Re: [ccp4bb] ample

[Randy Read]

Dear Patrick,

Apologies for a partly non-CCP4 answer!  You can use the HHPRED alignments in 
some of the software available in Phenix.  One option is to provide the .hhr 
file to MRage, which will fetch the PDB entries, run Sculptor to modify the 
templates with one or more protocols, based on that alignment, and then test 
all the models that have been generated.  That's fully automated and will often 
work.  If it doesn't, an alternative is to run phenix.mr_model_preparation, 
which again will fetch the PDB entries and run the single best Sculptor 
protocol on all of them.  I tend to prefer this option myself, because then you 
can look at whether it would be sensible to combine various alternative models 
as ensembles.  One of the most powerful approaches is to run Ensembler 
(available in both CCP4 and Phenix, as is Sculptor) to make an ensemble, with 
the "trim=True" option turned on to trim any bits that don't agree among the 
structures in the ensemble.  Cutting back to a conserved core has allowed a 
number of very recalcitrant structures to be solved with collections of models 
around the 20% sequence identity range.

Best wishes,

Randy

> On 20 Jul 2017, at 23:13, Patrick Loll  wrote:
> 
> I’m intrigued by the prospect of using AMPLE to test multiple distant 
> homologs in a MR problem. I’ve used HHPRED to identify about 20 
> high-probability homologs of known structure, each of which has about 20-25% 
> identity with the unknown protein. However, it’s not clear to me from the 
> documentation whether the program will use the alignments from HHPRED, and, 
> if so, how I should provide that information. 
> 
> Or does AMPLE perform its own alignment? I.e., do I simply point the program 
> to a directory containing 20 different PDB files and stand back?
> 
> Thanks for any insights.
> 
> Cheers,
> 
> Pat 
> ---
> Patrick J. Loll, Ph. D.  
> Professor of Biochemistry & Molecular Biology
> Drexel University College of Medicine
> Room 10-102 New College Building
> 245 N. 15th St., Mailstop 497
> Philadelphia, PA  19102-1192  USA
> 
> (215) 762-7706
> pjl...@gmail.com
> pj...@drexel.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] ample

[Daniel Rigden]

Dear Pat

Yes, AMPLE does it's own, purely structure-based, alignment of the 
homologs provided using GESAMT. You provide a directory of structures to 
work with and, crucially, give AMPLE the


-homologs True

flag so that it knows the inputs have different sequences (unlike in 
modelling mode), and need to be dealt with accordingly.


There's more explanation and example files here

http://ample.readthedocs.io/en/latest/examples/rst/homologs.html#example-dist-homologs

In this mode AMPLE first finds the common core shared by all inputs and 
then produces graded further truncations of that with different side 
chain treatments. This sampling is often necessary in the hardest cases. 
What this means, however, is if the input set are ultra-diverse, then 
the GESAMT shared common core can be quite small. It can therefore also 
be worth trying a smaller set of not quite so diverse structures which 
share a somewhat larger core structure.


Best wishes

Daniel

On 20/07/17 23:13, Patrick Loll wrote:

I’m intrigued by the prospect of using AMPLE to test multiple distant homologs 
in a MR problem. I’ve used HHPRED to identify about 20 high-probability 
homologs of known structure, each of which has about 20-25% identity with the 
unknown protein. However, it’s not clear to me from the documentation whether 
the program will use the alignments from HHPRED, and, if so, how I should 
provide that information.

Or does AMPLE perform its own alignment? I.e., do I simply point the program to 
a directory containing 20 different PDB files and stand back?

Thanks for any insights.

Cheers,

Pat
---
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu


--
Dr Daniel John Rigden Tel:(+44) 151 795 4467
Institute of Integrative Biology  FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool   http://pcwww.liverpool.ac.uk/~drigden/
Crown St.,
Liverpool L69 7ZB, U.K.

[ccp4bb] ample

[Patrick Loll]

I’m intrigued by the prospect of using AMPLE to test multiple distant homologs 
in a MR problem. I’ve used HHPRED to identify about 20 high-probability 
homologs of known structure, each of which has about 20-25% identity with the 
unknown protein. However, it’s not clear to me from the documentation whether 
the program will use the alignments from HHPRED, and, if so, how I should 
provide that information. 

Or does AMPLE perform its own alignment? I.e., do I simply point the program to 
a directory containing 20 different PDB files and stand back?

Thanks for any insights.

Cheers,

Pat 
---
Patrick J. Loll, Ph. D.  
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu

Re: [ccp4bb] AMPLE failure

[Ronan Keegan]

Hi Robert,

Thanks for your interest in AMPLE and reporting this bug. There is a 
small bug that has come about as a result of the latest MRBUMP update 
last week that causes this problem. We're preparing a fix for it which 
should be in the next ccp4 update towards the end of this week or early 
next week. In the meantime I can send you (off list) the latest version 
of the code that you can manually install.


Best wishes,

Ronan

On 12/07/14 18:58, Robert Kirchdoerfer wrote:

Hi,

I'm trying to run AMPLE from ccp4-6.4.0 on Linux Ubuntu.  It looks like it 
found all the program dependencies that it needs and Rosetta looks like it ran 
okay and I think MRBUMP looks alright, but then the program stopped with the 
following error message:

MR and shelx DONE

  ALL DONE  (in 1.64101706141 hours)



Saved results as file: 
/home/rob/Crystal/108_B7U_3/ccp4/ROSETTA_MR_1/resultsd.pkl


***
* Information from CCP4Interface script
***
The program run with command: 
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ccp4-python -u 
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample -mtz 
/home/rob/Crystal/108_B7U_3/ccp4/XDS_ASCII_scaled2.mtz -fasta 
/home/rob/Crystal/108_B7U_3/phenix/RNK149.fasta -nmodels 1000 -name MVD0 
-run_dir /home/rob/Crystal/108_B7U_3/ccp4 -nproc 8 -make_models True 
-rosetta_dir /home/rob/Xstal_Programs/Rosetta/rosetta-3.5 -frags_3mers 
/home/rob/Crystal/108_B7U_3/ccp4/aat000_03_05.200_v1_3 -frags_9mers 
/home/rob/Crystal/108_B7U_3/ccp4/aat000_09_05.200_v1_3 -make_frags False -F 
F_XDSdataset -SIGF SIGF_XDSdataset -FREE FreeR_flag  -early_terminate True   
-use_shelxe True -use_arpwarp False
has failed with error message
Traceback (most recent call last):
   File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample, 
line 838, in
 summary = amopt.final_summary()
   File 
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/share/ample/python/ample_options.py,
 line 197, in final_summary
 result_summary.append( getattr( result, title2attr[ h ] )  )
KeyError: 'SHELXE_ACL'

Any thoughts on how I might troubleshoot this?

Thanks and Best wishes,
Rob


--
Scanned by iCritical.

[ccp4bb] AMPLE failure

[Robert Kirchdoerfer]

Hi,

I'm trying to run AMPLE from ccp4-6.4.0 on Linux Ubuntu.  It looks like it 
found all the program dependencies that it needs and Rosetta looks like it ran 
okay and I think MRBUMP looks alright, but then the program stopped with the 
following error message:

MR and shelx DONE

 ALL DONE  (in 1.64101706141 hours) 



Saved results as file: 
/home/rob/Crystal/108_B7U_3/ccp4/ROSETTA_MR_1/resultsd.pkl


***
* Information from CCP4Interface script
***
The program run with command: 
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ccp4-python -u 
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample -mtz 
/home/rob/Crystal/108_B7U_3/ccp4/XDS_ASCII_scaled2.mtz -fasta 
/home/rob/Crystal/108_B7U_3/phenix/RNK149.fasta -nmodels 1000 -name MVD0 
-run_dir /home/rob/Crystal/108_B7U_3/ccp4 -nproc 8 -make_models True 
-rosetta_dir /home/rob/Xstal_Programs/Rosetta/rosetta-3.5 -frags_3mers 
/home/rob/Crystal/108_B7U_3/ccp4/aat000_03_05.200_v1_3 -frags_9mers 
/home/rob/Crystal/108_B7U_3/ccp4/aat000_09_05.200_v1_3 -make_frags False -F 
F_XDSdataset -SIGF SIGF_XDSdataset -FREE FreeR_flag  -early_terminate True   
-use_shelxe True -use_arpwarp False   
has failed with error message
Traceback (most recent call last):
  File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample, 
line 838, in 
summary = amopt.final_summary()
  File 
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/share/ample/python/ample_options.py,
 line 197, in final_summary
result_summary.append( getattr( result, title2attr[ h ] )  )
KeyError: 'SHELXE_ACL'

Any thoughts on how I might troubleshoot this?

Thanks and Best wishes,
Rob

Re: [ccp4bb] AMPLE failure

[Thomas, Jens]

Dear Rob,

Sorry to hear that this issue has affected you - it's a known bug which will be 
fixed in the next ccp4 update.

AMPLE has run to completion but crashed printing out the results.

To see the results, you can run the following command at the terminal 
(command-line):

/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ccp4-python  
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/share/ample/python/mrbump_results.py
 /home/rob/Crystal/108_B7U_3/ccp4/ROSETTA_MR_1/MRBUMP/cluster_1

If that doesn't work or you need any additional help, please contact me 
off-list.

Best wishes,

Jens



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Robert 
Kirchdoerfer [rkirc...@scripps.edu]
Sent: 12 July 2014 18:58
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AMPLE failure

Hi,

I'm trying to run AMPLE from ccp4-6.4.0 on Linux Ubuntu.  It looks like it 
found all the program dependencies that it needs and Rosetta looks like it ran 
okay and I think MRBUMP looks alright, but then the program stopped with the 
following error message:

MR and shelx DONE

 ALL DONE  (in 1.64101706141 hours)



Saved results as file: 
/home/rob/Crystal/108_B7U_3/ccp4/ROSETTA_MR_1/resultsd.pkl


***
* Information from CCP4Interface script
***
The program run with command: 
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ccp4-python -u 
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample -mtz 
/home/rob/Crystal/108_B7U_3/ccp4/XDS_ASCII_scaled2.mtz -fasta 
/home/rob/Crystal/108_B7U_3/phenix/RNK149.fasta -nmodels 1000 -name MVD0 
-run_dir /home/rob/Crystal/108_B7U_3/ccp4 -nproc 8 -make_models True 
-rosetta_dir /home/rob/Xstal_Programs/Rosetta/rosetta-3.5 -frags_3mers 
/home/rob/Crystal/108_B7U_3/ccp4/aat000_03_05.200_v1_3 -frags_9mers 
/home/rob/Crystal/108_B7U_3/ccp4/aat000_09_05.200_v1_3 -make_frags False -F 
F_XDSdataset -SIGF SIGF_XDSdataset -FREE FreeR_flag  -early_terminate True   
-use_shelxe True -use_arpwarp False
has failed with error message
Traceback (most recent call last):
  File /home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/bin/ample, 
line 838, in
summary = amopt.final_summary()
  File 
/home/rob/Xstal_Programs/ccp4v640/destination/ccp4-6.4.0/share/ample/python/ample_options.py,
 line 197, in final_summary
result_summary.append( getattr( result, title2attr[ h ] )  )
KeyError: 'SHELXE_ACL'

Any thoughts on how I might troubleshoot this?

Thanks and Best wishes,
Rob

[ccp4bb] Ample fails

[Florian Sauer]

Dear all,

I'm trying to use Ample from CCP4 (6.4) to solve a structure of 2x197
residues from 2.0 A data.
After the generation of initial (120) models by Rosetta (3.3) Ample
stops with the error-message below.
Could anyone provide me information about the origin of this error and
possibly how to solve the problem?

Thanks in advance for your replies!

Best wishes,

Florian

***

* Information from CCP4Interface script

***

The program run with command: 
/home/flo/crystallography/ccp4-6.4.0/bin/ccp4-python -u 
/home/flo/crystallography/ccp4-6.4.0/bin/ample -mtz 
/home/flo/crystallography/Virchow/ESRF_20140707/CM133A/ccp4/pos5wedge3scaled.mtz
 -fasta /home/flo/Desktop/arch.seq -name MVD0 -run_dir 
/home/flo/crystallography/Virchow/ESRF_20140707/pos7au/ccp4 -nproc 3 -F 
F_XDSdataset -SIGF SIGF_XDSdataset -FREE FreeR_flag  -models_dir 
/home/flo/crystallography/Virchow/ESRF_20140707/pos7au/ccp4/ROSETTA_MR_0/models/models_1
 -early_terminate True  -use_shelxe True -use_arpwarp False   

has failed with error message

Traceback (most recent call last):

  File /home/flo/crystallography/ccp4-6.4.0/bin/ample, line 757, in 

ensemble.create_ensembles( amopt.d )

  File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ensemble.py, 
line 85, in create_ensembles

ensembles = ensemble_models( amoptd['spicker_results'][ cluster-1 
].pdb_list, amoptd, ensemble_id=cluster )

  File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ensemble.py, 
line 58, in ensemble_models

percent=amoptd['percent'] )

  File 
/home/flo/crystallography/ccp4-6.4.0/share/ample/python/ample_ensemble.py, 
line 168, in generate_ensembles

self.make_truncated_ensembles()

  File 
/home/flo/crystallography/ccp4-6.4.0/share/ample/python/ample_ensemble.py, 
line 312, in make_truncated_ensembles

clusterer.generate_distance_matrix( self.truncated_models[tcount] )

  File 
/home/flo/crystallography/ccp4-6.4.0/share/ample/python/cluster_with_MAX.py, 
line 55, in generate_distance_matrix

retcode = ample_util.run_command( cmd, logfile=log_name )

  File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ample_util.py, 
line 274, in run_command

p = subprocess.Popen( cmd, stdin=stdin, stdout=logf, 
stderr=subprocess.STDOUT, cwd=directory, **kwargs )

  File /home/flo/crystallography/ccp4-6.4.0/lib/python2.7/subprocess.py, line 
711, in __init__

errread, errwrite)

  File /home/flo/crystallography/ccp4-6.4.0/lib/python2.7/subprocess.py, line 
1308, in _execute_child

raise child_exception

OSError: [Errno 8] Exec format error

***



-- 
Dr. Florian Sauer
Rudolf Virchow Zentrum für Experimentelle Biomedizin
Josef-Schneider-Str. 2, Haus D15
97080 Würzburg

Re: [ccp4bb] Ample fails

[Thomas, Jens]

Dear Florian,

Sorry to hear that Ample isn't working for you.

I haven't seen this error before, but my initial guess would be that you're 
trying to run Ample on Windows? If so then unfortunately the current release of 
Ample isn't supported on Windows. Most of the work to port Ample to Windows has 
been carried out, and it will be made available in a forthcoming release of 
CCP4, but until then the only solution is to run Ample on Linux or Mac OSX.

If you're not running on Windows, please could you send me (off list) the file 
debug.log, which should have been created in the directory:

/home/flo/crystallography/Virchow/ESRF_20140707/pos7au/ccp4/ROSETTA_MR_0

(the directory may be named ROSETTA_MR_0, ROSETTA_MR_1, ROSETTA_MR_2... etc. 
depending on how many runs you have attempted.)

Just for information, at 197 residues your protein is on the large side 
(although well within the bounds of what Ample is capable of solving), but 120 
models is far fewer then we would normally recommend. The usual recommendation 
is to make at least 1000 models.

Best wishes,

Jens


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Florian Sauer 
[florian.sau...@virchow.uni-wuerzburg.de]
Sent: 11 July 2014 08:37
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Ample fails

Dear all,

I'm trying to use Ample from CCP4 (6.4) to solve a structure of 2x197 residues 
from 2.0 A data.
After the generation of initial (120) models by Rosetta (3.3) Ample stops with 
the error-message below.
Could anyone provide me information about the origin of this error and possibly 
how to solve the problem?

Thanks in advance for your replies!

Best wishes,

Florian


***

* Information from CCP4Interface script

***

The program run with command: 
/home/flo/crystallography/ccp4-6.4.0/bin/ccp4-python -u 
/home/flo/crystallography/ccp4-6.4.0/bin/ample -mtz 
/home/flo/crystallography/Virchow/ESRF_20140707/CM133A/ccp4/pos5wedge3scaled.mtz
 -fasta /home/flo/Desktop/arch.seq -name MVD0 -run_dir 
/home/flo/crystallography/Virchow/ESRF_20140707/pos7au/ccp4 -nproc 3 -F 
F_XDSdataset -SIGF SIGF_XDSdataset -FREE FreeR_flag  -models_dir 
/home/flo/crystallography/Virchow/ESRF_20140707/pos7au/ccp4/ROSETTA_MR_0/models/models_1
 -early_terminate True  -use_shelxe True -use_arpwarp False

has failed with error message

Traceback (most recent call last):

  File /home/flo/crystallography/ccp4-6.4.0/bin/ample, line 757, in

ensemble.create_ensembles( amopt.d )

  File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ensemble.py, 
line 85, in create_ensembles

ensembles = ensemble_models( amoptd['spicker_results'][ cluster-1 
].pdb_list, amoptd, ensemble_id=cluster )

  File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ensemble.py, 
line 58, in ensemble_models

percent=amoptd['percent'] )

  File 
/home/flo/crystallography/ccp4-6.4.0/share/ample/python/ample_ensemble.py, 
line 168, in generate_ensembles

self.make_truncated_ensembles()

  File 
/home/flo/crystallography/ccp4-6.4.0/share/ample/python/ample_ensemble.py, 
line 312, in make_truncated_ensembles

clusterer.generate_distance_matrix( self.truncated_models[tcount] )

  File 
/home/flo/crystallography/ccp4-6.4.0/share/ample/python/cluster_with_MAX.py, 
line 55, in generate_distance_matrix

retcode = ample_util.run_command( cmd, logfile=log_name )

  File /home/flo/crystallography/ccp4-6.4.0/share/ample/python/ample_util.py, 
line 274, in run_command

p = subprocess.Popen( cmd, stdin=stdin, stdout=logf, 
stderr=subprocess.STDOUT, cwd=directory, **kwargs )

  File /home/flo/crystallography/ccp4-6.4.0/lib/python2.7/subprocess.py, line 
711, in __init__

errread, errwrite)

  File /home/flo/crystallography/ccp4-6.4.0/lib/python2.7/subprocess.py, line 
1308, in _execute_child

raise child_exception

OSError: [Errno 8] Exec format error

***



--
Dr. Florian Sauer
Rudolf Virchow Zentrum für Experimentelle Biomedizin
Josef-Schneider-Str. 2, Haus D15
97080 Würzburg

[ccp4bb] Ample, shelxe-beta and F to I conversion confusion

[Huw Jenkins]

Hi,

I've been running Ample and I'm a bit confused about the input for the 
shelxe-beta auto-tracing. The input mtz for Ample has F, SIGF and FreeR and it 
appears that Ample converts the structure factor amplitudes to intensities 
using mtz2various with the FSQUARED keyword as the log file contains the 
following:

Data line--- LABIN FP=F SIGFP=SIGF FREE=FreeR_flag
Data line--- OUTPUT SHELX 
Data line--- FSQUARED

   Fs are squared on output - better to use original Is from TRUNCATE output
 Data line--- END

However then shelxe is run with the command:

shelxe shelxe-input.pda -a15 -q -s0.4779 -o -f -n -t3

I thought that the -f flag tells shelxe that the input hkl file contains Fs not 
Is so this should not be present? 

When I run shelxe with the phaser/molrep solutions and a hkl file generated 
either from the merged intensities with mtz2hkl or unmerged intensities with 
xdsconv I get much lower CCs for the autotracing which makes sense as all of 
the solutions so far are rubbish! The Ample logs contain CCs 30 for all 
solutions which doesn't seem correct.

Any information would be greatly appreciated!

Thanks,



Huw

Re: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion

[George Sheldrick]

Dear Huw,

It looks as though you have correctly diagnosed a problem with AMPLE.

For expansion from borderline partial structures, I recommend the latest
SHELXE (on my beta-test server since Jan. 20th)  and experimenting with
the -O and -F switches, e.g.

-F0.9 -O100 -a30

However SHELXE is still a work in progress, so this may change in future
versions.

Best wishes, George


Hi,

I've been running Ample and I'm a bit confused about the input for the 
shelxe-beta auto-tracing. The input mtz for Ample has F, SIGF and FreeR and it 
appears that Ample converts the structure factor amplitudes to intensities 
using mtz2various with the FSQUARED keyword as the log file contains the 
following:

Data line--- LABIN FP=F SIGFP=SIGF FREE=FreeR_flag
Data line--- OUTPUT SHELX
Data line--- FSQUARED

Fs are squared on output - better to use original Is from TRUNCATE output
  Data line--- END

However then shelxe is run with the command:

shelxe shelxe-input.pda -a15 -q -s0.4779 -o -f -n -t3

I thought that the -f flag tells shelxe that the input hkl file contains Fs not 
Is so this should not be present?

When I run shelxe with the phaser/molrep solutions and a hkl file generated either 
from the merged intensities with mtz2hkl or unmerged intensities with xdsconv I 
get much lower CCs for the autotracing which makes sense as all of the solutions 
so far are rubbish! The Ample logs contain CCs30 for all solutions which 
doesn't seem correct.

Any information would be greatly appreciated!

Thanks,



Huw




--
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

Re: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion

[ronan . keegan]

Hi Huw,

Well spotted! We originally gave structure factors to SHELXE in our testing as 
for most of our test cases we only had F/SIGF available. We were advised to 
change to intensities but somehow in the released version the -f flag 
remained. I'll make the change and put it in a CCP4 update. Ideally we should 
be using the original intensities rather than converting the structure factors 
so we'll look to adding that as an input option. 

Thanks again for spotting this.

Best wishes,

Ronan 

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Huw 
Jenkins
Sent: 28 January 2013 10:14
To: ccp4bb
Subject: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion

Hi,

I've been running Ample and I'm a bit confused about the input for the 
shelxe-beta auto-tracing. The input mtz for Ample has F, SIGF and FreeR and it 
appears that Ample converts the structure factor amplitudes to intensities 
using mtz2various with the FSQUARED keyword as the log file contains the 
following:

Data line--- LABIN FP=F SIGFP=SIGF FREE=FreeR_flag
Data line--- OUTPUT SHELX 
Data line--- FSQUARED

   Fs are squared on output - better to use original Is from TRUNCATE output
 Data line--- END

However then shelxe is run with the command:

shelxe shelxe-input.pda -a15 -q -s0.4779 -o -f -n -t3

I thought that the -f flag tells shelxe that the input hkl file contains Fs not 
Is so this should not be present? 

When I run shelxe with the phaser/molrep solutions and a hkl file generated 
either from the merged intensities with mtz2hkl or unmerged intensities with 
xdsconv I get much lower CCs for the autotracing which makes sense as all of 
the solutions so far are rubbish! The Ample logs contain CCs 30 for all 
solutions which doesn't seem correct.

Any information would be greatly appreciated!

Thanks,



Huw

-- 
Scanned by iCritical.

Re: [ccp4bb] Ample, shelxe-beta and F to I conversion confusion

[George Sheldrick]

Correct, shelxe does not use the free -R flags, and works just
as well with the original unmerged unctruncated intensities.

George


Hi Ronan,

On 28 Jan 2013, at 12:18, ronan.kee...@stfc.ac.uk wrote:


Well spotted! We originally gave structure factors to SHELXE in our testing as for most 
of our test cases we only had F/SIGF available. We were advised to change to intensities 
but somehow in the released version the -f flag remained. I'll make the 
change and put it in a CCP4 update. Ideally we should be using the original intensities 
rather than converting the structure factors so we'll look to adding that as an input 
option.

Thanks for confirming that! Perhaps the option to add a hkl file for shelxe 
would be a useful? Since I use XDS to integrate and scale data it's as easy to 
generate the shelx format hkl file from the unmerged XDS_ASCII.HKL as it is to 
use the merged intensities in the mtz from the 
aimless/truncate/unique/freerflag pipeline. The only issue with this I can see 
is that there will be no freeR flags but I don't think that shelxe uses these 
anyway?

Thanks,


Huw




--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
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