Re: [ccp4bb] Phaser: tNCS present but correction not applied

[Eleanor Dodson]

That is a very high nTCS vector (78% of the origin. Are you sure your unit
cell isny doubled
ie cell is not 94.2073 148.003 72.9967 90 97.6686 90

But
47.136 148 7390 98 90
What does pointless suggest for theSG

Eleanor



On 26 November 2016 at 18:56, KAUSHIK H.S. <
02b42c18251e-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear Dr. Read,
>
> For the first time, Phaser gave the following warning.
> XXX
> Warning: Input/Default tNCS NMOL (2) does not match suggested NMOL (4):
> Please check cell content analysis and tNCS to confirm NMOL
>
> Warning: tNCS is present but correction factors NOT applied
> XXX
>
> Hence, I set NMOL=4 (under other setting using the Phenix GUI of Phaser)
> following which, only the second Warning message was displayed.  The LLG
> and TFZ scores remained the same in both the cases.  The warnings remain
> the same when I try to place more protomers in the ASU.
>
> XXX
> Warning: tNCS is present but correction factors NOT applied
> XXX
>
>
> However, I found the following message from the log file:
> 
> Large non-origin Patterson peaks indicate that multiple tNCS vectors are
> present
>Please analyse peaks for NMOL multiplicity
>tNCS correction will NOT be applied
>   To activate tNCS correction, enter tNCS vector manually
> 
>
> I (think, I have) identified the t-vector (0.500 0.000 0.000) but, don't
> know what parameters of Phaser to tweak with.  Any suggestions or pointers
> to related papers could be very helpful.
>
> I have a similar problem with another dataset of a different protein which
> is nearly cylindrical.
>
> Thank,
> Kaushik
>
>
> On Saturday, 26 November 2016 11:46 PM, Randy Read 
> wrote:
>
>
> Hi,
>
> That message should mean that you didn't ask for a number of molecules
> divisible by the order of the tNCS. With that vector you need to search for
> an even number of copies.
>
> Let me know if that doesn't explain what you're saying.
>
> Best wishes,
> Randy Read
>
> 
> Randy J. Read
>
> On 25 Nov 2016, at 21:27, KAUSHIK H.S. <02b42c18251e-dmarc-
> requ...@jiscmail.ac.uk> wrote:
>
> Hello,
>
> I have a crystal in C2 spacegroup (94.2073 148.003 72.9967 90 97.6686 90)
> and Xtriage predicts 923 residues in ASU.  My protein could be anywhere
> between 95 to 110 residues long (assuming the terminals could be cleaved).
> Using a homolog, Phaser gives me a solution with LLG=1072 and TFZ=45.
> Molrep placed 4 protomers in the ASU however, the crystal packing is poor.
>
> I understand from Phaser that the tNCS is not accounted for (because the
> structure is linear?).  Is there a way the exact location of the tNCS
> related protomers be predicted using information from SfCheck and Xtriage?
>
> Xtriage information:
> Fraqc. coord. : 0.500 0.000 0.000
> Distance to origin: 47.104
> Height relative to origin: 79.688%
> p_value(height) : 5.283e-07
>
> SFCHECK:
> Pseudo-translation is detected: 62.6%
> Pseudo-translation vector: 0.500 0.000 0.000
>
> Sorry if my question is too naive.
>
> Thanks in advance,
> Kaushik Hatti,
> Molecular Biophysics Unit,
> Indian Institute of Science,
> India.
>
>
>
>

Re: [ccp4bb] Problems finding the correct Cif file of a crystal structure

[Eleanor Dodson]

There is a data bae - cambridge Structural Data Base with most crystal
structures coordinates and measure data in it. if your university
subscribes you should be able to acess it.
Eleanor dodson

On 26 November 2016 at 21:00, Bianca Valdes 
wrote:

> Hello!
>
> I'm currently a PhD student. I'm taking a crystallography class and for
> our final project the professor wants us to compare the theoretical cif
> file of Copper Acetate with the experimental one we are generating. I found
> a cif file but is very incomplete,  do you guys now where I can find the
> complete and correct Cif file for Copper Acetate?
>
>
> Thanks a lot!
>
> Bianca
>

[ccp4bb] update 024

[Charles Ballard]

Dear All

hopefully this fixes the coot-0.8.7 issue on OS X and linux.

In this update

  * coot
   - new libcoot-coord-extra to address auto-mutate issue

  * crank2
   - update to 2.0.132

  * ccp4i2
   - gesamt chain selection
   - crank2

  * pointless
   - 1.10.28, fix for NaN with some centrosymmetric space groups

  * ccp4i
   - crank2 update

  * blend
   - 0.6.22

  * qtrview
  - fix for phaser log files
  
  * refmac
  - fix for atom name confusion when link involves monomers of same type

  * monomers
   - various additions and fixes.

All the best

Charles

[ccp4bb] Problems finding the correct Cif file of a crystal structure

[Bianca Valdes]

Hello!

I'm currently a PhD student. I'm taking a crystallography class and for our
final project the professor wants us to compare the theoretical cif file of
Copper Acetate with the experimental one we are generating. I found a cif
file but is very incomplete,  do you guys now where I can find the complete
and correct Cif file for Copper Acetate?


Thanks a lot!

Bianca

Re: [ccp4bb] Phaser: tNCS present but correction not applied

[KAUSHIK H.S.]

Dear Dr. Read,
For the first time, Phaser gave the following warning.XXXWarning: 
Input/Default tNCS NMOL (2) does not match suggested NMOL (4): Please check 
cell content analysis and tNCS to confirm NMOL
Warning: tNCS is present but correction factors NOT applied
XXX
Hence, I set NMOL=4 (under other setting using the Phenix GUI of Phaser) 
following which, only the second Warning message was displayed.  The LLG and 
TFZ scores remained the same in both the cases.  The warnings remain the same 
when I try to place more protomers in the ASU.
XXX Warning: tNCS is present but correction factors NOT appliedXXX

However, I found the following message from the log file:Large 
non-origin Patterson peaks indicate that multiple tNCS vectors are present   
Please analyse peaks for NMOL multiplicity   tNCS correction will NOT be 
applied      To activate tNCS correction, enter tNCS vector manually
I (think, I have) identified the t-vector (0.500 0.000 0.000) but, don't know 
what parameters of Phaser to tweak with.  Any suggestions or pointers to 
related papers could be very helpful.
I have a similar problem with another dataset of a different protein which is 
nearly cylindrical. 
Thank,Kaushik

On Saturday, 26 November 2016 11:46 PM, Randy Read  wrote:
 

 Hi,
That message should mean that you didn't ask for a number of molecules 
divisible by the order of the tNCS. With that vector you need to search for an 
even number of copies.
Let me know if that doesn't explain what you're saying. 
Best wishes,Randy Read 


Randy J. Read
On 25 Nov 2016, at 21:27, KAUSHIK H.S. 
<02b42c18251e-dmarc-requ...@jiscmail.ac.uk> wrote:


Hello,
I have a crystal in C2 spacegroup (94.2073 148.003 72.9967 90 97.6686 90) and 
Xtriage predicts 923 residues in ASU.  My protein could be anywhere between 95 
to 110 residues long (assuming the terminals could be cleaved).  Using a 
homolog, Phaser gives me a solution with LLG=1072 and TFZ=45.  Molrep placed 4 
protomers in the ASU however, the crystal packing is poor.
I understand from Phaser that the tNCS is not accounted for (because the 
structure is linear?).  Is there a way the exact location of the tNCS related 
protomers be predicted using information from SfCheck and Xtriage?  

Xtriage information:Fraqc. coord. : 0.500 0.000 0.000Distance to origin: 
47.104Height relative to origin: 79.688%p_value(height) : 5.283e-07
SFCHECK:
Pseudo-translation is detected: 62.6%Pseudo-translation vector: 0.500 0.000 
0.000
Sorry if my question is too naive.
Thanks in advance,Kaushik Hatti,Molecular Biophysics Unit,Indian Institute of 
Science,India.




   

Re: [ccp4bb] Phaser: tNCS present but correction not applied

[Randy Read]

Hi,

That message should mean that you didn't ask for a number of molecules 
divisible by the order of the tNCS. With that vector you need to search for an 
even number of copies.

Let me know if that doesn't explain what you're saying. 

Best wishes,
Randy Read 


Randy J. Read

> On 25 Nov 2016, at 21:27, KAUSHIK H.S. 
> <02b42c18251e-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hello,
> 
> I have a crystal in C2 spacegroup (94.2073 148.003 72.9967 90 97.6686 90) and 
> Xtriage predicts 923 residues in ASU.  My protein could be anywhere between 
> 95 to 110 residues long (assuming the terminals could be cleaved).  Using a 
> homolog, Phaser gives me a solution with LLG=1072 and TFZ=45.  Molrep placed 
> 4 protomers in the ASU however, the crystal packing is poor.
> 
> I understand from Phaser that the tNCS is not accounted for (because the 
> structure is linear?).  Is there a way the exact location of the tNCS related 
> protomers be predicted using information from SfCheck and Xtriage?  
> 
> Xtriage information:
> Fraqc. coord. : 0.500 0.000 0.000
> Distance to origin: 47.104
> Height relative to origin: 79.688%
> p_value(height) : 5.283e-07
> 
> SFCHECK:
> Pseudo-translation is detected: 62.6%
> Pseudo-translation vector: 0.500 0.000 0.000
> 
> Sorry if my question is too naive.
> 
> Thanks in advance,
> Kaushik Hatti,
> Molecular Biophysics Unit,
> Indian Institute of Science,
> India.
>