_project/libtbx/configure.py
 --repository=$CCP4/src/phaser/source phaser
 --build-boost-python-extensions=False --enable-openmp-if-possible=True
 
 $ . ./setpaths.sh (source ./setpaths.csh with csh) $ libtbx.scons (if
 you have several CPUs, add -jX where X is the number of CPUs you want to
 use for compilation)
 
 This will build phaser that is openmp-enabled. You can also try passing
 the --static-exe flag (to configure.py), in which case the executable is
 static and can be relocated without any headaches. This works with
 certain compilers.
 
 Let me know if there are any problems!
 
 BW, Gabor
 
 On Nov 8 2011, Ed Pozharski wrote:
 
 Could anyone point me towards instructions on how to get/build
 parallelized phaser binary on linux? I searched around but so far found
 nothing. The latest updated phaser binary doesn't seem to be
 parallelized.
 Apologies if this has been resolved before - just point at the relevant
 thread, please.
 
 

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

Re: [ccp4bb] phaser openmp

[Pascal]

Le Tue, 8 Nov 2011 16:25:22 -0800,
Nat Echols nathaniel.ech...@gmail.com a écrit :

 On Tue, Nov 8, 2011 at 4:22 PM, Francois Berenger beren...@riken.jp
 wrote:
  In the past I have been quite badly surprised by
  the no-acceleration I gained when using OpenMP
  with some of my programs... :(

You need big parallel jobs and avoid synchronisations, barriers or this
kind of things. Using data reduction is much more efficient. It's working 
very well for structure factors calculations for exemple.

 
 Amdahl's law is cruel:
 
 http://en.wikipedia.org/wiki/Amdahl's_law

You can have much less than 5% of serial code.

I have more problems with L2 misse cache events and memory bandwidth. A
quad cores means 4 times the bandwidth necessary for a single process... 
If your code is already a bit greedy, the scale up is not good.

Pascal

Re: [ccp4bb] phaser openmp

[Francois Berenger]

On 11/09/2011 07:21 PM, Pascal wrote:

Le Tue, 8 Nov 2011 16:25:22 -0800,
Nat Echolsnathaniel.ech...@gmail.com  a écrit :


On Tue, Nov 8, 2011 at 4:22 PM, Francois Berengerberen...@riken.jp
wrote:

In the past I have been quite badly surprised by
the no-acceleration I gained when using OpenMP
with some of my programs... :(


You need big parallel jobs and avoid synchronisations, barriers or this
kind of things. Using data reduction is much more efficient. It's working
very well for structure factors calculations for exemple.



Amdahl's law is cruel:

http://en.wikipedia.org/wiki/Amdahl's_law


You can have much less than 5% of serial code.

I have more problems with L2 misse cache events and memory bandwidth. A
quad cores means 4 times the bandwidth necessary for a single process...
If your code is already a bit greedy, the scale up is not good.


I never went down to this level of optimization.
Are you using valgrind to detect cache miss events?

After gprof, usually I am done with optimization.
I would prefer to change my algorithm and would be afraid
of introducing optimizations that are architecture-dependent
into my software.

Regards,
F.

[ccp4bb] [gsheldr: Re: [ccp4bb] phaser openmp]

[George M. Sheldrick]

-- 
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

---BeginMessage---
In my experience, writing efficient multithreaded code is much harder
than writing efficient single-thread code, and some algorithms scale
up much better than others. It is important to avoid cache misses, but 
because each CPU has its own cache, on rare occasions it is possible
to scale up by more than the number of CPUs, because by dividing up
the memory the number of cache misses can be reduced. In the case of
the multi-CPU version of SHELXD (part of the current beta-test, 
available on email request) I was able - with some effort - to keep
the effects of Amdahl's law within limits (on a 32 CPU machine it is
about 29 times faster than with one CPU).

George

On Wed, Nov 09, 2011 at 11:21:11AM +0100, Pascal wrote:
 Le Tue, 8 Nov 2011 16:25:22 -0800,
 Nat Echols nathaniel.ech...@gmail.com a écrit :
 
  On Tue, Nov 8, 2011 at 4:22 PM, Francois Berenger beren...@riken.jp
  wrote:
   In the past I have been quite badly surprised by
   the no-acceleration I gained when using OpenMP
   with some of my programs... :(
 
 You need big parallel jobs and avoid synchronisations, barriers or this
 kind of things. Using data reduction is much more efficient. It's working 
 very well for structure factors calculations for exemple.
 
  
  Amdahl's law is cruel:
  
  http://en.wikipedia.org/wiki/Amdahl's_law
 
 You can have much less than 5% of serial code.
 
 I have more problems with L2 misse cache events and memory bandwidth. A
 quad cores means 4 times the bandwidth necessary for a single process... 
 If your code is already a bit greedy, the scale up is not good.
 
 Pascal
 

-- 
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582

---End Message---

[ccp4bb] phaser openmp

[Ed Pozharski]

Could anyone point me towards instructions on how to get/build
parallelized phaser binary on linux?  I searched around but so far found
nothing.  The latest updated phaser binary doesn't seem to be
parallelized.  

Apologies if this has been resolved before - just point at the relevant
thread, please.

-- 
I'd jump in myself, if I weren't so good at whistling.
   Julian, King of Lemurs

Re: [ccp4bb] phaser openmp

[Dr G. Bunkoczi]

Hi Ed,

in the CCP4 distribution, openmp is not enabled by default, and there
seems to be no easy way to enable it (i.e. by setting a flag at the
configure stage).

On the other hand, you can easily create a separate build for phaser
that is openmp enabled and use phaser from there. To do this, create a
new folder, say phaser-build, cd into it, and issue the following
commands (this assumes you are using bash):

$ python $CCP4/lib/cctbx/cctbx_sources/cctbx_project/libtbx/configure.py
--repository=$CCP4/src/phaser/source phaser
--build-boost-python-extensions=False --enable-openmp-if-possible=True

$ . ./setpaths.sh (source ./setpaths.csh with csh) $ libtbx.scons (if you 
have several CPUs, add -jX where X is the number of CPUs you want to use 
for compilation)


This will build phaser that is openmp-enabled. You can also try passing
the --static-exe flag (to configure.py), in which case the executable is
static and can be relocated without any headaches. This works with
certain compilers.

Let me know if there are any problems!

BW, Gabor

On Nov 8 2011, Ed Pozharski wrote:


Could anyone point me towards instructions on how to get/build
parallelized phaser binary on linux?  I searched around but so far found
nothing.  The latest updated phaser binary doesn't seem to be
parallelized.  


Apologies if this has been resolved before - just point at the relevant
thread, please.

Re: [ccp4bb] phaser openmp

[Nat Echols]

On Tue, Nov 8, 2011 at 4:22 PM, Francois Berenger beren...@riken.jp wrote:
 In the past I have been quite badly surprised by
 the no-acceleration I gained when using OpenMP
 with some of my programs... :(

Amdahl's law is cruel:

http://en.wikipedia.org/wiki/Amdahl's_law

This is the same reason why GPU acceleration isn't very useful for
most crystallography software.

-Nat

Re: [ccp4bb] phaser openmp

[Ed Pozharski]

See page 3 of this

http://www-structmed.cimr.cam.ac.uk/phaser/ccp4-sw2011.pdf



On Wed, 2011-11-09 at 09:22 +0900, Francois Berenger wrote:
 Hello,
 
 How faster is the OpenMP version of Phaser
 versus number of cores used?
 
 In the past I have been quite badly surprised by
 the no-acceleration I gained when using OpenMP
 with some of my programs... :(
 
 Regards,
 F.
 
 On 11/09/2011 02:59 AM, Dr G. Bunkoczi wrote:
  Hi Ed,
 
  in the CCP4 distribution, openmp is not enabled by default, and there
  seems to be no easy way to enable it (i.e. by setting a flag at the
  configure stage).
 
  On the other hand, you can easily create a separate build for phaser
  that is openmp enabled and use phaser from there. To do this, create a
  new folder, say phaser-build, cd into it, and issue the following
  commands (this assumes you are using bash):
 
  $ python $CCP4/lib/cctbx/cctbx_sources/cctbx_project/libtbx/configure.py
  --repository=$CCP4/src/phaser/source phaser
  --build-boost-python-extensions=False --enable-openmp-if-possible=True
 
  $ . ./setpaths.sh (source ./setpaths.csh with csh) $ libtbx.scons (if
  you have several CPUs, add -jX where X is the number of CPUs you want to
  use for compilation)
 
  This will build phaser that is openmp-enabled. You can also try passing
  the --static-exe flag (to configure.py), in which case the executable is
  static and can be relocated without any headaches. This works with
  certain compilers.
 
  Let me know if there are any problems!
 
  BW, Gabor
 
  On Nov 8 2011, Ed Pozharski wrote:
 
  Could anyone point me towards instructions on how to get/build
  parallelized phaser binary on linux? I searched around but so far found
  nothing. The latest updated phaser binary doesn't seem to be
  parallelized.
  Apologies if this has been resolved before - just point at the relevant
  thread, please.
 
 

Re: [ccp4bb] phaser

[Eleanor Dodson]

The new Phaser GUI does not seem to let me reset the number of clashes 
for the packing search?

Is there something I have missed?
Eleanor

Re: [ccp4bb] phaser

[Randy Read]

Hi Eleanor,

I think you should find it in the Additional Parameters section, second line, 
labelled Packing criterion.  The default (chosen largely because you had been 
asking for something like this!) is to allow a number of clashes equal to 5% of 
the number of residues.

Let me know if it isn't there.  It's possible I've got a different version of 
the GUI on my machine...

Randy

On 7 Nov 2011, at 16:42, Eleanor Dodson wrote:

 The new Phaser GUI does not seem to let me reset the number of clashes for 
 the packing search?
 Is there something I have missed?
 Eleanor

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

[ccp4bb] Phaser: ensemble not set

[ROS]

Subject: Phaser: ensemble not set

Hello:
 
I try to use Phaser under MR. 
 
The program complain: ensemble not set. 
 
The ensemble box keeps blank and does not allow to click. 
 
I use: ccp4-6.2.0
Window Vista Business
 
Thanks for advice
 
ROS

[ccp4bb] phaser 2.3.0 floating point exception

[Petr Leiman]

Dear Randy and the Phaser team,

Phaser 2.3.0 brought us several enhancement, but similar to Alexander 
Schiffer's experience, Phaser has failed several times now with a floating 
point exception error at different stages of automated MR: it has stopped in 
the beginning of RF and then in a new run it stopped in the middle of TF. The 
remedy is to explicitly lower the resolution of the input data (that was a 1.2 
A resolution data with a smallish unit cell).  

I can provide the log files and the mtz file if necessary.

Sincerely,

Petr
---
Petr Leiman
EPFL
IPSB-LBBS
BSP-415
CH-1015 Lausanne, Suisse
http://lbbs.epfl.ch

Re: [ccp4bb] phaser 2.3.0 floating point exception

[Randy Read]

Dear Petr,

Yes, please do send the log files, MTZ file and anything else needed to run the 
job that shows the problem, so we can track it down.  It's probably best to 
send them off-line.

We couldn't reproduce Alexander's problem, but he tells me that it only occurs 
when the script is started from a mono application (and I confess that I 
don't really know yet what that means).  Once the problem he ran into has been 
defined a bit better, we can look into whether it's something we can fix on our 
end.

Regards,

Randy Read

On 6 Sep 2011, at 08:25, Petr Leiman wrote:

 Dear Randy and the Phaser team,
 
 Phaser 2.3.0 brought us several enhancement, but similar to Alexander 
 Schiffer's experience, Phaser has failed several times now with a floating 
 point exception error at different stages of automated MR: it has stopped in 
 the beginning of RF and then in a new run it stopped in the middle of TF. The 
 remedy is to explicitly lower the resolution of the input data (that was a 
 1.2 A resolution data with a smallish unit cell).  
 
 I can provide the log files and the mtz file if necessary.
 
 Sincerely,
 
 Petr
 ---
 Petr Leiman
 EPFL
 IPSB-LBBS
 BSP-415
 CH-1015 Lausanne, Suisse
 http://lbbs.epfl.ch

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

Re: [ccp4bb] Phaser 2.3.0

[Randy Read]

Hi,

Could you send me some representative logfiles (probably off-list)?  This might 
give a hint.  It must be something unusual, because we have a fairly wide range 
of test cases and none of them have any problems.

Thanks and best wishes,

Randy Read

On 1 Sep 2011, at 14:58, alexander.schif...@sanofi-aventis.com wrote:

 Dear all,
 
 We just upgraded to ccp4 6.2.0 and with that upgrade switched from Phaser 
 2.1.4 to 2.3.0. During testing we ran into the problem that for some of our 
 datasets phaser stops with a floating point exception . As it is not the case 
 for all datasets I asume it must be linked to the input mtz or pdb file.
 
 Is there a way to check the integrity of those files and identify the 
 specific problem?
 
 Best regards,
 
 Alexander
 
 Mit freundlichen Grüßen / Best regards / Cordialement 
 
 Dr. Alexander Schiffer 
 
 Sanofi-Aventis Deutschland GmbH
 RD LGCR/Struct.,Design  Informatics FF
 Industriepark Hoechst
 Bldg. G877, Room 029
 D-65926 Frankfurt am Main
 t: +49 69 305 24896
 f: +49 69 305 80169
 w:www.sanofi.de
 
 *
 Sanofi-Aventis Deutschland GmbH ·  Sitz der Gesellschaft: Frankfurt am Main · 
 Handelsregister: Frankfurt am Main, Abt. B Nr. 40661
 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer: Dr. Martin 
 Siewert (Vorsitzender), Dr. Matthias Braun,
 Peter Guenter, Prof. Dr. Jochen Maas, Dr. Klaus Menken, Dr. Heinz Riederer, 
 Dr. Emmanuel Siregar
 *
 

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

Re: [ccp4bb] phaser problem

[Randy Read]

Hi Amir,

When this error was reported before, it turned out that the sequence file used 
to define the composition had the one-letter code Z (presumably for Se-Met), 
which Phaser-2.1.4 doesn't recognise.  I'm not sure what the newer versions in 
CCP4 and Phenix would do with this, but at the time I recall we were at least 
going to make the error message more informative.  I'll check when I'm back at 
work (it's a bank holiday today in the UK).

Regards,

Randy

On 29 Aug 2011, at 00:22, Amir Khan wrote:

 Hi
 
 Has anyone a solution to the following problem with Phaser (version 2.1.4)?
 
 UNHANDLED ERROR: basic_string::_S_create
 
 It seems to be data and model independent – there was an old thread from 
 earlier this year, but I cannot find a follow-up.
 
 Thanks!
 
 Amir
 
 

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 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

[ccp4bb] phaser problem

[Amir Khan]

Hi

Has anyone a solution to the following problem with Phaser (version 2.1.4)?

UNHANDLED ERROR: basic_string::_S_create

It seems to be data and model independent – there was an old thread from 
earlier this year, but I cannot find a follow-up.

Thanks!

Amir

[ccp4bb] phaser openmp

[Jochen Kuper]

Dear all,


it would be really great if someone could point out to me how to enable the 
openmp option for phaser during the compilation of  the latest ccp4 release. 

The system will be a SUSE 11.3 64bit using gcc. 

Cheers,

Jochen


-
Dr. Jochen Kuper
Rudolf Virchow Center for Biomedical Research
Josef Schneider Strasse 2, Haus D15
97080 Wuerzburg
+49 (0) 9313180391
jochen.ku...@virchow.uni-wuerzburg.de

Re: [ccp4bb] Phaser and Molrep gave different solutions

[Hubing Lou]

Hi,

Thanks for those who replied to this thread.
I have been trying all the means that people suggested: search protein
alone, DNA alone. However, both not working out.
One thing Ray Brown suggested MR works if the molecules have identical
sequences. So I just played around with the following way: 1) use the
chainsaw editted model in MR; 2) mutate the protein sequence back to my
protein and refine the solution in Coot; 3) use the partially refined
protein-DNA as the new search model and run Phaser again then I get the
following results for the two copies in ASU:
RFZ=6.5 TFZ=10.7 LLG=903 RFZ=6.2 TFZ=17.4 LLG=1130.
After one round of rigid body and restraint refinement in Refmac5, the Rfac
and Rfree drops from 0.50/0.51 to 0.46/0.51. I did not refine the DNA
sequences yet.

I am not sure if this way I can further refine the structure, or do I bring
two much bias into the structure. Please correct me if any. Thanks.

Best,
Hubing




On Thu, Jul 21, 2011 at 11:31 PM, ray-br...@att.net wrote:

 I have also tried for years to solve a protein-DNA complex without sucess.
 If you have a lot more DNA than protein in the AU then MR will not work. You
 always get a good RFZ score but you cannot solve the translation if the
 DNA molecules are forming long stacks. With a plausible packing you will of
 course get model phases and a nice map but refinement will not work and you
 will get stuck at 40-50% Rf.

 You may have a chancewith MR if you only have a small DNA and a much bigger
 protein molecule or if the search models and the molecules have identical
 sequences.

 To solve this structure you probably have to do Se-labeled protein and SAD
 etc. or collect anomalous from metal ions if present.

 Cheers.

 Ray Brown

  --
 *From:* Hubing Lou louhub...@gmail.com

 *To:* CCP4BB@JISCMAIL.AC.UK
 *Sent:* Thu, July 21, 2011 6:39:49 AM
 *Subject:* Re: [ccp4bb] Phaser and Molrep gave different solutions

 I was worried as well with the low TFZ score. Usually successful cases with
 score 8. I am still puzzled why Phaser and Molrep gave different solutions.
 Does this mean molecular replacement do not work out in this case so more
 crystals have to be prepared?

 A little more information might be helpful to dissolve the problem here.
 The model I used is a protein-DNA complex. The protein was Chainsaw editted
 but the DNA sequence was directly borrowed from the original model.

 Best,
 Hubing

 On Thu, Jul 21, 2011 at 3:30 PM, Vellieux Frederic 
 frederic.velli...@ibs.fr wrote:

 Hi,

 It's not a bad idea to read the Phaser manual for molecular replacement;
 see http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement

 Soon after the start, in a table on the right hand side, there is: TFZ
 score  5, have I solved it ? No.

 Hence with a TFZ score of 3.8 you do not have a solution using Phaser.

 Fred.

 Hubing Lou wrote:

  Dear all,

 I am stuck in a molecular replacement case and looking for advices.
 I have been working on a protein-DNA complex structure.
 Data was processed by HKL2000 to 2.6Ang and some of the data statistics
 are shown below:

 Space group: P21,
 Unit Cell: 54.73, 104.91, 78.40, 90, 100.2, 90
 Redundancy: 2.8 (2.7)
 Completeness: 94.8 (93.1)
 Linear R-fac: 0.051 (0.442)

 Data quality was checked by Phenix.xtriage and there's no problem. I then
 prepared a model by Chainsaw. Our protein shares only 30% of sequence
 similarity with the model, but structurally they are in the same group and
 almost identical in apo form. Matthrews Coeff indaced two monomers in AU. I
 then ran Phaser in automated search mode and there's a solution with RFZ
 score 4.8, TFZ score 3.8. The electron density map was not bad with DNA
 double helix clearly seen. However Refmac5 couldn't get Rfree lower than
 50%.

 I then changed to MolRep, ran self rotation function first then used
 the first 10 peaks for translation search. Again there's a solution but it
 is different from that from Phaser. I attached a picture here. Checking in
 coot, the packing is the same. But, the refinement couldn't get Rfree lower
 than 50%.

 I have tried to include NCS, TLS refinement in Refmac, both not working.
 Hope someone out there can help.
 Thanks very much for your time.

 Hubing


 --**--**
 

Re: [ccp4bb] Phaser and Molrep gave different solutions

[ccp4]

That looks very hopeful. Do you know how the two molecules are related to
each other? Do they form a dimer or have some interesting relationship?
I would keep on improving the model - possibly use COOT to average the
density and build into that for a start. I presume there are still side
chains to mutate and fit, and other corrections to make? You can then save
molecule 1, and fit the molecule 1 model back over molecule 2 and save that
again.
You need to edit the two chains into one PDB in some way and refine again.
You might begin to see DNA at a low sigma level in those maps..

(By the way - I dont understand 2) mutate the protein sequence back to my
 protein and refine the solution in Coot. Chainsaw should output the
model with the correct sequence but with atoms missing where there are
changes. You would need to rebuild that but not change the sequence? ) 

And you would hope then that PHASER might find your 2 protein chains with
a very high LLG then perhaps place the DNA. but in my limited experience
DNA is usually more mobile and therefore harder to pick up than protein.

good luck Eleanor
 

On Mon, 25 Jul 2011 15:38:02 +0800, Hubing Lou louhub...@gmail.com
wrote:
 Hi,
 
 Thanks for those who replied to this thread.
 I have been trying all the means that people suggested: search protein
 alone, DNA alone. However, both not working out.
 One thing Ray Brown suggested MR works if the molecules have identical
 sequences. So I just played around with the following way: 1) use the
 chainsaw editted model in MR; 2) mutate the protein sequence back to my
 protein and refine the solution in Coot; 3) use the partially refined
 protein-DNA as the new search model and run Phaser again then I get the
 following results for the two copies in ASU:
 RFZ=6.5 TFZ=10.7 LLG=903 RFZ=6.2 TFZ=17.4 LLG=1130.
 After one round of rigid body and restraint refinement in Refmac5, the
Rfac
 and Rfree drops from 0.50/0.51 to 0.46/0.51. I did not refine the DNA
 sequences yet.
 
 I am not sure if this way I can further refine the structure, or do I
bring
 two much bias into the structure. Please correct me if any. Thanks.
 
 Best,
 Hubing
 
 
 
 
 On Thu, Jul 21, 2011 at 11:31 PM, ray-br...@att.net wrote:
 
 I have also tried for years to solve a protein-DNA complex without
 sucess.
 If you have a lot more DNA than protein in the AU then MR will not
work.
 You
 always get a good RFZ score but you cannot solve the translation if the
 DNA molecules are forming long stacks. With a plausible packing you
will
 of
 course get model phases and a nice map but refinement will not work and
 you
 will get stuck at 40-50% Rf.

 You may have a chancewith MR if you only have a small DNA and a much
 bigger
 protein molecule or if the search models and the molecules have
identical
 sequences.

 To solve this structure you probably have to do Se-labeled protein and
 SAD
 etc. or collect anomalous from metal ions if present.

 Cheers.

 Ray Brown

  --
 *From:* Hubing Lou louhub...@gmail.com

 *To:* CCP4BB@JISCMAIL.AC.UK
 *Sent:* Thu, July 21, 2011 6:39:49 AM
 *Subject:* Re: [ccp4bb] Phaser and Molrep gave different solutions

 I was worried as well with the low TFZ score. Usually successful cases
 with
 score 8. I am still puzzled why Phaser and Molrep gave different
 solutions.
 Does this mean molecular replacement do not work out in this case so
more
 crystals have to be prepared?

 A little more information might be helpful to dissolve the problem
here.
 The model I used is a protein-DNA complex. The protein was Chainsaw
 editted
 but the DNA sequence was directly borrowed from the original model.

 Best,
 Hubing

 On Thu, Jul 21, 2011 at 3:30 PM, Vellieux Frederic 
 frederic.velli...@ibs.fr wrote:

 Hi,

 It's not a bad idea to read the Phaser manual for molecular
replacement;
 see http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement

 Soon after the start, in a table on the right hand side, there is: TFZ
 score  5, have I solved it ? No.

 Hence with a TFZ score of 3.8 you do not have a solution using Phaser.

 Fred.

 Hubing Lou wrote:

  Dear all,

 I am stuck in a molecular replacement case and looking for advices.
 I have been working on a protein-DNA complex structure.
 Data was processed by HKL2000 to 2.6Ang and some of the data
statistics
 are shown below:

 Space group: P21,
 Unit Cell: 54.73, 104.91, 78.40, 90, 100.2, 90
 Redundancy: 2.8 (2.7)
 Completeness: 94.8 (93.1)
 Linear R-fac: 0.051 (0.442)

 Data quality was checked by Phenix.xtriage and there's no problem. I
 then
 prepared a model by Chainsaw. Our protein shares only 30% of sequence
 similarity with the model, but structurally they are in the same
group
 and
 almost identical in apo form. Matthrews Coeff indaced two monomers in
 AU. I
 then ran Phaser in automated search mode and there's a solution
with
 RFZ
 score 4.8, TFZ score 3.8. The electron density map was not bad with
DNA
 double helix clearly seen. However Refmac5 couldn't