Re: [ccp4bb] refmac output

[Pavel Afonine]

>
> I know space is cheap these days, but is there a reason for Refmac to
> generate all those extra columns in the output mtz file?  Refmac (as well
> as phenix.refine and buster-tnt) output mtz file is almost always used for
> only one purpose - look at the map in coot.  You only need 4 columns for
> that, not 14.  Other columns are useful for testing, but why not make them
> optional?
>

a phenix.refine run creates an MTZ file with four kinds of data:

1) Copy of input data. Why? For convenience and consistency. Inputs may not
necessarily be in MTZ format and may be spread across multiple files of
different format.

2) Data that were actually used in refinement. Why? A user has options to
cut resolution from both ends, as well as apply cutting by sigma. Plus,
phenix.refine may choose not to use a handful of reflections as outliers
(Read, 1999). So it may be good to have set of reflections that were used
in given refinement run.

3) Model in reciprocal space: Fmodel. Why? This is a reciprocal space
representation of what's in PDB file except that it is richer because
contains not only atomic model (Fcalc) but also solvent contributions (bulk
and non-uniform) as well as all scales. Fmodel taken from this array and
Fobs from "2)" are expected to reproduce reported R-factor exactly.

4) Fourier map coefficients (2mFobs-DFmodel, mFobs-DFmodel, anomalous map
if applicable).

"1)" and "3)" can be optional:
- with trivial scripting one can obtain Fmodel using data from "2)" and
"4)".
- "1)" duplicates inputs. It's not unreasonable to assume they are
still available by the time you finalize your structure.
But.. as you pointed out space is cheap and personally I find it much
easier to have relevant arrays of data centralized in one place (file)
rather than scattered across hard drive.

All the best,
Pavel

Re: [ccp4bb] Help needed finding hit condition

[khaja faisal tarique]

Hello everyone.

I remember the screen was again from Jenabioscience and this had happened
with one of my protein. The screen was very old and the condition was
peg3350, tris pH 8, lithium sulfate and NaCl as the salt. Hit was obtained
which was never reproducible. Luckily I solved the structure from the hit
itself which diffracted to 2.2A resolution. But it is still a mystery for
us but this is all crystallography is. Strange things happen.

Faisal
Postdoc
PHRI, NJ, USA

On Jul 31, 2017 5:19 PM, "Janet Newman"  wrote:

> ​Hi Jonathan,
>
>
> Hopefully you know about the trick of making any precious condition last
> longer - use the 'magic' solution only in the drop itself, and use the best
> approximation you can make in the reservoir of the experiment (if you are
> doing vapour diffusion)
>
>
> Regards, Janet
>
>
> Janet Newman
> Principal Scientist / Director, Collaborative Crystallisation Centre (C3)
> CSIRO Material Science and Engineering
> 343 Royal Parade
> Parkville.  VIC. 3052
> Australia
> Tel +613 9662 7326 <+61%203%209662%207326>
> Email janet.new...@csiro.au
> --
> *From:* CCP4 bulletin board  on behalf of Jonathan
> Bailey 
> *Sent:* 31 July 2017 22:34
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Help needed finding hit condition
>
>
> Dear CCP4bb community
>
>
> I apologies for the slightly off topic post.
>
>
> We have recently had success crystallizing a membrane protein (diffraction
> > 3 Å at a synchrotron source) using the *in meso* method, the hit
> condition was from the Jena Bioscience screen Pi-minimal condition number
> #57.
>
>
> Hit condition – 47.1 % w/v PEG1000, 150 mM Tris pH 8.0, 80 mM Potassium
> bromide
>
>
> The screen is old and expired 12/20/2013 (lot # JBS00013133), we have
> tried to reproduce the crystals using homemade optimization screens around
> the hit condition but have not had any success. We have tried reproducing
> the hit using a new (not expired) Pi-minimal screen but had no success. We
> are only able to reproduce the crystals using the expired screen and we do
> not have much of it left.
>
>
>
> We went back and tested the pH of the condition that had given crystals,
> the expected pH was 7.9 but we found it to be 6 – 6.5 using a pH indicator
> strip. We believe the drop in pH is caused by oxidative degradation of the
> PEG1000 resulting in the formation of carboxylic acid species.
>
>
> We have contacted Jena Bioscience to try and get some of the old screen
> stock but unfortunately they do not have any.
>
>
> My question is does anyone out there happen to have any expired screen
> stocks of this Pi-minimal condition (#57), ideally from the same lot (lot #
> JB200013133), that they would be willing to send us.
>
>
>
> Does anyone have any advice as to how to reproduce the condition? We’ve
> considered bubbling oxygen through and heating the sample to accelerate the
> oxidation process.
>
>
>
> King Regards
>
>
> Jonathan Bailey (PhD student)
>
>
> Professor Martin Caffrey Lab MS group Trinity College Dublin
>

Re: [ccp4bb] Help needed finding hit condition

[Janet Newman]

?Hi Jonathan,


Hopefully you know about the trick of making any precious condition last longer 
- use the 'magic' solution only in the drop itself, and use the best 
approximation you can make in the reservoir of the experiment (if you are doing 
vapour diffusion)


Regards, Janet


Janet Newman
Principal Scientist / Director, Collaborative Crystallisation Centre (C3)
CSIRO Material Science and Engineering
343 Royal Parade
Parkville.  VIC. 3052
Australia
Tel +613 9662 7326
Email janet.new...@csiro.au

From: CCP4 bulletin board  on behalf of Jonathan Bailey 

Sent: 31 July 2017 22:34
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Help needed finding hit condition

Dear CCP4bb community

I apologies for the slightly off topic post.

We have recently had success crystallizing a membrane protein (diffraction > 3 
Å at a synchrotron source) using the in meso method, the hit condition was from 
the Jena Bioscience screen Pi-minimal condition number #57.

Hit condition - 47.1 % w/v PEG1000, 150 mM Tris pH 8.0, 80 mM Potassium bromide

The screen is old and expired 12/20/2013 (lot # JBS00013133), we have tried to 
reproduce the crystals using homemade optimization screens around the hit 
condition but have not had any success. We have tried reproducing the hit using 
a new (not expired) Pi-minimal screen but had no success. We are only able to 
reproduce the crystals using the expired screen and we do not have much of it 
left.

We went back and tested the pH of the condition that had given crystals, the 
expected pH was 7.9 but we found it to be 6 - 6.5 using a pH indicator strip. 
We believe the drop in pH is caused by oxidative degradation of the PEG1000 
resulting in the formation of carboxylic acid species.

We have contacted Jena Bioscience to try and get some of the old screen stock 
but unfortunately they do not have any.

My question is does anyone out there happen to have any expired screen stocks 
of this Pi-minimal condition (#57), ideally from the same lot (lot # 
JB200013133), that they would be willing to send us.

Does anyone have any advice as to how to reproduce the condition? We've 
considered bubbling oxygen through and heating the sample to accelerate the 
oxidation process.

King Regards

Jonathan Bailey (PhD student)

Professor Martin Caffrey Lab MS group Trinity College Dublin

Re: [ccp4bb] Help needed finding hit condition

[Kevin Jin]

Hi Jonathan,

 Old buffer may have slow evaporation with some side reactions. The
concentration of each component may increase a little bit.  In this case,
 I would consider the condition as the origin for further optimization.
Each component may need to be considered separately.

For 150mM Tris pH 8.000,
The pH and concentration may  have a slight change (increase ?).  I will
try the concentration of 150mM, 155 mM and 160mM. For pH,  pH 8.1 and pH
8.2...

For KBr, the concentration may be 80, 85, 90mM or higher.

For 47.1% w/v PEG1K (Pretty high concentration),
As the result for ring-opening epoxide reaction, it is not very stable
anyway. The reaction always continued. Basic condition made the case even
worse. In this case, the Mn (MW) of PEG1K may not be that average anymore.
It is very possible that the polymer chain is elongated. Of course, the
concentration of PEG is increased too. In the meanwhile, the presence of
KBr may cause further chemical modification on the PEG chains.  You may try
PEG 95--1050 (Sigma P3515), PEG 1305-1595 (Sigma 202136), PEG3K or PEG
3350, etc.


Best,

Kevin

P.S. If you take a look from the top of your old solution in the tube,
what's the color? Slight Yellow? You can use a tube with dd water a
reference.


On Mon, Jul 31, 2017 at 5:34 AM, Jonathan Bailey  wrote:

> Dear CCP4bb community
>
>
> I apologies for the slightly off topic post.
>
>
> We have recently had success crystallizing a membrane protein (diffraction
> > 3 Å at a synchrotron source) using the *in meso* method, the hit
> condition was from the Jena Bioscience screen Pi-minimal condition number
> #57.
>
>
> Hit condition – 47.1 % w/v PEG1000, 150 mM Tris pH 8.0, 80 mM Potassium
> bromide
>
>
> The screen is old and expired 12/20/2013 (lot # JBS00013133), we have
> tried to reproduce the crystals using homemade optimization screens around
> the hit condition but have not had any success. We have tried reproducing
> the hit using a new (not expired) Pi-minimal screen but had no success. We
> are only able to reproduce the crystals using the expired screen and we do
> not have much of it left.
>
>
>
> We went back and tested the pH of the condition that had given crystals,
> the expected pH was 7.9 but we found it to be 6 – 6.5 using a pH indicator
> strip. We believe the drop in pH is caused by oxidative degradation of the
> PEG1000 resulting in the formation of carboxylic acid species.
>
>
> We have contacted Jena Bioscience to try and get some of the old screen
> stock but unfortunately they do not have any.
>
>
> My question is does anyone out there happen to have any expired screen
> stocks of this Pi-minimal condition (#57), ideally from the same lot (lot #
> JB200013133), that they would be willing to send us.
>
>
>
> Does anyone have any advice as to how to reproduce the condition? We’ve
> considered bubbling oxygen through and heating the sample to accelerate the
> oxidation process.
>
>
>
> King Regards
>
>
> Jonathan Bailey (PhD student)
>
>
> Professor Martin Caffrey Lab MS group Trinity College Dublin
>



-- 
Kevin Jin

Sharing knowledge each other is always very joyful..

Website: http://www.jinkai.org/

Re: [ccp4bb] refmac output

[Jon Agirre]

Perhaps a good opportunity for getting rid of (scaled) F and SIGF too?

Certain pipelines need Refmac's phase estimates (Buccaneer and Crank2 off
the top of my head), but I can't see how activating an 'expert mode' or
'developer mode' in order to get them would be a problem for their authors.

Cheers,

Jon


On 31 July 2017 at 16:57, Edwin Pozharski  wrote:

> I know space is cheap these days, but is there a reason for Refmac to
> generate all those extra columns in the output mtz file?  Refmac (as well
> as phenix.refine and buster-tnt) output mtz file is almost always used for
> only one purpose - look at the map in coot.  You only need 4 columns for
> that, not 14.  Other columns are useful for testing, but why not make them
> optional?
>
> This would certainly be a low priority - one can easily delete extra
> columns using, say, sftools.
>
> Cheers,
>
> Ed.
>
> ---
> Hurry up, before we all come to our senses!
> Julien, King of Lemurs
>
>


-- 
Dr Jon Agirre
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, England
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Twitter: @alwaysonthejazz
+44 (0) 1904 32 8270

[ccp4bb] refmac output

[Edwin Pozharski]

I know space is cheap these days, but is there a reason for Refmac to
generate all those extra columns in the output mtz file?  Refmac (as well
as phenix.refine and buster-tnt) output mtz file is almost always used for
only one purpose - look at the map in coot.  You only need 4 columns for
that, not 14.  Other columns are useful for testing, but why not make them
optional?

This would certainly be a low priority - one can easily delete extra
columns using, say, sftools.

Cheers,

Ed.

---
Hurry up, before we all come to our senses!
Julien, King of Lemurs

Re: [ccp4bb] Help needed finding hit condition

[R. Michael Garavito]

Jonathan,

While your claim of oxidative degradation of PEG1000 may be true -- I gather 
you mean that the conversion of the ends of the PEG polymers to aldehydes or 
peroxides, then to carboxylates --  you should check out Fran Jurnak’s old 
paper (Journal of Crystal Growth 76, 577, 1986).  The synthesis of PEG often 
contains some of phosphoric acid due to the way they terminated the chain 
elongation.  It is variable from batch to batch and from supplier to supplier; 
Merck (Germany) is a fairly good source, but Baker/Union Carbide isn't.   
Unless Jena took the time and effort to purify the PEG (see Bill Ray's article 
in the same issue, p. 562), you have another factor that can drop the pH.  You 
might ask where Jena buys their PEG stock.

Also, the way many companies make the screens are not always clear.  Some just 
mix stocks, meaning the pH of the Tris stock (perhaps at 1 M) was pH 8, but 
when diluted down with the other components to make the 150 mM concentration 
for the screen mixture, the pH can be significantly different.  The dilution of 
Tris would drop the pH.

Cheers,

Michael
 

R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
603 Wilson Rd., Rm. 513   
Michigan State University  
East Lansing, MI 48824-1319
Office:  (517) 355-9724 Lab:  (517) 353-9125
FAX:  (517) 353-9334Email:  rmgarav...@gmail.com





> On Jul 31, 2017, at 8:34 AM, Jonathan Bailey  wrote:
> 
> Dear CCP4bb community
> 
> 
> 
> I apologies for the slightly off topic post.
> 
> 
> 
> We have recently had success crystallizing a membrane protein (diffraction > 
> 3 Å at a synchrotron source) using the in meso method, the hit condition was 
> from the Jena Bioscience screen Pi-minimal condition number #57.
> 
> 
> 
> Hit condition – 47.1 % w/v PEG1000, 150 mM Tris pH 8.0, 80 mM Potassium 
> bromide
> 
> 
> 
> 
> The screen is old and expired 12/20/2013 (lot # JBS00013133), we have tried 
> to reproduce the crystals using homemade optimization screens around the hit 
> condition but have not had any success. We have tried reproducing the hit 
> using a new (not expired) Pi-minimal screen but had no success. We are only 
> able to reproduce the crystals using the expired screen and we do not have 
> much of it left.
> 
>   
> We went back and tested the pH of the condition that had given crystals, the 
> expected pH was 7.9 but we found it to be 6 – 6.5 using a pH indicator strip. 
> We believe the drop in pH is caused by oxidative degradation of the PEG1000 
> resulting in the formation of carboxylic acid species.
> 
> 
> 
> We have contacted Jena Bioscience to try and get some of the old screen stock 
> but unfortunately they do not have any.
> 
> 
> 
> My question is does anyone out there happen to have any expired screen stocks 
> of this Pi-minimal condition (#57), ideally from the same lot (lot # 
> JB200013133), that they would be willing to send us.
> 
>   
> Does anyone have any advice as to how to reproduce the condition? We’ve 
> considered bubbling oxygen through and heating the sample to accelerate the 
> oxidation process.
> 
>   
> King Regards
> 
> 
> 
> Jonathan Bailey (PhD student) 
> 
> 
> 
> Professor Martin Caffrey Lab MS group Trinity College Dublin 
> 

Re: [ccp4bb] Help needed finding hit condition

[Vellieux Frédéric]

Hello,

Such pH drifts are rather common with crystallisation screens. Have you tried 
to produce other precipitant solutions with ca. 47% PEG 1000, 80 mM Potassium 
bromide but having a pH of (say) 6.2 ? A pH rangle close to that where your 
crystals were obtained. This would mean changing buffering agent to… MES 
perhaps ?

Cheers,

Fred.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jonathan 
Bailey
Sent: Monday, July 31, 2017 2:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Help needed finding hit condition

Dear CCP4bb community

I apologies for the slightly off topic post.

We have recently had success crystallizing a membrane protein (diffraction > 3 
Å at a synchrotron source) using the in meso method, the hit condition was from 
the Jena Bioscience screen Pi-minimal condition number #57.

Hit condition – 47.1 % w/v PEG1000, 150 mM Tris pH 8.0, 80 mM Potassium bromide

The screen is old and expired 12/20/2013 (lot # JBS00013133), we have tried to 
reproduce the crystals using homemade optimization screens around the hit 
condition but have not had any success. We have tried reproducing the hit using 
a new (not expired) Pi-minimal screen but had no success. We are only able to 
reproduce the crystals using the expired screen and we do not have much of it 
left.

We went back and tested the pH of the condition that had given crystals, the 
expected pH was 7.9 but we found it to be 6 – 6.5 using a pH indicator strip. 
We believe the drop in pH is caused by oxidative degradation of the PEG1000 
resulting in the formation of carboxylic acid species.

We have contacted Jena Bioscience to try and get some of the old screen stock 
but unfortunately they do not have any.

My question is does anyone out there happen to have any expired screen stocks 
of this Pi-minimal condition (#57), ideally from the same lot (lot # 
JB200013133), that they would be willing to send us.

Does anyone have any advice as to how to reproduce the condition? We’ve 
considered bubbling oxygen through and heating the sample to accelerate the 
oxidation process.

King Regards

Jonathan Bailey (PhD student)

Professor Martin Caffrey Lab MS group Trinity College Dublin
-

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[ccp4bb] Help needed finding hit condition

[Jonathan Bailey]

Dear CCP4bb community


I apologies for the slightly off topic post.


We have recently had success crystallizing a membrane protein (diffraction
> 3 Å at a synchrotron source) using the *in meso* method, the hit
condition was from the Jena Bioscience screen Pi-minimal condition number
#57.


Hit condition – 47.1 % w/v PEG1000, 150 mM Tris pH 8.0, 80 mM Potassium
bromide


The screen is old and expired 12/20/2013 (lot # JBS00013133), we have tried
to reproduce the crystals using homemade optimization screens around the
hit condition but have not had any success. We have tried reproducing the
hit using a new (not expired) Pi-minimal screen but had no success. We are
only able to reproduce the crystals using the expired screen and we do not
have much of it left.



We went back and tested the pH of the condition that had given crystals,
the expected pH was 7.9 but we found it to be 6 – 6.5 using a pH indicator
strip. We believe the drop in pH is caused by oxidative degradation of the
PEG1000 resulting in the formation of carboxylic acid species.


We have contacted Jena Bioscience to try and get some of the old screen
stock but unfortunately they do not have any.


My question is does anyone out there happen to have any expired screen
stocks of this Pi-minimal condition (#57), ideally from the same lot (lot #
JB200013133), that they would be willing to send us.



Does anyone have any advice as to how to reproduce the condition? We’ve
considered bubbling oxygen through and heating the sample to accelerate the
oxidation process.



King Regards


Jonathan Bailey (PhD student)


Professor Martin Caffrey Lab MS group Trinity College Dublin

[ccp4bb]

[Daniel Rigden]

Dear Shijun

As the message suggests, AMPLE has not been able to find the executable 
of THESEUS, the program it uses for maximum likelihood superposition of 
structures. This error message is nothing to do with Rosetta. THESEUS is 
distributed with more recent versions of CCP4. To continue with your 
current version you can install THESEUS (if you haven't already) from 
http://theseus3d.org/ . You can then either put it in your $PATH or use 
the flag


  -theseus_exe /path/to/theseus

Best wishes

Daniel

On 31/07/17 12:55, 张士军 wrote:


Hi all

  It always fail when I run ccp4-AMPLE, and log file says


Cannot find executable theseus in PATH. Please give the path to theseus
***
* Information from CCP4Interface script
***
The program run with command: 
/usr/local/programs/ccp4/ccp4-6.4.0/bin/ccp4-python -u 
/usr/local/programs/ccp4/ccp4-6.4.0/bin/ample -mtz 
/home/xingqiang/ZSJ/kif5b/430-566/A12P422output.mtz -fasta 
/home/xingqiang/ZSJ/kif5b/430.seq -nmodels 500 -name MVD0 -run_dir 
/home/xingqiang/ZSJ/kif5b/430-566 -nproc 4 -make_models True 
-rosetta_dir /usr/local/programs/rosetta -frags_3mers 
/home/xingqiang/ZSJ/kif5b/aat000_03_05.200_v1_3 -frags_9mers 
/home/xingqiang/ZSJ/kif5b/aat000_09_05.200_v1_3 -make_frags False -F F 
-SIGF SIGF -FREE FreeR_flag -early_terminate True -use_shelxe True 
-use_arpwarp False

has failed with error message
Traceback (most recent call last):
File "/usr/local/programs/ccp4/ccp4-6.4.0/bin/ample", line 505, in
amopt.d['theseus_exe'] = ample_util.check_for_exe('theseus', 
amopt.d['theseus_exe'])
File 
"/usr/local/programs/ccp4/ccp4-6.4.0/share/ample/python/ample_util.py", 
line 93, in check_for_exe

raise RuntimeError,msg
RuntimeError: Cannot find executable theseus in PATH. Please give the 
path to theseus

***
#CCP4I TERMINATION STATUS 0 "Traceback (most recent call last): File 
"/usr/local/programs/ccp4/ccp4-6.4.0/bin/ample", line 505, in 
amopt.d['theseus_exe'] = ample_util.check_for_exe('theseus', 
amopt.d['theseus_exe']) File 
"/usr/local/programs/ccp4/ccp4-6.4.0/share/ample/python/ample_util.py", 
line 93, in check_for_exe raise RuntimeError,msg RuntimeError: Cannot 
find executable theseus in PATH. Please give the path to theseus"

#CCP4I TERMINATION TIME 31 Jul 2017 19:49:31
#CCP4I MESSAGE Task failed
 Anyone know what's wrong with it? Does it mean I don't install 
Rosseta successfully? Thanks


best regards

shijun



--
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]

[张士军]

Hi all

  It always fail when I run ccp4-AMPLE, and log file says 




Cannot find executable theseus in PATH. Please give the path to theseus
***
* Information from CCP4Interface script
***
The program run with command: 
/usr/local/programs/ccp4/ccp4-6.4.0/bin/ccp4-python -u 
/usr/local/programs/ccp4/ccp4-6.4.0/bin/ample -mtz 
/home/xingqiang/ZSJ/kif5b/430-566/A12P422output.mtz -fasta 
/home/xingqiang/ZSJ/kif5b/430.seq -nmodels 500 -name MVD0 -run_dir 
/home/xingqiang/ZSJ/kif5b/430-566 -nproc 4 -make_models True -rosetta_dir 
/usr/local/programs/rosetta -frags_3mers 
/home/xingqiang/ZSJ/kif5b/aat000_03_05.200_v1_3 -frags_9mers 
/home/xingqiang/ZSJ/kif5b/aat000_09_05.200_v1_3 -make_frags False -F F -SIGF 
SIGF -FREE FreeR_flag  -early_terminate True   -use_shelxe True -use_arpwarp 
False 
has failed with error message
Traceback (most recent call last):
 File "/usr/local/programs/ccp4/ccp4-6.4.0/bin/ample", line 505, in 
 amopt.d['theseus_exe'] = ample_util.check_for_exe('theseus', 
amopt.d['theseus_exe'])
 File "/usr/local/programs/ccp4/ccp4-6.4.0/share/ample/python/ample_util.py", 
line 93, in check_for_exe
 raise RuntimeError,msg
RuntimeError: Cannot find executable theseus in PATH. Please give the path to 
theseus
***
#CCP4I TERMINATION STATUS 0 "Traceback (most recent call last):   File 
"/usr/local/programs/ccp4/ccp4-6.4.0/bin/ample", line 505, in  
amopt.d['theseus_exe'] = ample_util.check_for_exe('theseus', 
amopt.d['theseus_exe'])   File 
"/usr/local/programs/ccp4/ccp4-6.4.0/share/ample/python/ample_util.py", line 
93, in check_for_exe raise RuntimeError,msg RuntimeError: Cannot find 
executable theseus in PATH. Please give the path to theseus"
#CCP4I TERMINATION TIME 31 Jul 2017  19:49:31
#CCP4I MESSAGE Task failed
 Anyone know what's wrong with it? Does it mean I don't install Rosseta 
successfully? Thanks 

best regards

shijun