Re: [ccp4bb] Coot installation issue

[Paul Emsley]

Coot is not (yet) an official part of brewsci, so the goocanvas update 
bonked coot.


This morning I uninstalled my coot and rebuilt it with YoshitakaMo's 
coot.rb. The second time it worked (i.e. build and installed just fine).


You can see from the patch

https://github.com/brewsci/homebrew-bio/commit/9f57646721018f584dffe700fccbfcb44105304e

that there are a couple of environment variables in the wrapper script. 
They didn't work for me, so I set them on the terminal (and that worked).


They were discovered (if that's the right verb - "ferreted out" or 
"unearthed" maybe?) by Charles Ballard's diligent reading of the 
Inkscape mailing list. For me they increased the fps by 70-100% - which 
makes GTK3 Coot almost usable (on an Intel MacBook Pro, maybe on an M1 
it is *actually* usable).



Paul.


On 30/09/2022 16:17, William G. Scott wrote:

homebrew heavy-handedly wiped out coocanvas v. 2 when upgrading.

I made a temp fix with a sym link as follows:

ln -s /usr/local/Cellar/goocanvas/3.0.0/lib/libgoocanvas-3.0.9.dylib 
/usr/local/lib/libgoocanvas-2.0.9.dylib

your path prefix will be different, but you get the idea.




On Sep 30, 2022, at 7:38 AM, tim smith  wrote:

Hi All,

I am having an issue with installing coot. Here is the outcome when I type coot 
in command line. I am using M1 mac pro. Thank you.

Best regards
Tim


CSI363227 ~ % coot
dyld[11265]: Library not loaded: 
'/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
   Referenced from: '/opt/homebrew/Cellar/coot/HEAD-4c7971f/libexec/coot-bin'
   Reason: tried: '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib' 
(no such file), 
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no such 
file), '/opt/homebrew/Cellar/goocanvas/3.0.0/lib/libgoocanvas-2.0.9.dylib' (no 
such file), 
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no such 
file)
/opt/homebrew/bin/coot: line 211: 11265 Abort trap: 6   $coot_bin "$@"
Coot crashed.



CSI363227 ~ % coot --version
dyld[11238]: Library not loaded: 
'/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
   Referenced from: '/opt/homebrew/Cellar/coot/HEAD-4c7971f/libexec/coot-bin'
   Reason: tried: '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib' 
(no such file), 
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no such 
file), '/opt/homebrew/Cellar/goocanvas/3.0.0/lib/libgoocanvas-2.0.9.dylib' (no 
such file), 
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no such 
file)
/opt/homebrew/bin/coot: line 211: 11238 Abort trap: 6   $coot_bin "$@"
Coot crashed.

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[ccp4bb] Deadline for LCLS screening proposals extended to Oct 4th

[Artem Lyubimov]

Hi everyone,

The deadline to submit a screening proposal to the LCLS XFEL has been
extended!  For delicate crystals and/or for crystals available in lower
quantities, the standard goniometer setup at LCLS-MFX is a useful option
available to all general users applying for beamtime.

See below for more information on how to apply.

___

We are pleased to announce the next call for LCLS Protein Crystal Screening
(PCS) Proposals. LCLS is seeking proposals for PCS beamtime to be awarded
during LCLS Run 21 expected to be scheduled between October 2022 and June
2023.

The LCLS Protein Crystal Screening (PCS) program aims to enable increased
access to LCLS beamtime for biological structure determination by making
use of short, 6-12 hour runs to screen the quality of different sample
preparations or potentially collect a full data set under good running
conditions. To enable measurements within such a short time frame and
maximize efficiency and the chances of success, these studies must be
carried out with limited instrumentation flexibility to minimize the time
impact of setup changes.

PCS experiments at atmospheric pressure are expected to be available at the
*MFX*

instrument
with multiple options likely to be available, including a fixed target
system, a Droplet-on-Demand system, and a liquid jet system compatible with
various types of jets.

The following sample delivery configurations (at the discretion of LCLS)
are expected to be supported at MFX (in atmosphere) for PCS in this current
call for proposals:

   - Gas Dynamic Virtual Nozzle (GDVN)
   - Dual Flow Focusing Nozzles (DFFN)
   - Lipidic Cubic Phase (LCP) jets
   - Microfluidic Electrokinetic Sample Holder (MESH)
   - Droplet-on-Demand (DoD)
   - Sheet Jets

Other sample delivery techniques supplied by user groups (i.e., liquid jet,
fixed target, goniometer, tape drive, etc.) that are compatible with the
basic MFX system could also be considered if the schedule allows it and at
the discretion of LCLS.

> For full details of the call, please visit 
> *https://lcls.slac.stanford.edu/proposals/run21-pcs
*

Questions about the LCLS PCS program should be directed to *Christopher
Kupitz* (*ckup...@slac.stanford.edu *). For more
general information about LCLS, please visit:
*http://lcls.slac.stanford.edu*




-- 
Art Lyubimov, PhD
Staff Scientist
SSRL SMB Crystallography
2525 Sand Hill Road mail stop 99
Menlo Park, CA 94025-7015
(415) 325-2057



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Re: [ccp4bb] PAIREF - Warning - not enough free reflections in resolution bin

[Eleanor Dodson]

Dear Matt,
Your data past 2.5A is awfully weak, and wont contribute much to any map
you calculate. Each term at the outer resolution will have a very low
weight.
I sometimes cling to the belief that the weak data may help the B factor
refinement, but there isnt much evidence of that. There is a feeling that
once I/SigI is << 1 the data is no use.. Looking at those statistics I
would cut the resolution to 2.75.

What does the I2 data processing report suggest as the cut off?
Eleanor

On Fri, 30 Sept 2022 at 17:21, Andrew Purkiss <
a.purk...@mail.cryst.bbk.ac.uk> wrote:

> Is the data anisotropic? This would explain the strange processing
> statistics beyond 3.0 Angstrom. If using Dials directly it is worth
> looking for abnormalities with the reciprocal lattice viewer.
>
> I've seen similar issues with the completeness being low, when data is
> weak in one direction, despite reflections being reported in the
> scaling output.
>
> It may also be worth running some analysis of the data with Staraniso
> (https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi) to try to
> help.
>
> Andy
>
>
>
>
> Quoting Martin Malý :
>
> > Dear Matt,
> >
> > thank you for asking. I am bit confused how you set up the PAIREF
> > run. In paired refinement, data are added step by step - going to
> > higher resolution, i.e. lower d_hkl. So the merged data in the
> > PAIREF input should not be cut to much. The data statistics look
> > from DIALS quite strange, there is very good completeness and CC1/2
> > for high resolution shells, but very poor  and Rmeas.
> >
> > I would suggest to refine the model at 3 A to be safe. Then, run
> > PAIREF with the initial resolution 3 A and using the cutoffs 2.8,
> > 2.6, 2.4 and 2.2 A. Diffraction data must be up to 2.2 A in that
> > case, no truncation to 2.4 A as you mentioned previously.
> >
> > I hope it will help. Please feel free to ask and let me know if it
> > was successful.
> >
> > Best regards,
> > Martin
> >
> >
> > On 30. 09. 22 17:29, Matt McLeod wrote:
> >> Hi all,
> >>
> >> I am having a bit of trouble with PAIREF.  I am trying to determine
> >> the resolution cutoff of a dataset which has a high Rwork
> >> (0.223)/free (0.275)value for the resolution (2.24A).  I have
> >> truncated this data further to 2.4A and the R values get better but
> >> the electron density maps do not improve whatsoever.  When I put
> >> this data into PAIREF I get this message.
> >>
> >> WARNING: There are only 40 < 50 free reflections in the resolution
> >> shell 2.75-2.70 A. Values of statistics Rfree and CCfree in this
> >> shell could be misleading. Consider setting thicker resolution
> >> shells.
> >>
> >> This error occurs for all resolution bins.  Looking at the pdb log
> >> of the refined structure (where the data looks quite reasonable,
> >> maybe not a 2.3 dataset but not much worse).
> >>
> >> REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).
> >> REMARK   3   BIN  RESOLUTION RANGE  COMPL.NWORK NFREE   RWORK
> >> RFREE  CCWORK CCFREE
> >> REMARK   3 1   60.08 -4.281.00 4135   213  0.1646
> >> 0.2213   0.940  0.901
> >> REMARK   3 24.28 -3.401.00 4095   201  0.1951
> >> 0.2672   0.928  0.857
> >> REMARK   3 33.40 -2.971.00 4099   204  0.2736
> >> 0.3303   0.861  0.739
> >> REMARK   3 42.97 -2.701.00 4026   212  0.3486
> >> 0.3508   0.726  0.551
> >> REMARK   3 52.70 -2.510.78 3178   154  0.4027
> >> 0.4062   0.637  0.594
> >> REMARK   3 62.50 -2.360.29 115460  0.4118
> >> 0.3984   0.647  0.547
> >> REMARK   3 72.36 -2.240.01   29 1  0.3366
> >> 0.4089   0.343  0.000
> >>
> >> Where I assume NFree is the issue, but doesn't suggest that there
> >> arent enough reflections.  There needs to be a higher cutoff as the
> >> completeness goes to pot, but the scaling log from DIALS suggested
> >> it was at least a good starting point.
> >>
> >>  Statistics by resolution bin:
> >>  d_max  d_min   #obs  #uniq   mult.  %comp   
> >> r_mrg   r_measr_pim   cc1/2   cc_ano
> >> 118.81   5.97  10436   15776.62  99.94 797.6
> >> 22.80.1100.1200.046   0.992*  -0.397
> >>   5.97   4.74   9602   15496.20 100.00 491.7
> >> 10.00.1720.1880.075   0.979*  -0.240
> >>   4.74   4.14  10410   15286.81 100.00 513.5
> >> 10.30.1910.2070.079   0.978*  -0.281
> >>   4.14   3.76  10833   15516.98 100.00 324.7
> >> 6.90.2380.2570.098   0.969*  -0.419
> >>   3.76   3.49  10956   15267.18 100.00 207.5
> >> 4.60.2590.2800.105   0.975*  -0.271
> >>   3.49   3.29  10899   15467.05 100.00 133.4
> >> 3.10.2720.2940.111   0.966*  -0.258
> >>   3.29   3.12   9565   15286.26  99.93  86.9
> >> 2.00.3140.3430.136   0.935*  -0.346
> >>   3.12   2.99   9256   1519

Re: [ccp4bb] PAIREF - Warning - not enough free reflections in resolution bin

[Andrew Purkiss]

Is the data anisotropic? This would explain the strange processing
statistics beyond 3.0 Angstrom. If using Dials directly it is worth
looking for abnormalities with the reciprocal lattice viewer.

I've seen similar issues with the completeness being low, when data is
weak in one direction, despite reflections being reported in the
scaling output.

It may also be worth running some analysis of the data with Staraniso
(https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi) to try to
help.

Andy




Quoting Martin Malý :


Dear Matt,

thank you for asking. I am bit confused how you set up the PAIREF
run. In paired refinement, data are added step by step - going to
higher resolution, i.e. lower d_hkl. So the merged data in the
PAIREF input should not be cut to much. The data statistics look
from DIALS quite strange, there is very good completeness and CC1/2
for high resolution shells, but very poor  and Rmeas.

I would suggest to refine the model at 3 A to be safe. Then, run
PAIREF with the initial resolution 3 A and using the cutoffs 2.8,
2.6, 2.4 and 2.2 A. Diffraction data must be up to 2.2 A in that
case, no truncation to 2.4 A as you mentioned previously.

I hope it will help. Please feel free to ask and let me know if it
was successful.

Best regards,
Martin


On 30. 09. 22 17:29, Matt McLeod wrote:

Hi all,

I am having a bit of trouble with PAIREF.  I am trying to determine
the resolution cutoff of a dataset which has a high Rwork
(0.223)/free (0.275)value for the resolution (2.24A).  I have
truncated this data further to 2.4A and the R values get better but
the electron density maps do not improve whatsoever.  When I put
this data into PAIREF I get this message.

WARNING: There are only 40 < 50 free reflections in the resolution
shell 2.75-2.70 A. Values of statistics Rfree and CCfree in this
shell could be misleading. Consider setting thicker resolution
shells.

This error occurs for all resolution bins.  Looking at the pdb log
of the refined structure (where the data looks quite reasonable,
maybe not a 2.3 dataset but not much worse).

REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK   3   BIN  RESOLUTION RANGE  COMPL.NWORK NFREE   RWORK
RFREE  CCWORK CCFREE
REMARK   3 1   60.08 -4.281.00 4135   213  0.1646
0.2213   0.940  0.901
REMARK   3 24.28 -3.401.00 4095   201  0.1951
0.2672   0.928  0.857
REMARK   3 33.40 -2.971.00 4099   204  0.2736
0.3303   0.861  0.739
REMARK   3 42.97 -2.701.00 4026   212  0.3486
0.3508   0.726  0.551
REMARK   3 52.70 -2.510.78 3178   154  0.4027
0.4062   0.637  0.594
REMARK   3 62.50 -2.360.29 115460  0.4118
0.3984   0.647  0.547
REMARK   3 72.36 -2.240.01   29 1  0.3366
0.4089   0.343  0.000

Where I assume NFree is the issue, but doesn't suggest that there
arent enough reflections.  There needs to be a higher cutoff as the
completeness goes to pot, but the scaling log from DIALS suggested
it was at least a good starting point.

 Statistics by resolution bin:
 d_max  d_min   #obs  #uniq   mult.  %comp   
r_mrg   r_measr_pim   cc1/2   cc_ano
118.81   5.97  10436   15776.62  99.94 797.6
22.80.1100.1200.046   0.992*  -0.397
  5.97   4.74   9602   15496.20 100.00 491.7
10.00.1720.1880.075   0.979*  -0.240
  4.74   4.14  10410   15286.81 100.00 513.5
10.30.1910.2070.079   0.978*  -0.281
  4.14   3.76  10833   15516.98 100.00 324.7
6.90.2380.2570.098   0.969*  -0.419
  3.76   3.49  10956   15267.18 100.00 207.5
4.60.2590.2800.105   0.975*  -0.271
  3.49   3.29  10899   15467.05 100.00 133.4
3.10.2720.2940.111   0.966*  -0.258
  3.29   3.12   9565   15286.26  99.93  86.9
2.00.3140.3430.136   0.935*  -0.346
  3.12   2.99   9256   15196.09 100.00  57.1
1.30.3540.3870.154   0.932*  -0.354
  2.99   2.87   9317   15246.11 100.00  43.6
1.00.4030.4410.177   0.934*  -0.198
  2.87   2.77  10087   15496.51 100.00  30.9
0.70.4550.4940.192   0.923*  -0.116
  2.77   2.69  10157   15246.66 100.00  26.4
0.60.5030.5460.210   0.927*  -0.132
  2.69   2.61  10351   15416.72 100.00  19.3
0.40.6130.6650.255   0.925*  -0.155
  2.61   2.54  10121   15046.73 100.00  15.5
0.40.7350.7970.306   0.906*  -0.088
  2.54   2.48  10510   15396.83 100.00  12.4
0.30.9321.0090.385   0.857*   0.006
  2.48   2.42  10432   15196.87 100.00  11.2
0.20.9721.0520.399   0.829*  -0.111
  2.42   2.37  10596   15326.92 100.00  10.2
0.21.0951.1840.447   0.844*  -0.083
  2.37   2.32  10577   

Re: [ccp4bb] PAIREF - Warning - not enough free reflections in resolution bin

[Martin Malý]

Dear Matt,

thank you for asking. I am bit confused how you set up the PAIREF run. 
In paired refinement, data are added step by step - going to higher 
resolution, i.e. lower d_hkl. So the merged data in the PAIREF input 
should not be cut to much. The data statistics look from DIALS quite 
strange, there is very good completeness and CC1/2 for high resolution 
shells, but very poor  and Rmeas.


I would suggest to refine the model at 3 A to be safe. Then, run PAIREF 
with the initial resolution 3 A and using the cutoffs 2.8, 2.6, 2.4 and 
2.2 A. Diffraction data must be up to 2.2 A in that case, no truncation 
to 2.4 A as you mentioned previously.


I hope it will help. Please feel free to ask and let me know if it was 
successful.


Best regards,
Martin


On 30. 09. 22 17:29, Matt McLeod wrote:

Hi all,

I am having a bit of trouble with PAIREF.  I am trying to determine the 
resolution cutoff of a dataset which has a high Rwork (0.223)/free (0.275)value 
for the resolution (2.24A).  I have truncated this data further to 2.4A and the 
R values get better but the electron density maps do not improve whatsoever.  
When I put this data into PAIREF I get this message.

WARNING: There are only 40 < 50 free reflections in the resolution shell 
2.75-2.70 A. Values of statistics Rfree and CCfree in this shell could be 
misleading. Consider setting thicker resolution shells.

This error occurs for all resolution bins.  Looking at the pdb log of the 
refined structure (where the data looks quite reasonable, maybe not a 2.3 
dataset but not much worse).

REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK   3   BIN  RESOLUTION RANGE  COMPL.NWORK NFREE   RWORK  RFREE  
CCWORK CCFREE
REMARK   3 1   60.08 -4.281.00 4135   213  0.1646 0.2213   
0.940  0.901
REMARK   3 24.28 -3.401.00 4095   201  0.1951 0.2672   
0.928  0.857
REMARK   3 33.40 -2.971.00 4099   204  0.2736 0.3303   
0.861  0.739
REMARK   3 42.97 -2.701.00 4026   212  0.3486 0.3508   
0.726  0.551
REMARK   3 52.70 -2.510.78 3178   154  0.4027 0.4062   
0.637  0.594
REMARK   3 62.50 -2.360.29 115460  0.4118 0.3984   
0.647  0.547
REMARK   3 72.36 -2.240.01   29 1  0.3366 0.4089   
0.343  0.000

Where I assume NFree is the issue, but doesn't suggest that there arent enough 
reflections.  There needs to be a higher cutoff as the completeness goes to 
pot, but the scaling log from DIALS suggested it was at least a good starting 
point.

  Statistics by resolution bin:
  d_max  d_min   #obs  #uniq   mult.  %comp r_mrg  
 r_measr_pim   cc1/2   cc_ano
 118.81   5.97  10436   15776.62  99.94 797.622.80.110  
  0.1200.046   0.992*  -0.397
   5.97   4.74   9602   15496.20 100.00 491.710.00.172  
  0.1880.075   0.979*  -0.240
   4.74   4.14  10410   15286.81 100.00 513.510.30.191  
  0.2070.079   0.978*  -0.281
   4.14   3.76  10833   15516.98 100.00 324.7 6.90.238  
  0.2570.098   0.969*  -0.419
   3.76   3.49  10956   15267.18 100.00 207.5 4.60.259  
  0.2800.105   0.975*  -0.271
   3.49   3.29  10899   15467.05 100.00 133.4 3.10.272  
  0.2940.111   0.966*  -0.258
   3.29   3.12   9565   15286.26  99.93  86.9 2.00.314  
  0.3430.136   0.935*  -0.346
   3.12   2.99   9256   15196.09 100.00  57.1 1.30.354  
  0.3870.154   0.932*  -0.354
   2.99   2.87   9317   15246.11 100.00  43.6 1.00.403  
  0.4410.177   0.934*  -0.198
   2.87   2.77  10087   15496.51 100.00  30.9 0.70.455  
  0.4940.192   0.923*  -0.116
   2.77   2.69  10157   15246.66 100.00  26.4 0.60.503  
  0.5460.210   0.927*  -0.132
   2.69   2.61  10351   15416.72 100.00  19.3 0.40.613  
  0.6650.255   0.925*  -0.155
   2.61   2.54  10121   15046.73 100.00  15.5 0.40.735  
  0.7970.306   0.906*  -0.088
   2.54   2.48  10510   15396.83 100.00  12.4 0.30.932  
  1.0090.385   0.857*   0.006
   2.48   2.42  10432   15196.87 100.00  11.2 0.20.972  
  1.0520.399   0.829*  -0.111
   2.42   2.37  10596   15326.92 100.00  10.2 0.21.095  
  1.1840.447   0.844*  -0.083
   2.37   2.32  10577   15356.89 100.00   8.9 0.21.259  
  1.3610.514   0.825*  -0.082
   2.32   2.28  10217   15136.75 100.00   7.8 0.21.421  
  1.5400.587   0.725*  -0.056
   2.28   2.24   9702   15216.38 100.00   6.4 0.11.683  
  1.8340.721   0.600*  -0.001
   2.24   2.20   9551   15386.21 100.00   6.1 0.11.895  
  2.071   

[ccp4bb] PAIREF - Warning - not enough free reflections in resolution bin

[Matt McLeod]

Hi all,

I am having a bit of trouble with PAIREF.  I am trying to determine the 
resolution cutoff of a dataset which has a high Rwork (0.223)/free (0.275)value 
for the resolution (2.24A).  I have truncated this data further to 2.4A and the 
R values get better but the electron density maps do not improve whatsoever.  
When I put this data into PAIREF I get this message. 

WARNING: There are only 40 < 50 free reflections in the resolution shell 
2.75-2.70 A. Values of statistics Rfree and CCfree in this shell could be 
misleading. Consider setting thicker resolution shells.

This error occurs for all resolution bins.  Looking at the pdb log of the 
refined structure (where the data looks quite reasonable, maybe not a 2.3 
dataset but not much worse). 

REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK   3   BIN  RESOLUTION RANGE  COMPL.NWORK NFREE   RWORK  RFREE  
CCWORK CCFREE
REMARK   3 1   60.08 -4.281.00 4135   213  0.1646 0.2213   
0.940  0.901
REMARK   3 24.28 -3.401.00 4095   201  0.1951 0.2672   
0.928  0.857
REMARK   3 33.40 -2.971.00 4099   204  0.2736 0.3303   
0.861  0.739
REMARK   3 42.97 -2.701.00 4026   212  0.3486 0.3508   
0.726  0.551
REMARK   3 52.70 -2.510.78 3178   154  0.4027 0.4062   
0.637  0.594
REMARK   3 62.50 -2.360.29 115460  0.4118 0.3984   
0.647  0.547
REMARK   3 72.36 -2.240.01   29 1  0.3366 0.4089   
0.343  0.000

Where I assume NFree is the issue, but doesn't suggest that there arent enough 
reflections.  There needs to be a higher cutoff as the completeness goes to 
pot, but the scaling log from DIALS suggested it was at least a good starting 
point.

 Statistics by resolution bin:
 d_max  d_min   #obs  #uniq   mult.  %comp r_mrg   
r_measr_pim   cc1/2   cc_ano
118.81   5.97  10436   15776.62  99.94 797.622.80.110   
 0.1200.046   0.992*  -0.397
  5.97   4.74   9602   15496.20 100.00 491.710.00.172   
 0.1880.075   0.979*  -0.240
  4.74   4.14  10410   15286.81 100.00 513.510.30.191   
 0.2070.079   0.978*  -0.281
  4.14   3.76  10833   15516.98 100.00 324.7 6.90.238   
 0.2570.098   0.969*  -0.419
  3.76   3.49  10956   15267.18 100.00 207.5 4.60.259   
 0.2800.105   0.975*  -0.271
  3.49   3.29  10899   15467.05 100.00 133.4 3.10.272   
 0.2940.111   0.966*  -0.258
  3.29   3.12   9565   15286.26  99.93  86.9 2.00.314   
 0.3430.136   0.935*  -0.346
  3.12   2.99   9256   15196.09 100.00  57.1 1.30.354   
 0.3870.154   0.932*  -0.354
  2.99   2.87   9317   15246.11 100.00  43.6 1.00.403   
 0.4410.177   0.934*  -0.198
  2.87   2.77  10087   15496.51 100.00  30.9 0.70.455   
 0.4940.192   0.923*  -0.116
  2.77   2.69  10157   15246.66 100.00  26.4 0.60.503   
 0.5460.210   0.927*  -0.132
  2.69   2.61  10351   15416.72 100.00  19.3 0.40.613   
 0.6650.255   0.925*  -0.155
  2.61   2.54  10121   15046.73 100.00  15.5 0.40.735   
 0.7970.306   0.906*  -0.088
  2.54   2.48  10510   15396.83 100.00  12.4 0.30.932   
 1.0090.385   0.857*   0.006
  2.48   2.42  10432   15196.87 100.00  11.2 0.20.972   
 1.0520.399   0.829*  -0.111
  2.42   2.37  10596   15326.92 100.00  10.2 0.21.095   
 1.1840.447   0.844*  -0.083
  2.37   2.32  10577   15356.89 100.00   8.9 0.21.259   
 1.3610.514   0.825*  -0.082
  2.32   2.28  10217   15136.75 100.00   7.8 0.21.421   
 1.5400.587   0.725*  -0.056
  2.28   2.24   9702   15216.38 100.00   6.4 0.11.683   
 1.8340.721   0.600*  -0.001
  2.24   2.20   9551   15386.21 100.00   6.1 0.11.895   
 2.0710.826   0.603*  -0.041
118.64   2.20 203575  306636.64  99.99 142.0 3.30.222   
 0.2410.093   0.989*  -0.265



Does anyone have any insight into where PAIREF is getting hung up? I am welcome 
to any other suggestions with regards to handling this dataset to determine 
resolution cutoff.  I can also supply any other log files that may be useful

Matt



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Re: [ccp4bb] Coot installation issue

[William G. Scott]

homebrew heavy-handedly wiped out coocanvas v. 2 when upgrading.

I made a temp fix with a sym link as follows:

ln -s /usr/local/Cellar/goocanvas/3.0.0/lib/libgoocanvas-3.0.9.dylib 
/usr/local/lib/libgoocanvas-2.0.9.dylib

your path prefix will be different, but you get the idea.



> On Sep 30, 2022, at 7:38 AM, tim smith  wrote:
> 
> Hi All,
> 
> I am having an issue with installing coot. Here is the outcome when I type 
> coot in command line. I am using M1 mac pro. Thank you. 
> 
> Best regards
> Tim
> 
> 
> CSI363227 ~ % coot
> dyld[11265]: Library not loaded: 
> '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
>   Referenced from: '/opt/homebrew/Cellar/coot/HEAD-4c7971f/libexec/coot-bin'
>   Reason: tried: '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib' 
> (no such file), 
> '/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no 
> such file), 
> '/opt/homebrew/Cellar/goocanvas/3.0.0/lib/libgoocanvas-2.0.9.dylib' (no such 
> file), '/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' 
> (no such file)
> /opt/homebrew/bin/coot: line 211: 11265 Abort trap: 6   $coot_bin "$@"
> Coot crashed.
> 
> 
> 
> CSI363227 ~ % coot --version
> dyld[11238]: Library not loaded: 
> '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
>   Referenced from: '/opt/homebrew/Cellar/coot/HEAD-4c7971f/libexec/coot-bin'
>   Reason: tried: '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib' 
> (no such file), 
> '/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no 
> such file), 
> '/opt/homebrew/Cellar/goocanvas/3.0.0/lib/libgoocanvas-2.0.9.dylib' (no such 
> file), '/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' 
> (no such file)
> /opt/homebrew/bin/coot: line 211: 11238 Abort trap: 6   $coot_bin "$@"
> Coot crashed.
> 
> 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] Coot installation issue

[tim smith]

Hi All,

I am having an issue with installing coot. Here is the outcome when I type
coot in command line. I am using M1 mac pro. Thank you.

Best regards
Tim


CSI363227 ~ % coot
dyld[11265]: Library not loaded:
'/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
  Referenced from: '/opt/homebrew/Cellar/coot/HEAD-4c7971f/libexec/coot-bin'
  Reason: tried: '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
(no such file),
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no
such file),
'/opt/homebrew/Cellar/goocanvas/3.0.0/lib/libgoocanvas-2.0.9.dylib' (no
such file),
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no
such file)
/opt/homebrew/bin/coot: line 211: 11265 Abort trap: 6   $coot_bin
"$@"
Coot crashed.



CSI363227 ~ % coot --version
dyld[11238]: Library not loaded:
'/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
  Referenced from: '/opt/homebrew/Cellar/coot/HEAD-4c7971f/libexec/coot-bin'
  Reason: tried: '/opt/homebrew/opt/goocanvas/lib/libgoocanvas-2.0.9.dylib'
(no such file),
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no
such file),
'/opt/homebrew/Cellar/goocanvas/3.0.0/lib/libgoocanvas-2.0.9.dylib' (no
such file),
'/opt/homebrew/Cellar/coot/HEAD-4c7971f/lib/libgoocanvas-2.0.9.dylib' (no
such file)
/opt/homebrew/bin/coot: line 211: 11238 Abort trap: 6   $coot_bin
"$@"
Coot crashed.



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[ccp4bb] PhD position in Luebeck (Northern Germany)

[Thomas Krey]

Dear colleagues,

We invite applications for a

Ph.D. position in Structural Virology

in the lab of Thomas Krey, Institute of Biochemistry, University of Luebeck 
(Germany). Our group is interested in the study of viruses that constitute a 
global public health and/or veterinary concern and uses mostly structural 
biology/biophysical techniques with a special focus on X-ray crystallography 
and more recently also cryo electron microscopy. The structural knowledge 
gained from our experiments can be used for structure-based design of 
antivirals and/or vaccines, i.e., has a direct translational potential.
The collaborative project of interest aims at the structural characterization 
of a γ-herpesviral protein that plays a key role for the control of the 
complement system and the position is available immediately.

We:

•  Are structural virologists with a special interest in how viruses 
manipulate the host’s immune response
•  Use a wide range of methodologies including but not limited to 
protein biochemistry, X-ray crystallography, electron microscopy, Next 
Generation Sequencing (NGS)
•  Offer state-of-the-art equipment in protein purification and 
crystallization
•  Provide an international, interdisciplinary, exciting and 
stimulating scientific environment at the University of Luebeck
•  Have access to

· An on-campus FACS facility with single-cell sequencing 
instrumentation and a Next-Generation Sequencing platform

· Excellent biophysical instrumentation (Biacore, SEC-MALLS, DLS, ITC, 
AUC)

· A state-of-the-art cryo EM platform at the CSSB in Hamburg

You:

•  Are interested in structural virology
•  Hold a Master degree in a relevant field and have profound practical 
and theoretical knowledge in protein biochemistry
•  Enjoy working both on your own and as part of an international and 
interdisciplinary team
•  Like to visit international conferences and present your data
•  Are a creative and enthusiastic individual committed to solve 
problems
•  Experience in protein purification, structural biology techniques 
(preferably X-ray crystallography) would be beneficial

Please send a cover letter, CV, relevant certificates as well as names, e-mail 
addresses and telephone numbers of at least two references in a single PDF file 
to Thomas Krey 
(k...@biochem.uni-luebeck.de). Additional 
information can be found here 
(https://www.biochem.uni-luebeck.de/fileadmin/files/pdf/KR2880-8-1-Ausschreibung_Englisch.pdf).

Best wishes
Thomas


Prof. Dr. Thomas Krey
[University of Luebeck]
University of Lübeck
Institute of Biochemistry
phone: +49-451-3101-3100
fax: +49-451-3101-3104
e-mail: k...@biochem.uni-luebeck.de
www.biochem.uni-luebeck.de
Ratzeburger Allee 160
23562 Lübeck
Germany






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[ccp4bb] CCPBioSim Industry Talk

[Sarah Fegan - STFC UKRI]

Hi all,

Registration is now open for our next Industry Talk. It will take place on 
Thursday 20 October 2022 from 2pm UK time. It will be on Zoom and registration 
is free but required to get the webinar link. The speakers are Alex R. Jones 
and Amy E. Danson from the National Physical Laboratory and the title is 
"Biomolecular Metrology: Ensuring Reproducible Measurement for the Life 
Sciences".

Details and registration can be found at https://www.ccpbiosim.ac.uk/npl2022.

Best wishes,
Sarah



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