Re: [ccp4bb] Pymol Map range

[Horrell, Sam (DLSLtd,RAL,LSCI)]

Thanks Paul, that has worked just fine.

Cheers,

Sam

From: CCP4 bulletin board  On Behalf Of Paul Emsley
Sent: 26 February 2021 16:12
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Pymol Map range



On 26/02/2021 16:07, Horrell, Sam (DLSLtd,RAL,LSCI) wrote:
Hello BB,

I'm trying to make an image of some electron density in pymol but am running 
into a problem, my atoms are half in and half out of the unit cell so I only 
get half the density.
Has anyone ran into this problem previously, and if so, is there a way to shift 
the origin, extend the map, or something so everything is covered?
I realise this is not a ccp4 problem exactly, so I am ready for the inevitable 
replies, but I imagine a program in ccp4 might be the answer.




You can do it in Coot.  Do the masking or whatever, then File -> Export Map 
Fragment

Then use that map in PyMOL

Paul.







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Re: [ccp4bb] File System Problems

[Horrell, Sam (DLSLtd,RAL,LSCI)]

Hi Stuart,

That has cracked It thanks! I can open files again.

Much appreciated,

Sam

From: Stuart McNicholas 
Sent: 01 October 2020 13:34
To: Horrell, Sam (DLSLtd,RAL,LSCI) 
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] File System Problems

Dear Sam,
   We have heard reports that running as Administrator the first time fixes 
some issues on Windows. It might be worth testing this before anything else.

Best wishes,
Stuart


On Thu, 1 Oct 2020 at 11:53, Horrell, Sam (DLSLtd,RAL,LSCI) 
mailto:sam.horr...@diamond.ac.uk>> wrote:
Hello CCP4bb,

I’m having a serious problem with my CCP4i2 installation on my windows 10 
computer, whenever I try and upload a file via the GUI it fails to open the 
file system and stops responding, then it just hangs until I kill the program. 
I’ve uninstalled and reinstalled CCP4 and rolled back the latest updates but 
nothing has changed. Obviously this makes using CCP4 completely impossible. Any 
suggestions for how I might fix this problem?

Cheers,

Sam




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[ccp4bb] File System Problems

[Horrell, Sam (DLSLtd,RAL,LSCI)]

Hello CCP4bb,

I'm having a serious problem with my CCP4i2 installation on my windows 10 
computer, whenever I try and upload a file via the GUI it fails to open the 
file system and stops responding, then it just hangs until I kill the program. 
I've uninstalled and reinstalled CCP4 and rolled back the latest updates but 
nothing has changed. Obviously this makes using CCP4 completely impossible. Any 
suggestions for how I might fix this problem?

Cheers,

Sam


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This e-mail and any attachments may contain confidential, copyright and or 
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are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
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Re: [ccp4bb] Coot CCP4i2 extensions

[Horrell, Sam (DLSLtd,RAL,LSCI)]

HI Stuart,

I’m not sure what has changed but the extension menu is back and working now.

I guess it sorted itself out somewhere between opening and closing ccp4i2 and 
restarting my computer a few times.

Cheers,

Sam

From: Stuart McNicholas 
Sent: 04 June 2020 14:09
To: Horrell, Sam (DLSLtd,RAL,LSCI) 
Subject: Re: [ccp4bb] Coot CCP4i2 extensions

Dear Sam,
   We can check if the i2 server is starting and is accessible outside of Coot.

Could you please:

i) Start a "CCP4 Console". You should have an icon CCP4Console on your desktop. 
Double-click this.

ii) In the window that opens, type ccp4i2. You should see a line somewhere in 
the output:

 CCP4i2 starting HTTP server on 127.0.0.1 port 43434

iii) In a web browser go to. The port number may be different, see above, it is 
usually 43434:

  127.0.0.1:43434<http://127.0.0.1:43434>

You should see a page "CCP4i2 User Interface Documentation"

Then try:

  127.0.0.1:43434/database/<http://127.0.0.1:43434/database/>

You should see a list of your projects.

If any of these steps fail then we should try to go from there to diagnose the 
problem.

Best wishes,
Stuart


On Thu, 4 Jun 2020 at 12:17, Horrell, Sam (DLSLtd,RAL,LSCI) 
mailto:sam.horr...@diamond.ac.uk>> wrote:
My firewall settings haven’t changed since yesterday when it was working so it 
feels unlikely.

Sam

From: Stuart McNicholas 
mailto:stuart.mcnicho...@york.ac.uk>>
Sent: 04 June 2020 12:05
To: Horrell, Sam (DLSLtd,RAL,LSCI) 
mailto:sam.horr...@diamond.ac.uk>>; Paul Emsley 
mailto:pems...@mrc-lmb.cam.ac.uk>>
Subject: Re: [ccp4bb] Coot CCP4i2 extensions

Could it be a firewall issue?

On Thu, 4 Jun 2020 at 12:02, Horrell, Sam (DLSLtd,RAL,LSCI) 
mailto:sam.horr...@diamond.ac.uk>> wrote:
Hey Paul,

I’ve attached a copy of the log after opening up coot. There is an error in 
there but not sure what it means.

IOError: [Errno socket error] [Errno 10061] No connection could be made because 
the target machine actively refused it

Cheers,

Sam

From: Paul Emsley mailto:pems...@mrc-lmb.cam.ac.uk>>
Sent: 04 June 2020 11:46
To: Horrell, Sam (DLSLtd,RAL,LSCI) 
mailto:sam.horr...@diamond.ac.uk>>
Subject: Re: [ccp4bb] Coot CCP4i2 extensions




Coot should write a log somewhere - not sure where it is - and that will record 
problems reading startup scripts. If you can find it it might be useful.



Paul.




On 04/06/2020 11:43, Horrell, Sam (DLSLtd,RAL,LSCI) wrote:
Hi Stuart,

Thanks for the reply, I am running on a windows 10 machine so maybe it’s OS 
specific.

I went to the file menu and it no longer has the save mol to ccp4i2 option. I 
have tried rebooting, rolling back the update, reinstalling the update and 
nothing has changed I’m afraid. The full path to the coot executable in the 
preferences is blank but if there was a problem I don’t think coot would have 
loaded at all from the interface.

Cheers,

Sam

From: Stuart McNicholas 
<mailto:stuart.mcnicho...@york.ac.uk>
Sent: 04 June 2020 11:38
To: Horrell, Sam (DLSLtd,RAL,LSCI) 
<mailto:sam.horr...@diamond.ac.uk>
Cc: CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk>
Subject: Re: [ccp4bb] Coot CCP4i2 extensions

Dear Sam,
   Apologies for your problem. I have tested myself on Mac and do not see the 
problem, however I will try on Linux and Windows as well.

However, this menu not functioning may not mean that you cannot saves. Do "Save 
mol to CCP4i2.." and "Save to CCP4i2" appear in Coot's File menu? If so you can 
use those. If not, then you do indeed still have a problem. One simple thought 
might be to reboot, if you have not already done so. Clearly Coot is, for some 
reason, not able to communicate properly. A reboot might help.

Best wishes,
Stuart

On Thu, 4 Jun 2020 at 10:57, Horrell, Sam (DLSLtd,RAL,LSCI) 
mailto:sam.horr...@diamond.ac.uk>> wrote:
Hello CCP4bb,

I just installed the latest update and it seems to have a problem with Coot’s 
CCP4i2 extensions.
The dropdown menu no longer appears when clicked so it’s impossible to save to 
the i2 gui.
I’ve rolled back the update but the bug is still present.

Cheers,

Sam





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Diamond Light Source Limited (company no. 4

Re: [ccp4bb] Coot CCP4i2 extensions

[Horrell, Sam (DLSLtd,RAL,LSCI)]

Hey Paul,

I’ve attached a copy of the log after opening up coot. There is an error in 
there but not sure what it means.

IOError: [Errno socket error] [Errno 10061] No connection could be made because 
the target machine actively refused it

Cheers,

Sam

From: Paul Emsley 
Sent: 04 June 2020 11:46
To: Horrell, Sam (DLSLtd,RAL,LSCI) 
Subject: Re: [ccp4bb] Coot CCP4i2 extensions




Coot should write a log somewhere - not sure where it is - and that will record 
problems reading startup scripts. If you can find it it might be useful.



Paul.




On 04/06/2020 11:43, Horrell, Sam (DLSLtd,RAL,LSCI) wrote:
Hi Stuart,

Thanks for the reply, I am running on a windows 10 machine so maybe it’s OS 
specific.

I went to the file menu and it no longer has the save mol to ccp4i2 option. I 
have tried rebooting, rolling back the update, reinstalling the update and 
nothing has changed I’m afraid. The full path to the coot executable in the 
preferences is blank but if there was a problem I don’t think coot would have 
loaded at all from the interface.

Cheers,

Sam

From: Stuart McNicholas 
<mailto:stuart.mcnicho...@york.ac.uk>
Sent: 04 June 2020 11:38
To: Horrell, Sam (DLSLtd,RAL,LSCI) 
<mailto:sam.horr...@diamond.ac.uk>
Cc: CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk>
Subject: Re: [ccp4bb] Coot CCP4i2 extensions

Dear Sam,
   Apologies for your problem. I have tested myself on Mac and do not see the 
problem, however I will try on Linux and Windows as well.

However, this menu not functioning may not mean that you cannot saves. Do "Save 
mol to CCP4i2.." and "Save to CCP4i2" appear in Coot's File menu? If so you can 
use those. If not, then you do indeed still have a problem. One simple thought 
might be to reboot, if you have not already done so. Clearly Coot is, for some 
reason, not able to communicate properly. A reboot might help.

Best wishes,
Stuart

On Thu, 4 Jun 2020 at 10:57, Horrell, Sam (DLSLtd,RAL,LSCI) 
mailto:sam.horr...@diamond.ac.uk>> wrote:
Hello CCP4bb,

I just installed the latest update and it seems to have a problem with Coot’s 
CCP4i2 extensions.
The dropdown menu no longer appears when clicked so it’s impossible to save to 
the i2 gui.
I’ve rolled back the update but the bug is still present.

Cheers,

Sam





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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
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I

Re: [ccp4bb] Coot CCP4i2 extensions

[Horrell, Sam (DLSLtd,RAL,LSCI)]

Hi Stuart,

Thanks for the reply, I am running on a windows 10 machine so maybe it’s OS 
specific.

I went to the file menu and it no longer has the save mol to ccp4i2 option. I 
have tried rebooting, rolling back the update, reinstalling the update and 
nothing has changed I’m afraid. The full path to the coot executable in the 
preferences is blank but if there was a problem I don’t think coot would have 
loaded at all from the interface.

Cheers,

Sam

From: Stuart McNicholas 
Sent: 04 June 2020 11:38
To: Horrell, Sam (DLSLtd,RAL,LSCI) 
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Coot CCP4i2 extensions

Dear Sam,
   Apologies for your problem. I have tested myself on Mac and do not see the 
problem, however I will try on Linux and Windows as well.

However, this menu not functioning may not mean that you cannot saves. Do "Save 
mol to CCP4i2.." and "Save to CCP4i2" appear in Coot's File menu? If so you can 
use those. If not, then you do indeed still have a problem. One simple thought 
might be to reboot, if you have not already done so. Clearly Coot is, for some 
reason, not able to communicate properly. A reboot might help.

Best wishes,
Stuart

On Thu, 4 Jun 2020 at 10:57, Horrell, Sam (DLSLtd,RAL,LSCI) 
mailto:sam.horr...@diamond.ac.uk>> wrote:
Hello CCP4bb,

I just installed the latest update and it seems to have a problem with Coot’s 
CCP4i2 extensions.
The dropdown menu no longer appears when clicked so it’s impossible to save to 
the i2 gui.
I’ve rolled back the update but the bug is still present.

Cheers,

Sam





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privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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[ccp4bb] Coot CCP4i2 extensions

[Horrell, Sam (DLSLtd,RAL,LSCI)]

Hello CCP4bb,

I just installed the latest update and it seems to have a problem with Coot's 
CCP4i2 extensions.
The dropdown menu no longer appears when clicked so it's impossible to save to 
the i2 gui.
I've rolled back the update but the bug is still present.

Cheers,

Sam



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This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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Re: [ccp4bb] CCP4i2 Text size

[Horrell, Sam (DLSLtd,RAL,LSCI)]

Hi Huw,

Thanks for the advice, but I'm afraid my display scaling is actually at 250%. 
I've changed the setting you suggested but it hasn't changed much.

Sounds like a bug fix is on the way for the scaling problem though.

Cheers,

Sam
From: Huw Jenkins 
Sent: 02 April 2020 14:04
To: Horrell, Sam (DLSLtd,RAL,LSCI) 
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] CCP4i2 Text size

Hi Sam,


On 2 Apr 2020, at 11:32, Horrell, Sam (DLSLtd,RAL,LSCI) 
mailto:sam.horr...@diamond.ac.uk>> wrote:

 If anyone has any other suggestions it would be greatly appreciated.

What settings do you have for Windows display scaling? From your screenshot it 
appears that the Windows task bar and window title bar are drawn at >100%

If so and your whole desktop is scaled can you try turning off "Let Windows try 
to fix apps so they're not blurry" in the Advanced scaling settings please? 
Then restart CCP4i2 and set the font sizes back to more normal sizes. This will 
make the text look less crisp but should make CCP4i2 more usable.

Best wishes,


Huw

[cid:image001.png@01D608FE.35407360]

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Re: [ccp4bb] teaching question: graphics for chromebook?

[Horrell, Sam]

Being on the ccp4bb I feel I should ask if ccp4mg isn't suitable for your 
purposes? 

Sam 


From: "Phoebe A. Rice"  
To: "ccp4bb"  
Sent: Wednesday, 23 May, 2018 22:01:16 
Subject: [ccp4bb] teaching question: graphics for chromebook? 



One for fellow educators: 

For years, I’ve given students pymol-heavy homework assignments. Today I found 
out that at least one has a chromebook and can’t install Pymol. 

I gather that these chrome thingies are becoming more and more popular with 
students, so I’m wondering if someone out there already come up with a good 
solution – either an easy way to install pymol, or an alternative 
undergraduate-user-friendly, free macromolecular graphic program that will work 
for chromebook users. 

Thanks, 

Phoebe 



~~~ 

Phoebe A. Rice 

Dept. of Biochem & Mol. Biol. and 

Committee on Microbiology 

[ https://voices.uchicago.edu/phoebericelab/ | 
https://voices.uchicago.edu/phoebericelab/ ] 

[ccp4bb] CCP4i2 Error in wrapper

[Horrell, Sam]

Hello CCP4bb, 

I'm having some trouble with my installation of CCP4i2. I keep getting a 
persistent error about the "Wrapper" in various programs and am not sure what I 
need to do to fix it. I have tried reinstalling via the package manager (64b 
linux) and still get the error. So far it has happened in Molrep, Phaser, 
Refmac and Morda (see below). I can provide log files if anyone thinks they can 
help. 

Cheers, 

Sam 

MORDA 

-ERROR- morda_i2_gui:9 Error in wrapper morda_i2 0.1:: Failed starting external 
process - is this program installed/accessible? 
Process: /home/horrells/ccp4-7.0/libexec/python2.7 

-ERROR- morda_i2_gui:47 Error in wrapper morda_i2 0.1:: Error in checking 
external process after completion 
exit status and code: 1 1 

REFMAC 

-ERROR- None:201 Error in wrapper refmac 0.0:: Refmac returned with non zero 
status 
Exit code: 1 

MOLREP 

-ERROR- None:9 Error in wrapper refmac 0.0:: Failed starting external process - 
is this program installed/accessible? 
Process: /home/horrells/ccp4-7.0/bin/refmac5 

-ERROR- None:47 Error in wrapper refmac 0.0:: Error in checking external 
process after completion 
exit status and code: 1 1 

PHASER (Expert and Basic) 

-ERROR- phaser_MR_AUTO_gui:48 Error in wrapper phaser_MR_AUTO 0.0:: No 
description available 
-ERROR- phaser_pipeline_gui:207 Error in wrapper phaser_pipeline 0.0:: No 
description available 
No output files in list 

Re: [ccp4bb] Manual His-Tag Purification

[Horrell, Sam]

This should give you everything you need to know about the column 
http://www.sigmaaldrich.com/technical-documents/protocols/biology/roche/complete-his-tag-purification-column.html



I'd definitely say load all of your lysate, possibly run it through twice if 
you really want to. If you're worried about it not binding run it at a slower 
flow rate. You would have to have a lot of expression from one litre of media 
to saturate the column. Not sure what exactly you mean by retention time but 
the protein should stay there indefinitely until you elute it.


Cheers,


Sam

[http://www.sigmaaldrich.com/etc/designs/sigma-aldrich/images/sial-logo-sharing.png]

cOmplete™ His-Tag Purification Column Protocol 
...
www.sigmaaldrich.com
Protocol. Purification Protocols. cOmplete His-Tag Purification Columns are 
compatible with automated chromatography systems such as ÄKTAexplorer.




From: CCP4 bulletin board  on behalf of Sundaram 

Sent: 01 February 2017 09:24:09
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Manual His-Tag Purification

Hello ,

It's an off topic question.

I'm planning to do manual purification a 6 his tagged protein of size around 
20kDa from 1L E.coli culture using
COHISC-RO Roche cOmplete™ His-Tag Purification Column.


Can I get some advice regarding the lysate loading volume and retention time.
This is the first time I going to use this column and I have no idea about my 
protein yield from 1L culture.

Sorry if I spammed your inbox.


Thanks!

Yours Sincerely,
Sundaram.S

Re: [ccp4bb] off topic pymol

[Horrell, Sam]

Hi Almudena,

Have a look in your PDB file in the second to last colum, if it looks something 
like the example below then delete the As from the fine and it should connect 
up. I've had this before, not sure where it came from but removing it fixed the 
problem.

ATOM371  CA  PRO A  48 -11.300 -19.315 -35.308  1.00 91.62   C
ATOM372  CB  PRO A  48 -10.546 -20.584 -35.726  1.00 90.06   C
ATOM373  CG  PRO A  48  -9.106 -20.254 -35.548  1.00 91.26   C
ATOM374  CD  PRO A  48  -8.992 -19.119 -34.570  1.00 91.06   C
ATOM375  C   PRO A  48 -12.669 -19.668 -34.722  1.00 85.38   C
ATOM376  O   PRO A  48 -13.686 -19.209 -35.228  1.00 79.05   O
ATOM377  N   ARG A  49 -12.683 -20.461 -33.658  1.00 91.80  AN
ATOM378  CA  ARG A  49 -13.936 -20.872 -33.022  1.00101.75  AC
ATOM379  CB  ARG A  49 -13.717 -22.064 -32.077  1.00109.37  AC
ATOM380  CG  ARG A  49 -15.008 -22.749 -31.637  1.00106.33  AC
ATOM381  CD  ARG A  49 -14.933 -23.259 -30.207  1.00104.16  AC

Hope that helps,

Sam

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Almudena Ponce 
Salvatierra [maps.fa...@gmail.com]
Sent: 04 February 2015 17:07
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] off topic pymol

Dear all,

does anyone know why if I open a pdb in pymol (that appears normal and fully 
connected in coot) it appears as if it was broken into pieces?

Thanks,

Almudena.

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

Re: [ccp4bb] fitting peptide with non-standard and standard amino acids

[Horrell, Sam]

Hi Emmanuel, 

I've never tried something quite as complex as a pseudopeptide but if you can 
build your lingand in the coot ligand builder coot will generate a cif file for 
you. Previously I have built my ligand, used real space refinement to get it 
into position, merged the protein and ligand and saved the model. Your coot may 
be different but my cif file always ended up in 
wincoot/new/examples/coot-ccp4/prodrg-out.cif. Make sure you rename this cif 
and move it to a new directory as I believe coot will just save over this when 
you make your next ligand.

Good luck, 

Sam

Sam Horrell BSc (Hons)
Research Student
School of Life Sciences
Life Sciences Building
University of Liverpool
Crown Street
Liverpool L69 7ZB
United Kingdom


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of ΕΜΜΑΝΟΥΗΛ 
ΣΑΡΕΙΔΑΚΗΣ [e.sarida...@inn.demokritos.gr]
Sent: 20 January 2015 15:32
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] fitting peptide with non-standard and standard amino acids

Dear All,

I wonder if you could help me with this. I am trying to do some 
regularisation/real space refinement of a ligand with Coot. The ligand is a 
pseudopeptide with two non-standard aminoacids, followed by several standard 
ones. I assume that to do this correctly, I would need a cif file that 
specifies the two non-standard aa's plus the links between these two and 
between second and third (which is a standard one). When trying to generate a 
cif with a program such as eLBOW (using a pdb as the starting reference), each 
of the non-standard aa's gets a cif of its own, and the third, standard one, is 
ignored, meaning that there are no specified links between the first two 
(non-standard) and even less between second (non-standard) and third 
(standard). Coot of course keeps each aa as it should be, but breaks up the 
peptide chain completely.

Could you direct me how to built a cif that includes such bond specifications, 
starting from a reference pdb or otherwise? Is there an altogether different 
way of getting Coot to do what I want?

Many thanks,

Emmanuel



Dr. Emmanuel Saridakis
Researcher C
Institute of Nanoscience and Nanotechnology
National Centre for Scientific Research DEMOKRITOS
15310 Athens
GREECE

[ccp4bb] Processing files from XSCALE in Aimless

[Horrell, Sam]

Hi Everyone,

I've been trying to process some data using Xia2, XSCALE, Pointless and 
Aimless. I have a large number of datasets (over 100) so have used Xia2 to 
produce the XDS_ASCII.HKL files using the 3daii pipeline. I now want to process 
them manually (with a script) using XSCALE and pointless to find the resolution 
limit and finally run them through Aimless to get the merging statistics. I'm 
not looking to solve the structures just to compare the merging statistics 
between datasets subjected to different treatments.

I've managed to put the the XDS_ASCII.HKL files through XSCALE and pointless 
without any problems but when I try and run aimless with the output from XSCALE 
in CCP4i I get the error message

FATAL ERROR message:

ERROR in ScaleModel: run1 has insuffient information for smooth scaling

And when trying to run it by command line Aimless won't recognize the 
XSCALE.HKL file.
I've tried converting the XDS file with XDSCONV to the ccp4 format but Aimless 
still didn't like it on command line or ccp4i so I tried using sortmtz but this 
just fails with a very uninformative message


“SORTMTZ: *** ERROR: Program Terminating

Times: User: 0.1s System: 0.0s Elapsed: 0:01”

The command line I've been trying to use for aimless is

“aimless hklin XSCALE.HKL hklout scaled.mtz “

Running Aimless with the XDS_ASCII.HKL from Xia2 using ccp4i works fine.

Is there a conversion step I'm missing when trying to run the XSCALE.HKL files 
through Aimless?
Maybe something I've done wrong in the XDSCONV stage or I need to get sortmtz 
working somehow?

Any advice would be greatly appreciated.

Best regards,

Sam

Re: [ccp4bb] Processing files from XSCALE in Aimless

[Horrell, Sam]

Thanks for the replies Harry, Joe and Kay, 

@Harry 
(1) I've had a look at the com files and the the run with the file from XSCALE 
reaches the ROGUEPLOT stage (command line) and says mtz MERGED (Script from 
file), when I press continue from that stage it switches from running to 
failed. The run with the ASCII file before running XSCALE continues on normally 
to completion. 
(2) Yes both the command line and ccp4i are running Aimless 0.1.29.  

@Joe The XDS_ASCII.HKL that is running through Aimless on ccp4i and finishing 
is from CORRECT. I've tried running the output from XSCALE through pointless 
using the commands you suggested and Aimless is still giving out the same error 
message on ccp4i and on the command line. 

@Kay I had a look at the output from XSCALE and it has !GENERATED BY: XSCALE 
(VERSION  July 4, 2012). I'm using the computer systems at Diamond so don't 
think I'm able to update this easily, I still don't really know how the 
permissions work here. From my relatively inexperienced perspective, the 
statistics look very similar between XSCALE and AIMLESS but the main reason for 
running through Aimless after XSCALE is it gives a value for Rp.i.m. which I 
don't see in the XSCALE.LP file. Unless it is under a different name somewhere? 

Thanks again, 

Sam

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kay Diederichs 
[kay.diederi...@uni-konstanz.de]
Sent: 26 July 2013 17:49
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Processing files from XSCALE in Aimless

On Fri, 26 Jul 2013 15:19:57 +0100, Joe.Lyons joe.ly...@ul.ie wrote:


Hi Sam,

Assuming the XDS_ASCII.HKL is from XSCALE. I generally run it through 
Pointless then aimless with (a scales constant command) using something like 
the following.
pointless -copy xdsin XDS_ASCII.HKL hklout sorted.mtz  eof  pointless.log
eof

aimless hklin sorted.mtz hklout Scaled_1.mtz  eof  aimless.log
run 1 all
scales constant
resolution 60.00 4.00
anomalous on
eof

If the reflection file is from the CORRECT step I would remove the scales 
constant command when running aimless.

I do hope you know that CORRECT scales the data, and when you remove the 
scales constant command  then you scale them again in aimless. Are you certain 
that this is good for the signal in your data?

best,

Kay


Hope this helps,

Regards,

Joe

-Original Message-
From: CCP4 bulletin board on behalf of Horrell, Sam
Sent: Fri 7/26/2013 1:32 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Processing files from XSCALE in Aimless

Hi Everyone,

I've been trying to process some data using Xia2, XSCALE, Pointless and 
Aimless. I have a large number of datasets (over 100) so have used Xia2 to 
produce the XDS_ASCII.HKL files using the 3daii pipeline. I now want to 
process them manually (with a script) using XSCALE and pointless to find the 
resolution limit and finally run them through Aimless to get the merging 
statistics. I'm not looking to solve the structures just to compare the 
merging statistics between datasets subjected to different treatments.

I've managed to put the the XDS_ASCII.HKL files through XSCALE and pointless 
without any problems but when I try and run aimless with the output from 
XSCALE in CCP4i I get the error message

FATAL ERROR message:

ERROR in ScaleModel: run1 has insuffient information for smooth scaling

And when trying to run it by command line Aimless won't recognize the 
XSCALE.HKL file.
I've tried converting the XDS file with XDSCONV to the ccp4 format but Aimless 
still didn't like it on command line or ccp4i so I tried using sortmtz but 
this just fails with a very uninformative message


SORTMTZ: *** ERROR: Program Terminating

Times: User: 0.1s System: 0.0s Elapsed: 0:01

The command line I've been trying to use for aimless is

aimless hklin XSCALE.HKL hklout scaled.mtz 

Running Aimless with the XDS_ASCII.HKL from Xia2 using ccp4i works fine.

Is there a conversion step I'm missing when trying to run the XSCALE.HKL files 
through Aimless?
Maybe something I've done wrong in the XDSCONV stage or I need to get sortmtz 
working somehow?

Any advice would be greatly appreciated.

Best regards,

Sam