date:20210625

Re: [ccp4bb] problems with running PARROT

2021-06-25 Thread Eleanor Dodson

Hmm - that looks almost too good - Mask volumes are expected to be less
than 1..


NCS operator statistics:
 Operator_number  Mask_volume/ASU  Correlation
11.0010.911
20.9980.912
30.9540.863
40.8880.854



And the rotation angles etc look as though chains A B C & D could be
symmetry euivalents?

rotation ~ 90 0 180 - ie a crystallographic two fold

Are you sure you arent giving PARROT a model with actual symmetry
equivalent molecules?

Eleanor


On Fri, 25 Jun 2021 at 14:38, Savvas Savvides 
wrote:

> There you go Eleanor
>
> Best wishes, — Savvas
>
> 
>
>
> # Task 41 parrot running cparrot
> # Mini-MTZ input to HKLIN:
> #   Data type   parameter  jobannotation
> #   Reflections F_SIGF 39 il_phaser.1.259: NULL_dname 
> imported by job 39
> #   Phases  ABCD   39 il_phaser.1.259: NULL_dname 
> imported by job 39
> mtzin /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklin.mtz
> colin-fo F_SIGF_F,F_SIGF_SIGF
> colin-phifom ABCD_PHI,ABCD_FOM
> seqin /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/seqin.fasta
> pdbin-mr 
> /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/XYZIN_MR-coordinates.pdb
> mtzout /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklout.mtz
> xmlout /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/program.xml
> cycles 3
> anisotropy-correction
> solvent-content 0.6
> ncs-mask-filter-radius 20.0
>
> 
>  
> 
> 
>
>  ###
>  ###
>  ###
>  ### CCP4 7.1.014: cparrotversion 1.0.6 : 20/04/21##
>  ###
>  User: root  Run date: 25/ 6/2021 Run time: 12:41:49
>
>
>  Please reference: Collaborative Computational Project, Number 4. 2011.
>  "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 
> 235-242.
>  as well as any specific reference in the program write-up.
>
> 
>
> Copyright 2008-2010 Kevin Cowtan and University of York.
>
> 
> $TEXT:Reference: $$ Please reference $$
>
>  'Recent developments in classical density modification.'
>  Cowtan K. (2010) Acta Cryst. D66, 470-478.
>
> $$
>
> mtzin /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklin.mtz
> colin-fo  F_SIGF_F,F_SIGF_SIGF
> colin-phifom  ABCD_PHI,ABCD_FOM
> seqin 
> /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/seqin.fasta
> pdbin-mr  
> /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/XYZIN_MR-coordinates.pdb
> mtzout/Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklout.mtz
> xmlout
> /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/program.xml
> cycles3
> anisotropy-correction
> solvent-content   0.6
> ncs-mask-filter-radius20.0
>
>
> PDB file: 
> /Applications/ccp4-7.1/lib/data/reference_structures/reference-1tqw.pdb
>   Number of atoms read: 9432
> PDB file: 
> /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/XYZIN_MR-coordinates.pdb
>   Number of atoms read: 7264
>
> MTZ file: /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklin.mtz
>   Number of reflections: 22867Number of columns:   7
>
> Applying anisotropy correction:
> |  -0.05391,  8.59e-17,0.1649|
> |  8.59e-17,   -0.1351, -3.06e-17|
> |0.1649, -3.06e-17,   -0.5043|
>
> NCS from atomic model:
>
> NCS operator found relating chains A and B
>  Polar rotation/deg: 89.9215,-0.233543,179.754
>  Euler rotation/deg: -57.6965,179.708,122.771
>  Source: xyz = (-5.624, 9.951, 36.36)
>  Target: xyz = (-5.528, 38.96, 64.43)
>
> NCS operator found relating chains B and A
>  Polar rotation/deg: 90.0785,179.766,179.754
>  Euler rotation/deg: 57.2294,179.708,-122.303
>  Source: xyz = (-5.528, 38.96, 64.43)
>  Target: xyz = (-5.624, 9.951, 36.36)
>
> NCS operator found relating chains C and D
>  Polar rotation/deg: 90.1347,-0.132348,178.552
>  Euler rotation/deg: -100.677,178.528,79.5875
>  Source: xyz = (-17.66, 33.01, 93.38)
>  Target: xyz = (-17.88, 16.06, 7.398)
>
> NCS operator found relating chains D and C
>  Polar rotation/deg: 89.8653,179.868,178.552
>  Euler rotation/deg: 100.412,178.528,-79.3228
>  Source: xyz = (-17.88, 16.06, 7.398)
>  Target: xyz = (-17.66, 33.01, 93.38)
>
>
> -- Cycle: 1 
>
> Suggested radius for solvent mask determination: 5.68666
>
> NCS operator:   1
>  NCS masking: Mask volume as fraction of ASU: 1.00   Multiplicity: 10
>   Contiguity score:  1.000   Self-overlap score:  0.151
>  NXop refinement- correlation before:  0.539, after:  0.581
>  NXop old:  -57.7  179.7  122.8 -5.6   10.0   36.4 -5.5   39.0   64.4
>  NXo

Re: [ccp4bb] problems with running PARROT

2021-06-25 Thread Savvas Savvides

There you go Eleanor
Best wishes, — Savvas


# Task 41 parrot running cparrot
# Mini-MTZ input to HKLIN:
#   Data type   parameter  jobannotation

#   Reflections F_SIGF 39 il_phaser.1.259: NULL_dname imported 
by job 39  
#   Phases  ABCD   39 il_phaser.1.259: NULL_dname imported 
by job 39  
mtzin /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklin.mtz
colin-fo F_SIGF_F,F_SIGF_SIGF
colin-phifom ABCD_PHI,ABCD_FOM
seqin /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/seqin.fasta
pdbin-mr 
/Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/XYZIN_MR-coordinates.pdb
mtzout /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklout.mtz
xmlout /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/program.xml
cycles 3
anisotropy-correction
solvent-content 0.6
ncs-mask-filter-radius 20.0

 


 
 ###
 ###
 ###
 ### CCP4 7.1.014: cparrotversion 1.0.6 : 20/04/21##
 ###
 User: root  Run date: 25/ 6/2021 Run time: 12:41:49 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 
235-242.
 as well as any specific reference in the program write-up.



Copyright 2008-2010 Kevin Cowtan and University of York.


$TEXT:Reference: $$ Please reference $$

 'Recent developments in classical density modification.'
 Cowtan K. (2010) Acta Cryst. D66, 470-478.

$$

mtzin   /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklin.mtz
colin-foF_SIGF_F,F_SIGF_SIGF
colin-phifomABCD_PHI,ABCD_FOM
seqin   /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/seqin.fasta
pdbin-mr
/Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/XYZIN_MR-coordinates.pdb
mtzout  /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklout.mtz
xmlout  /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/program.xml
cycles  3
anisotropy-correction
solvent-content 0.6
ncs-mask-filter-radius  20.0


PDB file: 
/Applications/ccp4-7.1/lib/data/reference_structures/reference-1tqw.pdb
  Number of atoms read: 9432
PDB file: 
/Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/XYZIN_MR-coordinates.pdb
  Number of atoms read: 7264

MTZ file: /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklin.mtz
  Number of reflections: 22867Number of columns:   7

Applying anisotropy correction:
|  -0.05391,  8.59e-17,0.1649|
|  8.59e-17,   -0.1351, -3.06e-17|
|0.1649, -3.06e-17,   -0.5043|

NCS from atomic model: 

NCS operator found relating chains A and B
 Polar rotation/deg: 89.9215,-0.233543,179.754
 Euler rotation/deg: -57.6965,179.708,122.771
 Source: xyz = (-5.624, 9.951, 36.36)
 Target: xyz = (-5.528, 38.96, 64.43)

NCS operator found relating chains B and A
 Polar rotation/deg: 90.0785,179.766,179.754
 Euler rotation/deg: 57.2294,179.708,-122.303
 Source: xyz = (-5.528, 38.96, 64.43)
 Target: xyz = (-5.624, 9.951, 36.36)

NCS operator found relating chains C and D
 Polar rotation/deg: 90.1347,-0.132348,178.552
 Euler rotation/deg: -100.677,178.528,79.5875
 Source: xyz = (-17.66, 33.01, 93.38)
 Target: xyz = (-17.88, 16.06, 7.398)

NCS operator found relating chains D and C
 Polar rotation/deg: 89.8653,179.868,178.552
 Euler rotation/deg: 100.412,178.528,-79.3228
 Source: xyz = (-17.88, 16.06, 7.398)
 Target: xyz = (-17.66, 33.01, 93.38)


-- Cycle: 1 

Suggested radius for solvent mask determination: 5.68666

NCS operator:   1
 NCS masking: Mask volume as fraction of ASU: 1.00   Multiplicity: 10
  Contiguity score:  1.000   Self-overlap score:  0.151
 NXop refinement- correlation before:  0.539, after:  0.581
 NXop old:  -57.7  179.7  122.8 -5.6   10.0   36.4 -5.5   39.0   64.4
 NXop new:  105.8  180.0  -74.1 -7.4   11.2   40.1 -7.3   37.8   60.9

NCS operator:   2
 NCS masking: Mask volume as fraction of ASU: 1.00   Multiplicity: 10
  Contiguity score:  1.000   Self-overlap score:  0.154
 NXop refinement- correlation before:  0.528, after:  0.577
 NXop old:   57.2  179.7 -122.3 -5.5   39.0   64.4 -5.6   10.0   36.4
 NXop new:  -94.6  179.8   85.4 -3.8   36.5   60.3 -3.8   12.5   40.6

NCS operator:   3
 NCS masking: Mask volume as fraction of ASU: 0.95   Multiplicity: 9
  Contiguity score:  0.999   Self-overlap score:  0.149
 NXop refinement- correlation before:  0.447, after:  0.606
 NXop old: -100.7  178.5   79.6-17.7   33.0   93.4-17.9   16.17.4
 NXop new: -140.4  179.8   39.7 -9.8   36.7   79.4 -9.9   12.4   21.6

NCS operator:

Re: [ccp4bb] problems with running PARROT

2021-06-25 Thread Eleanor Dodson

The extract from the  log file looks OK - can you send the whole log.txt?
Eleanor

On Fri, 25 Jun 2021 at 12:09, Savvas Savvides 
wrote:

> Dear colleagues,
>
> I am trying to run Parrot via CCP4-7.1.014 and the CCP4i2 GUI on a
> MacBookPro (OSX 10.15.7) and keep getting the following error report as the
> program is in the process of outputting SigmaA statistics.
>
> Below, I provide two pieces of information:
> (1) The Error message
> (2) The last page of the ouput file where the program ends up crashing
> with the error message.
>
> Thank you in advance for any insights/input on this issue.
>
> Best wishes,
> Savvas
>
>
>
> 
>
>
> Error Report for Job 41: Density modification - PARROT
>
> -ERROR- CTaskParrot:9 Error in wrapper parrot 0.0:: Failed starting external 
> process
>
> - this can be due to a number of things, but usually is due to the command 
> used by subprocess/QProcess not working for some reason.
>
> Missing input files, bad commands, non-functional programs etc. Check log 
> files and stdout.
> Process: cparrot
>
>  -ERROR- CTaskParrot:47 Error in wrapper parrot 0.0:: Error in checking 
> external process after completion
> exit status and  code: -11 -11
>
>
>
> ———
>
> -- Cycle: 1 
>
> Suggested radius for solvent mask determination: 5.68666
>
> NCS operator:   1
>  NCS masking: Mask volume as fraction of ASU: 1.00   Multiplicity: 10
>   Contiguity score:  1.000   Self-overlap score:  0.151
>  NXop refinement- correlation before:  0.539, after:  0.581
>  NXop old:  -57.7  179.7  122.8 -5.6   10.0   36.4 -5.5   39.0   64.4
>  NXop new:  105.8  180.0  -74.1 -7.4   11.2   40.1 -7.3   37.8   60.9
>
> NCS operator:   2
>  NCS masking: Mask volume as fraction of ASU: 1.00   Multiplicity: 10
>   Contiguity score:  1.000   Self-overlap score:  0.154
>  NXop refinement- correlation before:  0.528, after:  0.577
>  NXop old:   57.2  179.7 -122.3 -5.5   39.0   64.4 -5.6   10.0   36.4
>  NXop new:  -94.6  179.8   85.4 -3.8   36.5   60.3 -3.8   12.5   40.6
>
> NCS operator:   3
>  NCS masking: Mask volume as fraction of ASU: 0.95   Multiplicity: 9
>   Contiguity score:  0.999   Self-overlap score:  0.149
>  NXop refinement- correlation before:  0.447, after:  0.606
>  NXop old: -100.7  178.5   79.6-17.7   33.0   93.4-17.9   16.17.4
>  NXop new: -140.4  179.8   39.7 -9.8   36.7   79.4 -9.9   12.4   21.6
>
> NCS operator:   4
>  NCS masking: Mask volume as fraction of ASU: 0.89   Multiplicity: 9
>   Contiguity score:  0.998   Self-overlap score:  0.179
>  NXop refinement- correlation before:  0.423, after:  0.588
>  NXop old:  100.4  178.5  -79.3-17.9   16.17.4-17.7   33.0   93.4
>  NXop new:  144.0  179.8  -36.0-24.0   11.7   20.5-23.7   37.5   80.6
>
> 
> NCS operator statistics:
>  Operator_number  Mask_volume/ASU  Correlation
> 11.0010.911
> 20.9980.912
> 30.9540.863
> 40.8880.854
> 
>
> $TABLE :Cycle 1 Electron density histograms:
> $GRAPHS :Protein:N:1,4,5,6::Solvent:N:1,7,8::Simulation:N:1,3,4: $$
> rho_min rho_max   Simulatn P_init P_trgt P_mod  S_init S_mod $$
> $$
>  -0.317  -0.282  0.000  0.000  0.017  0.008  0.000  0.000
>  -0.282  -0.247  0.000  0.000  0.026  0.014  0.000  0.000
>  -0.247  -0.212  0.002  0.002  0.036  0.024  0.000  0.000
>  -0.212  -0.177  0.007  0.007  0.045  0.039  0.000  0.000
>  -0.177  -0.143  0.022  0.019  0.057  0.056  0.003  0.000
>  -0.143  -0.108  0.050  0.048  0.064  0.076  0.020  0.000
>  -0.108  -0.073  0.093  0.094  0.071  0.081  0.069  0.000
>  -0.073  -0.038  0.142  0.147  0.070  0.090  0.156  0.000
>  -0.038  -0.003  0.172  0.175  0.072  0.091  0.234  0.000
>  -0.003   0.032  0.172  0.173  0.068  0.085  0.237  1.000
>   0.032   0.067  0.141  0.141  0.063  0.075  0.167  0.000
>   0.067   0.101  0.099  0.094  0.057  0.071  0.080  0.000
>   0.101   0.136  0.056  0.053  0.053  0.063  0.026  0.000
>   0.136   0.171  0.029  0.026  0.049  0.053  0.006  0.000
>   0.171   0.206  0.011  0.012  0.044  0.048  0.001  0.000
>   0.206   0.241  0.004  0.005  0.038  0.038  0.000  0.000
>   0.241   0.276  0.001  0.002  0.033  0.033  0.000  0.000
>   0.276   0.311  0.000  0.001  0.030  0.025  0.000  0.000
>   0.311   0.345  0.000  0.000  0.025  0.016  0.000  0.000
>   0.345   0.380  0.000  0.000  0.021  0.014  0.000  0.000
> $$
>
>
> Gamma 0.24162
>
> Log likelihood:  2.920853e+04  Log likelihood (free):  0.00e+00
>
> $TABLE :Cycle 1 SigmaA statistics:
> $GRAPHS :SigmaA statistics:N:1,2,3: $$
>  1/resol^2  sigmaA(s)  sigmaA(w) $$
> $$
> 0.012  0.682  0.675
> 0.025  0.629  0.635
> 0.035  0.659  0.664
> 0.043

Re: [ccp4bb] Eukaryotic protein expression

2021-06-25 Thread Jared Sampson

Hi Dhiraj - In addition to the other good suggestions, you may also wish to
try codon optimization and different secretion signal peptides if your
target protein is secreted.

Hope that helps.

Cheers,
Jared

On Thu, Jun 24, 2021 at 4:42 PM Srivastava, Dhiraj <
dhiraj-srivast...@uiowa.edu> wrote:

> Hi all
> I am trying to express my protein in HEK293 cells for
> crystallization purpose but getting poor expression. I am using cmv
> promoter. Which promoter/vector people use to get good expression in
> eukaryotic expression system?
>
> Thank you
>
> Dhiraj
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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[ccp4bb] problems with running PARROT

2021-06-25 Thread Savvas Savvides

Dear colleagues,

I am trying to run Parrot via CCP4-7.1.014 and the CCP4i2 GUI on a MacBookPro 
(OSX 10.15.7) and keep getting the following error report as the program is in 
the process of outputting SigmaA statistics.

Below, I provide two pieces of information:
(1) The Error message
(2) The last page of the ouput file where the program ends up crashing with the 
error message.

Thank you in advance for any insights/input on this issue.

Best wishes,
Savvas






Error Report for Job 41: Density modification - PARROT
-ERROR- CTaskParrot:9 Error in wrapper parrot 0.0:: Failed starting external 
process
- this can be due to a number of things, but usually is due to the command used 
by subprocess/QProcess not working for some reason.
Missing input files, bad commands, non-functional programs etc. Check log files 
and stdout.
Process: cparrot

 -ERROR- CTaskParrot:47 Error in wrapper parrot 0.0:: Error in checking 
external process after completion
exit status and  code: -11 -11


———

-- Cycle: 1 

Suggested radius for solvent mask determination: 5.68666

NCS operator:   1
 NCS masking: Mask volume as fraction of ASU: 1.00   Multiplicity: 10
  Contiguity score:  1.000   Self-overlap score:  0.151
 NXop refinement- correlation before:  0.539, after:  0.581
 NXop old:  -57.7  179.7  122.8 -5.6   10.0   36.4 -5.5   39.0   64.4
 NXop new:  105.8  180.0  -74.1 -7.4   11.2   40.1 -7.3   37.8   60.9

NCS operator:   2
 NCS masking: Mask volume as fraction of ASU: 1.00   Multiplicity: 10
  Contiguity score:  1.000   Self-overlap score:  0.154
 NXop refinement- correlation before:  0.528, after:  0.577
 NXop old:   57.2  179.7 -122.3 -5.5   39.0   64.4 -5.6   10.0   36.4
 NXop new:  -94.6  179.8   85.4 -3.8   36.5   60.3 -3.8   12.5   40.6

NCS operator:   3
 NCS masking: Mask volume as fraction of ASU: 0.95   Multiplicity: 9
  Contiguity score:  0.999   Self-overlap score:  0.149
 NXop refinement- correlation before:  0.447, after:  0.606
 NXop old: -100.7  178.5   79.6-17.7   33.0   93.4-17.9   16.17.4
 NXop new: -140.4  179.8   39.7 -9.8   36.7   79.4 -9.9   12.4   21.6

NCS operator:   4
 NCS masking: Mask volume as fraction of ASU: 0.89   Multiplicity: 9
  Contiguity score:  0.998   Self-overlap score:  0.179
 NXop refinement- correlation before:  0.423, after:  0.588
 NXop old:  100.4  178.5  -79.3-17.9   16.17.4-17.7   33.0   93.4
 NXop new:  144.0  179.8  -36.0-24.0   11.7   20.5-23.7   37.5   80.6


NCS operator statistics:
 Operator_number  Mask_volume/ASU  Correlation
11.0010.911
20.9980.912
30.9540.863
40.8880.854


$TABLE :Cycle 1 Electron density histograms:
$GRAPHS :Protein:N:1,4,5,6::Solvent:N:1,7,8::Simulation:N:1,3,4: $$
rho_min rho_max   Simulatn P_init P_trgt P_mod  S_init S_mod $$
$$
 -0.317  -0.282  0.000  0.000  0.017  0.008  0.000  0.000
 -0.282  -0.247  0.000  0.000  0.026  0.014  0.000  0.000
 -0.247  -0.212  0.002  0.002  0.036  0.024  0.000  0.000
 -0.212  -0.177  0.007  0.007  0.045  0.039  0.000  0.000
 -0.177  -0.143  0.022  0.019  0.057  0.056  0.003  0.000
 -0.143  -0.108  0.050  0.048  0.064  0.076  0.020  0.000
 -0.108  -0.073  0.093  0.094  0.071  0.081  0.069  0.000
 -0.073  -0.038  0.142  0.147  0.070  0.090  0.156  0.000
 -0.038  -0.003  0.172  0.175  0.072  0.091  0.234  0.000
 -0.003   0.032  0.172  0.173  0.068  0.085  0.237  1.000
  0.032   0.067  0.141  0.141  0.063  0.075  0.167  0.000
  0.067   0.101  0.099  0.094  0.057  0.071  0.080  0.000
  0.101   0.136  0.056  0.053  0.053  0.063  0.026  0.000
  0.136   0.171  0.029  0.026  0.049  0.053  0.006  0.000
  0.171   0.206  0.011  0.012  0.044  0.048  0.001  0.000
  0.206   0.241  0.004  0.005  0.038  0.038  0.000  0.000
  0.241   0.276  0.001  0.002  0.033  0.033  0.000  0.000
  0.276   0.311  0.000  0.001  0.030  0.025  0.000  0.000
  0.311   0.345  0.000  0.000  0.025  0.016  0.000  0.000
  0.345   0.380  0.000  0.000  0.021  0.014  0.000  0.000
$$


Gamma 0.24162

Log likelihood:  2.920853e+04  Log likelihood (free):  0.00e+00

$TABLE :Cycle 1 SigmaA statistics:
$GRAPHS :SigmaA statistics:N:1,2,3: $$
 1/resol^2  sigmaA(s)  sigmaA(w) $$
$$
0.012  0.682  0.675
0.025  0.629  0.635
0.035  0.659  0.664
0.043  0.666  0.670
0.051  0.619  0.638
0.059  0.515  0.593
0.066  0.452  0.656
$$




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Re: [ccp4bb] S=O converted to S-OH during refinement

2021-06-25 Thread Pedro Matias



That's right. The S-OH configuration is imposed by the CIF dictionary 
for the ligand that you are using in REFMAC. You can edit the dictionary 
with e.g., jligand, save a local copy and feed that copy to REFMAC - it 
will override the library definition of the ligand.



On 25/06/2021 10:58, Peat, Tom (Manufacturing, Parkville) wrote:

Hello Shipra,

If you have defined the small molecule with a cif dictionary file 
(used for refinement in REFMAC), then take a look at that file and see 
whether it is correctly defined.
You can manually edit these files or remake them using any number of 
programs to get the parameters you think are correct.

Best of luck, tom

Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


*From:* CCP4 bulletin board  on behalf of 
Shipra Bijpuria 

*Sent:* Friday, June 25, 2021 7:04 PM
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* [ccp4bb] S=O converted to S-OH during refinement
Hello everyone,

I am trying to refine a protein-ligand complex structure.

The ligand is a small molecule and at one end has Sulfur that has 
three branches of O, NH and CH3.
Sulfur is attached to oxygen by a double bond (S=O). After fitting the 
ligand, I did refinement using Refmac5 with default settings.


But after the refinement the S=O gets converted to S-OH. Please let me 
know how can I retain the S=O during refinement.


Thanks,
Shipra



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--

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Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
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Re: [ccp4bb] S=O converted to S-OH during refinement

2021-06-25 Thread Peat, Tom (Manufacturing, Parkville)

Hello Shipra,

If you have defined the small molecule with a cif dictionary file (used for 
refinement in REFMAC), then take a look at that file and see whether it is 
correctly defined.
You can manually edit these files or remake them using any number of programs 
to get the parameters you think are correct.
Best of luck, tom

Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au


From: CCP4 bulletin board  on behalf of Shipra Bijpuria 

Sent: Friday, June 25, 2021 7:04 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] S=O converted to S-OH during refinement

Hello everyone,

I am trying to refine a protein-ligand complex structure.

The ligand is a small molecule and at one end has Sulfur that has three 
branches of O, NH and CH3.
Sulfur is attached to oxygen by a double bond (S=O). After fitting the ligand, 
I did refinement using Refmac5 with default settings.

But after the refinement the S=O gets converted to S-OH. Please let me know how 
can I retain the S=O during refinement.

Thanks,
Shipra



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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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[ccp4bb] S=O converted to S-OH during refinement

2021-06-25 Thread Shipra Bijpuria

Hello everyone,

I am trying to refine a protein-ligand complex structure.

The ligand is a small molecule and at one end has Sulfur that has three
branches of O, NH and CH3.
Sulfur is attached to oxygen by a double bond (S=O). After fitting the
ligand, I did refinement using Refmac5 with default settings.

But after the refinement the S=O gets converted to S-OH. Please let me know
how can I retain the S=O during refinement.

Thanks,
Shipra



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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 
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[ccp4bb] S=O converted to S-OH during refinement

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