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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[ccp4bb] Deadline Thursday June 18: Facility Manager for CPHSAXS at Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Denmark

[Michael Gajhede]

We are looking for a highly motivated and independent academic research staff 
for a position as facility manager for a new In-House bioSAXS facility CPHSAXS 
funded by the Novo Nordisk Foundation. The position is available from August 1 
2020 or as soon as possible thereafter until the end of 2024.

Our research
The facility is established in a group of collaborators; Michael Gajhede and 
Annette Eva Langkilde (Dept. Drug Design and Pharmacology), Vito Foderà and 
Martin Malmsteen (Dept. of Pharmacy), Lise Arleth (Niels Bohr Institute) and 
Søren Skou (SAXSLAB/Xenocs); with research projects covering discovery, 
formulation and delivery of biopharmaceutics, amyloid research, enzymatic 
catalysis, membrane proteins, disordered systems and colloid research, as well 
as technological and methodological developments within the use of solution 
scattering.

In addition to the core collaborators, the facility will be open to a broader 
user community, facilitating the use of SAXS in a range interdisciplinary 
research projects in the region. The facility will be located at the Department 
of Drug Design within the Peptides and Proteins discipline.

Your job
The tasks includes attracting and training of new users, advising on e.g. 
sample preparation and requirements, support with data collection and 
assistance with data analysis on collaborative projects. Your tasks will also 
include setting up and managing the scheduling/access platform, user accounts, 
and providing material for annual reports on the use and outcomes, organize 
annual user meetings and contribute to training courses, and represent the 
facility. You will be responsible for the daily maintenance of the instrument 
and, in collaboration with SAXSLAB/Xenocs, contribute to continued 
technological developments. You will have the opportunity to contribute to 
research projects primarily of the core collaborators but also the projects 
from a broader user community.

Profile
We are looking for a highly motivated and enthusiastic facility manager with 
solid technical knowledge and capabilities to build the frame and network 
around the facility. Specifically we are looking for the following competencies 
and experience:

Essential experience and skills

You have a PhD in structural biology, biophysics, biochemistry, or related.
Solid knowledge of SAXS data acquisition and analysis.
You have documented experience in SAXS for biologically relevant samples
You have an active interest in instrument and/or method development.
You have proven an ability to envision, plan and execute a research project
Service-minded with clear communication and networking  skills
Good English skills, written and spoken

Desirable experience and skills

Experience and knowledge with X-ray scattering hardware and/or programming
Knowledge of protein expression and purification is an advantage
Experience with DLS, HPLC and/or SEC-SAXS
Previous collaborations with industrial partners
Place of employment
The place of employment is at the Department of Drug Design and Pharmacology, 
University of Copenhagen. We offer creative and stimulating working conditions 
in dynamic and international research environment.

Terms of salary and employment
The employment as academic research staff with the title 'facility manager' 
(AC-TAP) is a full time and fixed-term position until 31 December 2024. 
Starting date is 1 August 2020 or after agreement. Employment will be in 
accordance with the provisions of the collective agreement between the Danish 
Ministry of Finance and AC (the Danish Confederation of Professional 
Associations). The monthly salary will be based on the number of years of work 
experience (seniority) with the possibility to negotiate a salary supplement 
based on prior experiences and qualifications. The employer will pay an 
additional 17.1 % to your pension fund.

Questions
For further information regarding the position, please contact Michael Gajhede; 
m...@sund.ku.dk or Annette E Langkilde; 
annette.langki...@sund.ku.dk.

Learn more:

Department of Drug Design and Pharmacology: https://drug.ku.dk/.

Integrative Structural Biology at UCPH: https://isbuc.ku.dk/.

Application
Your application should be in English and include:

Letter of application addressing the requirements (max. one page).
Curriculum Vitae (incl. two references)
A certified/signed copy of certificate(s) of education
Please submit your application by clicking on "Apply Now" below. Only online 
applications will be accepted.

Application deadline: 18 June 2020, 23.59 CET.

We reserve the right not to consider material received after the deadline, and 
not to consider applications that do not live up to the abovementioned 
requirements.

Interviews are expected to be held in week 25 and 26.

University of Copenhagen wish to reflect the diversity of society and welcome 
applications from all qualified candidates regardless of age, 

Re: [ccp4bb] COOT 0.9 cuts pdb header

[Paul Emsley]

On 16/06/2020 11:17, Dirk Maurer wrote:

Hi,


Hi.



I noticed that, while saving my pdb model in COOT 0.9, sometimes a big part of the header (compared to the 
originally loaded file) is just left out in the new pdb-file. This results in that COOT cannot reopen this 
file at another time. Any ideas how I can fix this?




This is not a problem with which I am familiar. How might I reproduce the 
problem?
I have a thought and a question:
 - it might not be coot that is the root of the problem, but something that is 
wrapping it.
 - coot displays information, when reading and writing files, in the console. 
What does it say?



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[ccp4bb] COOT 0.9 cuts pdb header

[Dirk Maurer]

Hi,

I noticed that, while saving my pdb model in COOT 0.9, sometimes a big 
part of the header (compared to the originally loaded file) is just left 
out in the new pdb-file. This results in that COOT cannot reopen this 
file at another time. Any ideas how I can fix this?


Best regards

Dirk



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Re: [ccp4bb] Question about Refmac

[Eleanor Dodson]

Thank you for cell.
For P32 21 2 spacegroup with this cell the only higher Laue symmetry you
could generate is P6/mmm, so as Jonathan says I wouldnt worry about the
FreeR assignment..
I can look at possible NCS operators if you like - the most informative
output is to run MOLREP Self Rotation on your data..
And maybe PISA on the coordinates to see what sort of assembly it suggests..
Eleanor

On Tue, 16 Jun 2020 at 01:29, Jonathan Cooper <
0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:

> I remember we discussed this a lot about a year ago when Ed Berry revived
> a thread from 2003!
>
>
> https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind1905=CCP4BB=D=72099
>
> I think the upshot of it all was that you do not need to use shells even
> with quite high NCS since Ian Tickle rightly persuaded us that over-fitting
> is due to measurement errors and there is no reason to expect these to be
> correlated for NCS-related reflections. However, as you have probably found
> out by now, you can make an R-free set in shells using the reflection file
> editor in phenix. From memory you may also need to make sure that you use a
> CCP4-style R-free flag (i.e. the free-set reflections should be flagged
> zero) if you are going to use Refmac. There's a screenshot here:
>
> http://u.cubeupload.com/jbcooper/202006160114071280x8.png
>
> Hope this helps!
> On Monday, 15 June 2020, 17:42:15 BST, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>
> Hmm - this finally was rather deprecated - there are some less happy
> consequences to have all reflections in a particular resolution shell
> excluded.
> If your NCS means there is pseudo- symmetry in the diffraction and it
> would be possible to have a cell with higher point symmetry (an example
> might be be Pmmm or P4mm  if a(Pmmm) ~  b(P). ) then you could assign
> freer flags in the higher symmetry group and extend then to the lower...
>
> What is your cell, and do you know the NCS operators?
> Eleanor
>
>
> On Mon, 15 Jun 2020 at 16:54,  
> wrote:
>
> Hello,
>
> I'm refining protein structure in Refmac and I have NCS greater than 4 (
> I've 8 identical subunits in the asymmetric unit).
>
> In the "Refinement parameters" section in Refmac, how can I pick Rfree set
> based on thin resolution shells rather than in the normal random method?
>
> I've read about the program "dataman" from the usf suite which could help
> with this but found it very complicated.
>
> Do you have any advice to solve this? or would you recommend any other
> program?
>
>
> Thank you in advance
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] Deadline Thursday June 18: Facility Manager for CPHSAXS at Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Denmark

[Michael Gajhede]

We are looking for a highly motivated and independent academic research staff 
for a position as facility manager for a new In-House bioSAXS facility CPHSAXS 
funded by the Novo Nordisk Foundation. The position is available from August 1 
2020 or as soon as possible thereafter until the end of 2024.

Our research
The facility is established in a group of collaborators; Michael Gajhede and 
Annette Eva Langkilde (Dept. Drug Design and Pharmacology), Vito Foderà and 
Martin Malmsteen (Dept. of Pharmacy), Lise Arleth (Niels Bohr Institute) and 
Søren Skou (SAXSLAB/Xenocs); with research projects covering discovery, 
formulation and delivery of biopharmaceutics, amyloid research, enzymatic 
catalysis, membrane proteins, disordered systems and colloid research, as well 
as technological and methodological developments within the use of solution 
scattering.

In addition to the core collaborators, the facility will be open to a broader 
user community, facilitating the use of SAXS in a range interdisciplinary 
research projects in the region. The facility will be located at the Department 
of Drug Design within the Peptides and Proteins discipline.

Your job
The tasks includes attracting and training of new users, advising on e.g. 
sample preparation and requirements, support with data collection and 
assistance with data analysis on collaborative projects. Your tasks will also 
include setting up and managing the scheduling/access platform, user accounts, 
and providing material for annual reports on the use and outcomes, organize 
annual user meetings and contribute to training courses, and represent the 
facility. You will be responsible for the daily maintenance of the instrument 
and, in collaboration with SAXSLAB/Xenocs, contribute to continued 
technological developments. You will have the opportunity to contribute to 
research projects primarily of the core collaborators but also the projects 
from a broader user community.

Profile
We are looking for a highly motivated and enthusiastic facility manager with 
solid technical knowledge and capabilities to build the frame and network 
around the facility. Specifically we are looking for the following competencies 
and experience:

Essential experience and skills

You have a PhD in structural biology, biophysics, biochemistry, or related.
Solid knowledge of SAXS data acquisition and analysis.
You have documented experience in SAXS for biologically relevant samples
You have an active interest in instrument and/or method development.
You have proven an ability to envision, plan and execute a research project
Service-minded with clear communication and networking  skills
Good English skills, written and spoken

Desirable experience and skills

Experience and knowledge with X-ray scattering hardware and/or programming
Knowledge of protein expression and purification is an advantage
Experience with DLS, HPLC and/or SEC-SAXS
Previous collaborations with industrial partners
Place of employment
The place of employment is at the Department of Drug Design and Pharmacology, 
University of Copenhagen. We offer creative and stimulating working conditions 
in dynamic and international research environment.

Terms of salary and employment
The employment as academic research staff with the title 'facility manager' 
(AC-TAP) is a full time and fixed-term position until 31 December 2024. 
Starting date is 1 August 2020 or after agreement. Employment will be in 
accordance with the provisions of the collective agreement between the Danish 
Ministry of Finance and AC (the Danish Confederation of Professional 
Associations). The monthly salary will be based on the number of years of work 
experience (seniority) with the possibility to negotiate a salary supplement 
based on prior experiences and qualifications. The employer will pay an 
additional 17.1 % to your pension fund.

Questions
For further information regarding the position, please contact Michael Gajhede; 
m...@sund.ku.dk or Annette E Langkilde; annette.langki...@sund.ku.dk.

Learn more:

Department of Drug Design and Pharmacology: https://drug.ku.dk/.

Integrative Structural Biology at UCPH: https://isbuc.ku.dk/.

Application
Your application should be in English and include:

Letter of application addressing the requirements (max. one page).
Curriculum Vitae (incl. two references)
A certified/signed copy of certificate(s) of education
Please submit your application by clicking on "Apply Now" below. Only online 
applications will be accepted.

Application deadline: 18 June 2020, 23.59 CET.

We reserve the right not to consider material received after the deadline, and 
not to consider applications that do not live up to the abovementioned 
requirements.

Interviews are expected to be held in week 25 and 26.

University of Copenhagen wish to reflect the diversity of society and welcome 
applications from all qualified candidates regardless of age, disability, 
gender, nationality, race, religion or sexual 

Re: [ccp4bb] Questions regarding MTZFIX and EDSTATS

[Ian Tickle]

Hi Joao

Can you post the mtzdmp output?

Cheers

Ian



On Tue, 16 Jun 2020, 09:30 Joao Ramos,  wrote:

> Dear Ian,
>
> I'm trying to use the edstats.pl script but I'm having problems with the
> column labels. mtzdmp can read the mtz file, but edstats.pl gives me a
> message saying that mtzfix cannot find the labels. I'm using a mtz file
> from a refinement job in Phenix.
>
> Best regards,
> Joao Ramos
>
> Ian Tickle  escreveu no dia terça, 16/06/2020 à(s)
> 09:39:
>
>> Hi João
>>
>> In cases like this it's always a good idea to check whether you can read
>> the same MTZ file with mtzdmp.  If that fails with the same error message
>> it means that the pathname/filename was indeed incorrectly specified, or it
>> could possibly be a permissions issue (the file needs to be given read
>> permission).
>>
>> Cheers
>>
>> Ian
>>
>>
>> On Mon, 15 Jun 2020, 19:09 Ian Tickle,  wrote:
>>
>>>
>>> Hi Joao
>>>
>>> The top of the page was cut off in your screenshot so I can't see the
>>> command line you typed.  It would be better to copy/paste the entire text,
>>> including the input command line and the output, into the email rather than
>>> taking a screenshot.  'Cannot open file' most likely means that the input
>>> filename was not typed correctly or the path was not specified correctly if
>>> it's in another directory.  Anyway you really shouldn't be calling the
>>> MTZFIX or EDSTATS programs directly.  Using the Perl script 'edstats.pl
>>> ' http://www.ccp4.ac.uk/dist/checkout/edstats/edstats.pl is much
>>> easier.  It should be in your path after running the CCP4 setup script.
>>>
>>> Cheers
>>>
>>> -- Ian
>>>
>>>
>>> On Mon, 15 Jun 2020 at 18:41, Joao Ramos 
>>> wrote:
>>>
 Dear Ian,

 Thanks for the reply!

 I've sourced the setup script, but now I get a 'cannot open file' error
 message (screenshot attached) when trying to run MTZFIX.

 Best regards,
 Joao Ramos

 Ian Tickle  escreveu no dia segunda, 15/06/2020
 à(s) 16:57:

>
> Hi Joao
>
> For all CCP4 programs you need to source your CCP4 setup script.
>
> Cheers
>
> -- Ian
>
>
> On Mon, 15 Jun 2020 at 15:29, Joao Ramos 
> wrote:
>
>> Dear CCP4bb,
>>
>> I'm trying to obtain RSC metrics using the CCP4 program EDSTATS for a
>> Phenix refinement job, in order to have a more reliable analysis of model
>> quality. From what I read, one should go through the program MTZFIX and
>> then create the FFT maps (density and difference maps). However, while
>> attempting to run the Phenix output mtz file in MTZFIX, I receive an 
>> error
>> message saying: "Cannot open environ.def".
>>
>> My questions are:
>> 1) Is the way to go from the Phenix refinement output files to
>> EDSTATS described earlier correct? Are there alternative programs 
>> included
>> in Phenix?
>> 2) How to fix the error and run MTZFIX?
>>
>> I'm currently using the new ccp4 v7.1, in macOS v10.14.5.
>>
>> Best regards,
>> Joao Ramos
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/wa.exe?SUBED1=CCP4BB=1
>>
>



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Re: [ccp4bb] Questions regarding MTZFIX and EDSTATS

[Joao Ramos]

Dear Ian,

I'm trying to use the edstats.pl script but I'm having problems with the
column labels. mtzdmp can read the mtz file, but edstats.pl gives me a
message saying that mtzfix cannot find the labels. I'm using a mtz file
from a refinement job in Phenix.

Best regards,
Joao Ramos

Ian Tickle  escreveu no dia terça, 16/06/2020 à(s) 09:39:

> Hi João
>
> In cases like this it's always a good idea to check whether you can read
> the same MTZ file with mtzdmp.  If that fails with the same error message
> it means that the pathname/filename was indeed incorrectly specified, or it
> could possibly be a permissions issue (the file needs to be given read
> permission).
>
> Cheers
>
> Ian
>
>
> On Mon, 15 Jun 2020, 19:09 Ian Tickle,  wrote:
>
>>
>> Hi Joao
>>
>> The top of the page was cut off in your screenshot so I can't see the
>> command line you typed.  It would be better to copy/paste the entire text,
>> including the input command line and the output, into the email rather than
>> taking a screenshot.  'Cannot open file' most likely means that the input
>> filename was not typed correctly or the path was not specified correctly if
>> it's in another directory.  Anyway you really shouldn't be calling the
>> MTZFIX or EDSTATS programs directly.  Using the Perl script 'edstats.pl'
>> http://www.ccp4.ac.uk/dist/checkout/edstats/edstats.pl is much easier.
>> It should be in your path after running the CCP4 setup script.
>>
>> Cheers
>>
>> -- Ian
>>
>>
>> On Mon, 15 Jun 2020 at 18:41, Joao Ramos 
>> wrote:
>>
>>> Dear Ian,
>>>
>>> Thanks for the reply!
>>>
>>> I've sourced the setup script, but now I get a 'cannot open file' error
>>> message (screenshot attached) when trying to run MTZFIX.
>>>
>>> Best regards,
>>> Joao Ramos
>>>
>>> Ian Tickle  escreveu no dia segunda, 15/06/2020 à(s)
>>> 16:57:
>>>

 Hi Joao

 For all CCP4 programs you need to source your CCP4 setup script.

 Cheers

 -- Ian


 On Mon, 15 Jun 2020 at 15:29, Joao Ramos 
 wrote:

> Dear CCP4bb,
>
> I'm trying to obtain RSC metrics using the CCP4 program EDSTATS for a
> Phenix refinement job, in order to have a more reliable analysis of model
> quality. From what I read, one should go through the program MTZFIX and
> then create the FFT maps (density and difference maps). However, while
> attempting to run the Phenix output mtz file in MTZFIX, I receive an error
> message saying: "Cannot open environ.def".
>
> My questions are:
> 1) Is the way to go from the Phenix refinement output files to EDSTATS
> described earlier correct? Are there alternative programs included in
> Phenix?
> 2) How to fix the error and run MTZFIX?
>
> I'm currently using the new ccp4 v7.1, in macOS v10.14.5.
>
> Best regards,
> Joao Ramos
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/wa.exe?SUBED1=CCP4BB=1
>




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Re: [ccp4bb] Questions regarding MTZFIX and EDSTATS

[Ian Tickle]

Hi João

In cases like this it's always a good idea to check whether you can read
the same MTZ file with mtzdmp.  If that fails with the same error message
it means that the pathname/filename was indeed incorrectly specified, or it
could possibly be a permissions issue (the file needs to be given read
permission).

Cheers

Ian


On Mon, 15 Jun 2020, 19:09 Ian Tickle,  wrote:

>
> Hi Joao
>
> The top of the page was cut off in your screenshot so I can't see the
> command line you typed.  It would be better to copy/paste the entire text,
> including the input command line and the output, into the email rather than
> taking a screenshot.  'Cannot open file' most likely means that the input
> filename was not typed correctly or the path was not specified correctly if
> it's in another directory.  Anyway you really shouldn't be calling the
> MTZFIX or EDSTATS programs directly.  Using the Perl script 'edstats.pl'
> http://www.ccp4.ac.uk/dist/checkout/edstats/edstats.pl is much easier.
> It should be in your path after running the CCP4 setup script.
>
> Cheers
>
> -- Ian
>
>
> On Mon, 15 Jun 2020 at 18:41, Joao Ramos 
> wrote:
>
>> Dear Ian,
>>
>> Thanks for the reply!
>>
>> I've sourced the setup script, but now I get a 'cannot open file' error
>> message (screenshot attached) when trying to run MTZFIX.
>>
>> Best regards,
>> Joao Ramos
>>
>> Ian Tickle  escreveu no dia segunda, 15/06/2020 à(s)
>> 16:57:
>>
>>>
>>> Hi Joao
>>>
>>> For all CCP4 programs you need to source your CCP4 setup script.
>>>
>>> Cheers
>>>
>>> -- Ian
>>>
>>>
>>> On Mon, 15 Jun 2020 at 15:29, Joao Ramos 
>>> wrote:
>>>
 Dear CCP4bb,

 I'm trying to obtain RSC metrics using the CCP4 program EDSTATS for a
 Phenix refinement job, in order to have a more reliable analysis of model
 quality. From what I read, one should go through the program MTZFIX and
 then create the FFT maps (density and difference maps). However, while
 attempting to run the Phenix output mtz file in MTZFIX, I receive an error
 message saying: "Cannot open environ.def".

 My questions are:
 1) Is the way to go from the Phenix refinement output files to EDSTATS
 described earlier correct? Are there alternative programs included in
 Phenix?
 2) How to fix the error and run MTZFIX?

 I'm currently using the new ccp4 v7.1, in macOS v10.14.5.

 Best regards,
 Joao Ramos

 --

 To unsubscribe from the CCP4BB list, click the following link:
 https://www.jiscmail.ac.uk/cgi-bin/wa.exe?SUBED1=CCP4BB=1

>>>



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