[ccp4bb] Open position: University Lecturer in Biochemistry (Structural bioinformatics) Abo Akademi University, Turku, Finland

[Tiina Salminen]

Dear all,


We have an open position as a University Lecturer in Biochemistry (Structural 
bioinformatics) and you can find more information about the position and how to 
apply on the web-page: 
https://abo.rekrytointi.com/paikat/index.php?jid=489==A_RJ=3yytrx2g9osg44cwogw088c00gck084.


The examination language at Abo Akademi University is Swedish and while English 
is the main teaching language.


The application deadline is 14.2.


Please spread the message through all your channels and apply if you are our 
candidate!


Best regards,

Tiina


**

Tiina A. Salminen, Professor

Structural Bioinformatics Laboratory

Biochemistry, Faculty of Science and Engineering

Abo Akademi University

Tykistökatu 6A

FI-20520 Turku

Finland


+358 40 515 3941



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Re: [ccp4bb] COOT FLEV error

[Xavier Brazzolotto]

This is probably a FLEV specific issue.
Have you tried external software such as LigPlot+ or Schrodinger’s Maestro to 
see if they can better handle the modified residue ?

> Le 27 janv. 2022 à 01:03, Sergio A. Sampieri  a écrit :
> 
> Greetings all,
> 
> Sorry for the naive question, but I'm having problems trying to FLEV a 
> modified residue in COOT.
> 
> I have modeled a modified CYS into an structure following these steps:
> 
> Generate a SMILES string for L-cysteine bonded the modification.  
> C1=CC=C(C=C1)C(=O)SCC(C(O)=O)N. 
> https://pubchem.ncbi.nlm.nih.gov/compound/262741 
> 
> Input the SMILES string to PHENIX eLBOW using the graphical user interface 
> with quantum optimization enabled to generate restraints (.cif) and 
> coordinates (.pdb).
> Used the eLBOW graphical user interface to change the atom names for the 
> backbone atoms of the modified cysteine to the standard ones for amino acids 
> (N, CA, C, O, OXT, CB), (additional atom names remain as they are)
> Save the new coordinates and restraints.
>  Modified the cif file, especially the definition as a L-peptide and not as 
> Ligand.
> Move the modified cysteine saved in step 5 into the density using Coot.
> Delete the extra OXT atom of the cysteine carboxylate and save the 
> coordinates of the modified Cys.
> In coot "replace residue" CYS with the Modified CYS ("MCY").
> Refine the structure.
> Open the refined model in COOT, and the cif dictionary generated.
> 
> But when trying to FLEV the modified residue I get the next errors:
> 
> WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for 
> atom name: " OXT" ele : O:
> Failed to get atom index for atom name " OXT"" in residue of type MCY [spec: 
> 1 "A" 165 ""]
> [17:43:23] Explicit valence for atom # 12 O, 3, is greater than permitted
> std::exception
> WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for 
> atom name: " OXT" ele : O:
> Failed to get atom index for atom name " OXT"" in residue of type MCY [spec: 
> 1 "A" 165 ""]
> [17:43:23] Explicit valence for atom # 12 O, 3, is greater than permitted
> std::exception
> WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for 
> atom name: " OXT" ele : O:
> ERROR:: (runtime error) in fle_view_with_rdkit(): Failed to get atom index 
> for atom name " OXT"" in residue of type MCY [spec: 1 "A" 165 ""]
> 
> Also tried to modify the atom names in the CIF file but still get the same 
> error (with different atom numbers instead of OXT, O09 and so):
> 
> WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for 
> atom name: " C10" ele : C:
> ERROR:: (runtime error) in fle_view_with_rdkit(): Failed to get atom index 
> for atom name " C10"" in residue of type MCY [spec: 1 "A" 165 ""]
> 
> Any help or ideas would be greatly appreciated, thanks in advance, stay safe!
> 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 
Xavier Brazzolotto, PhD
Département de Toxicologie et Risques Chimiques
Institut de Recherche Biomédicale des Armées
BP 73
91223 Brétigny sur Orge
France

Phone   +33 (0) 1 78 65 14 00
Alt Phone   +33 (0) 4 57 42 87 19
Cell+33 (0) 6 58 36 39 09

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[ccp4bb] COOT FLEV error

[Sergio A. Sampieri]

Greetings all,

Sorry for the naive question, but I'm having problems trying to FLEV a
modified residue in COOT.

I have modeled a modified CYS into an structure following these steps:


   1. Generate a SMILES string for L-cysteine bonded the modification.
   C1=CC=C(C=C1)C(=O)SCC(C(O)=O)N.
   https://pubchem.ncbi.nlm.nih.gov/compound/262741
   2. Input the SMILES string to PHENIX eLBOW using the graphical user
   interface with quantum optimization enabled to generate restraints (.cif)
   and coordinates (.pdb).
   3. Used the eLBOW graphical user interface to change the atom names for
   the backbone atoms of the modified cysteine to the standard ones for amino
   acids (N, CA, C, O, OXT, CB), (additional atom names remain as they are)
   4. Save the new coordinates and restraints.
   5.  Modified the cif file, especially the definition as a L-peptide and
   not as Ligand.
   6. Move the modified cysteine saved in step 5 into the density using
   Coot.
   7. Delete the extra OXT atom of the cysteine carboxylate and save the
   coordinates of the modified Cys.
   8. In coot "replace residue" CYS with the Modified CYS ("MCY").
   9. Refine the structure.
   10. Open the refined model in COOT, and the cif dictionary generated.


But when trying to FLEV the modified residue I get the next errors:

WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for
atom name: " OXT" ele : O:
Failed to get atom index for atom name " OXT"" in residue of type MCY
[spec: 1 "A" 165 ""]
[17:43:23] Explicit valence for atom # 12 O, 3, is greater than permitted
std::exception
WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for
atom name: " OXT" ele : O:
Failed to get atom index for atom name " OXT"" in residue of type MCY
[spec: 1 "A" 165 ""]
[17:43:23] Explicit valence for atom # 12 O, 3, is greater than permitted
std::exception
WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for
atom name: " OXT" ele : O:
ERROR:: (runtime error) in fle_view_with_rdkit(): Failed to get atom index
for atom name " OXT"" in residue of type MCY [spec: 1 "A" 165 ""]

Also tried to modify the atom names in the CIF file but still get the same
error (with different atom numbers instead of OXT, O09 and so):

WARNING:: oops, bonding in rdkit_mol() failed to get atom index idx_1 for
atom name: " C10" ele : C:
ERROR:: (runtime error) in fle_view_with_rdkit(): Failed to get atom index
for atom name " C10"" in residue of type MCY [spec: 1 "A" 165 ""]

Any help or ideas would be greatly appreciated, thanks in advance, stay
safe!



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] freezing in ethane / propane - unipucks ?

[Guenter Fritz]

Hi Steve,


Hi ,
1) If you are collecting the data at the APS  the samples frozen in propane can 
be legally shipped there (check APS web site for information)
2) The samples CANNOT be mounted using either the ACTOR or ALS Style auto 
mounter. But the samples can be shipped using either the Rigaku pucks or the 
Uni-pucks with a vial cover adapter. In any case you would need to manually 
mount and collect data or have the samples retrieved after the propane melted 
with the robotic mounter and mounted later by the robot for data collection.

I am in Europe, so I would go for ESRF / SLS.


 From my extensive experience quenching samples using propane it has been 
possible to freeze ALL in LN2 after a) perfecting cryoprotectant, b) perfecting 
freezing technique, c) modifying crystal growth conditions.


:)) yes better crystals is always the best solution. But we are happy 
that we have crystals at all after some efforts (insect cells, low 
solubility, crystallization in the glove box, )


Cheers Guenter



Steve Ginell



On Jan 26, 2022, at 1:31 PM, Joseph Ferrara  wrote:

When using Xe derivatization for SAD phasing, we (mostly Jim Pflugrath) used 
carbon tetrafluoride. CF4 has a melting point of 89.5K, just four degrees 
warmer than propane and is not flammable.

Joe Ferrara

-Original Message-
From: CCP4 bulletin board  On Behalf Of James Holton
Sent: Wednesday, January 26, 2022 13:07
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] freezing in ethane / propane - unipucks ?

I think the issue with propane at at least some light sources is that it is 
flammable.  Makes shipping and safety more complicated.

How hard would it be to let the propane melt off in a cryo gas stream at your 
home lab?  Then use tongs to transfer the pin into liquid N2 for handling as 
usual?  If you don't have a working N2 gas stream and are on a budget they are 
not that hard to build:
https://doi.org/10.1107/S0021889894006357

Cheers,

-James Holton
MAD Scientist


On 1/26/2022 9:25 AM, Guenter Fritz wrote:

Dear Dom,

thanks a lot. Yes, this might work sending a combipuck alongside with
a good bottle for the local contact.
I was wondering whether the grippers can handle a block of propane?

Best wishes,
guenter

Dear Guenter,

Would the use of vials inside combi-pucks
(https://www.mitegen.com/product/combipuck-system/) and some
arrangements with your local contact at the other end, perhaps help
with using propane remotely?

BW,

D

On 26/01/2022 16:53, Guenter Fritz wrote:

Dear all,

we have some  delicate crystals which might benefit from freezing in
propane. In former times (when I was still travelling to the
beamlines) we waited until the propane was solid in the vial and
then let the propane thaw in the cryo stream at the beamline.

But how can we  do this in these days with unipucks and no manual
mounting?

I was thinking about freezing in ethane and then transfer the loops
to liquid nitrogen, similarly we handle grids for cryo EM. Does
somebody has tried that? Any experience, tips & tricks would be very
welcome! Thanks in advance and best regards,

Guenter





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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] freezing in ethane / propane - unipucks ?

[Guenter Fritz]

Hi Joe,

thanks. I have never used CF4. Good point and worth a try.
Best,
Guenter

When using Xe derivatization for SAD phasing, we (mostly Jim Pflugrath) used 
carbon tetrafluoride. CF4 has a melting point of 89.5K, just four degrees 
warmer than propane and is not flammable.

Joe Ferrara

-Original Message-
From: CCP4 bulletin board  On Behalf Of James Holton
Sent: Wednesday, January 26, 2022 13:07
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] freezing in ethane / propane - unipucks ?

I think the issue with propane at at least some light sources is that it is 
flammable.  Makes shipping and safety more complicated.

How hard would it be to let the propane melt off in a cryo gas stream at your 
home lab?  Then use tongs to transfer the pin into liquid N2 for handling as 
usual?  If you don't have a working N2 gas stream and are on a budget they are 
not that hard to build:
https://doi.org/10.1107/S0021889894006357

Cheers,

-James Holton
MAD Scientist


On 1/26/2022 9:25 AM, Guenter Fritz wrote:

Dear Dom,

thanks a lot. Yes, this might work sending a combipuck alongside with
a good bottle for the local contact.
I was wondering whether the grippers can handle a block of propane?

Best wishes,
guenter

Dear Guenter,

Would the use of vials inside combi-pucks
(https://www.mitegen.com/product/combipuck-system/) and some
arrangements with your local contact at the other end, perhaps help
with using propane remotely?

BW,

D

On 26/01/2022 16:53, Guenter Fritz wrote:

Dear all,

we have some  delicate crystals which might benefit from freezing in
propane. In former times (when I was still travelling to the
beamlines) we waited until the propane was solid in the vial and
then let the propane thaw in the cryo stream at the beamline.

But how can we  do this in these days with unipucks and no manual
mounting?

I was thinking about freezing in ethane and then transfer the loops
to liquid nitrogen, similarly we handle grids for cryo EM. Does
somebody has tried that? Any experience, tips & tricks would be very
welcome! Thanks in advance and best regards,

Guenter





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Re: [ccp4bb] freezing in ethane / propane - unipucks ?

[Guenter Fritz]

Hi James,

I think the issue with propane at at least some light sources is that 
it is flammable.  Makes shipping and safety more complicated.


How hard would it be to let the propane melt off in a cryo gas stream 
at your home lab?  Then use tongs to transfer the pin into liquid N2 
for handling as usual?  If you don't have a working N2 gas stream and 
are on a budget they are not that hard to build:

https://doi.org/10.1107/S0021889894006357

Yes, that would be straightforward,  but was looking for a kind of 
shortcut :).


Cheers Guenter


Cheers,

-James Holton
MAD Scientist


On 1/26/2022 9:25 AM, Guenter Fritz wrote:

Dear Dom,

thanks a lot. Yes, this might work sending a combipuck alongside with 
a good bottle for the local contact.

I was wondering whether the grippers can handle a block of propane?

Best wishes,
guenter

Dear Guenter,

Would the use of vials inside combi-pucks 
(https://www.mitegen.com/product/combipuck-system/) and some 
arrangements with your local contact at the other end, perhaps help 
with using propane remotely?


BW,

D

On 26/01/2022 16:53, Guenter Fritz wrote:

Dear all,

we have some  delicate crystals which might benefit from freezing 
in propane. In former times (when I was still travelling to the 
beamlines) we waited until the propane was solid in the vial and 
then let the propane thaw in the cryo stream at the beamline.


But how can we  do this in these days with unipucks and no manual 
mounting?


I was thinking about freezing in ethane and then transfer the loops 
to liquid nitrogen, similarly we handle grids for cryo EM. Does 
somebody has tried that? Any experience, tips & tricks would be 
very welcome! Thanks in advance and best regards,


Guenter

 



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] freezing in ethane / propane - unipucks ?

[Ginell, Stephan L.]

Hi ,
1) If you are collecting the data at the APS  the samples frozen in propane can 
be legally shipped there (check APS web site for information)
2) The samples CANNOT be mounted using either the ACTOR or ALS Style auto 
mounter. But the samples can be shipped using either the Rigaku pucks or the 
Uni-pucks with a vial cover adapter. In any case you would need to manually 
mount and collect data or have the samples retrieved after the propane melted 
with the robotic mounter and mounted later by the robot for data collection.

>From my extensive experience quenching samples using propane it has been 
>possible to freeze ALL in LN2 after a) perfecting cryoprotectant, b) 
>perfecting freezing technique, c) modifying crystal growth conditions.

Steve Ginell


> On Jan 26, 2022, at 1:31 PM, Joseph Ferrara  wrote:
> 
> When using Xe derivatization for SAD phasing, we (mostly Jim Pflugrath) used 
> carbon tetrafluoride. CF4 has a melting point of 89.5K, just four degrees 
> warmer than propane and is not flammable. 
> 
> Joe Ferrara
> 
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of James Holton
> Sent: Wednesday, January 26, 2022 13:07
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [EXTERNAL] Re: [ccp4bb] freezing in ethane / propane - unipucks ?
> 
> I think the issue with propane at at least some light sources is that it is 
> flammable.  Makes shipping and safety more complicated.
> 
> How hard would it be to let the propane melt off in a cryo gas stream at your 
> home lab?  Then use tongs to transfer the pin into liquid N2 for handling as 
> usual?  If you don't have a working N2 gas stream and are on a budget they 
> are not that hard to build:
> https://doi.org/10.1107/S0021889894006357
> 
> Cheers,
> 
> -James Holton
> MAD Scientist
> 
> 
> On 1/26/2022 9:25 AM, Guenter Fritz wrote:
>> Dear Dom,
>> 
>> thanks a lot. Yes, this might work sending a combipuck alongside with 
>> a good bottle for the local contact.
>> I was wondering whether the grippers can handle a block of propane?
>> 
>> Best wishes,
>> guenter
>>> Dear Guenter,
>>> 
>>> Would the use of vials inside combi-pucks
>>> (https://www.mitegen.com/product/combipuck-system/) and some 
>>> arrangements with your local contact at the other end, perhaps help 
>>> with using propane remotely?
>>> 
>>> BW,
>>> 
>>> D
>>> 
>>> On 26/01/2022 16:53, Guenter Fritz wrote:
 Dear all,
 
 we have some  delicate crystals which might benefit from freezing in 
 propane. In former times (when I was still travelling to the
 beamlines) we waited until the propane was solid in the vial and 
 then let the propane thaw in the cryo stream at the beamline.
 
 But how can we  do this in these days with unipucks and no manual 
 mounting?
 
 I was thinking about freezing in ethane and then transfer the loops 
 to liquid nitrogen, similarly we handle grids for cryo EM. Does 
 somebody has tried that? Any experience, tips & tricks would be very 
 welcome! Thanks in advance and best regards,
 
 Guenter
 
 
 
 
 
 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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 mailing list hosted by www.jiscmail.ac.uk, terms & conditions are 
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>>> 
>> 
>> ##
>> ##
>> 
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> 
> 
> 
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This 

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] freezing in ethane / propane - unipucks ?

[Joseph Ferrara]

When using Xe derivatization for SAD phasing, we (mostly Jim Pflugrath) used 
carbon tetrafluoride. CF4 has a melting point of 89.5K, just four degrees 
warmer than propane and is not flammable. 

Joe Ferrara

-Original Message-
From: CCP4 bulletin board  On Behalf Of James Holton
Sent: Wednesday, January 26, 2022 13:07
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] freezing in ethane / propane - unipucks ?

I think the issue with propane at at least some light sources is that it is 
flammable.  Makes shipping and safety more complicated.

How hard would it be to let the propane melt off in a cryo gas stream at your 
home lab?  Then use tongs to transfer the pin into liquid N2 for handling as 
usual?  If you don't have a working N2 gas stream and are on a budget they are 
not that hard to build:
https://doi.org/10.1107/S0021889894006357

Cheers,

-James Holton
MAD Scientist


On 1/26/2022 9:25 AM, Guenter Fritz wrote:
> Dear Dom,
>
> thanks a lot. Yes, this might work sending a combipuck alongside with 
> a good bottle for the local contact.
> I was wondering whether the grippers can handle a block of propane?
>
> Best wishes,
> guenter
>> Dear Guenter,
>>
>> Would the use of vials inside combi-pucks
>> (https://www.mitegen.com/product/combipuck-system/) and some 
>> arrangements with your local contact at the other end, perhaps help 
>> with using propane remotely?
>>
>> BW,
>>
>> D
>>
>> On 26/01/2022 16:53, Guenter Fritz wrote:
>>> Dear all,
>>>
>>> we have some  delicate crystals which might benefit from freezing in 
>>> propane. In former times (when I was still travelling to the
>>> beamlines) we waited until the propane was solid in the vial and 
>>> then let the propane thaw in the cryo stream at the beamline.
>>>
>>> But how can we  do this in these days with unipucks and no manual 
>>> mounting?
>>>
>>> I was thinking about freezing in ethane and then transfer the loops 
>>> to liquid nitrogen, similarly we handle grids for cryo EM. Does 
>>> somebody has tried that? Any experience, tips & tricks would be very 
>>> welcome! Thanks in advance and best regards,
>>>
>>> Guenter
>>>
>>> 
>>> 
>>>
>>>
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>>
>
> ##
> ##
>
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Re: [ccp4bb] freezing in ethane / propane - unipucks ?

[James Holton]

I think the issue with propane at at least some light sources is that it 
is flammable.  Makes shipping and safety more complicated.


How hard would it be to let the propane melt off in a cryo gas stream at 
your home lab?  Then use tongs to transfer the pin into liquid N2 for 
handling as usual?  If you don't have a working N2 gas stream and are on 
a budget they are not that hard to build:

https://doi.org/10.1107/S0021889894006357

Cheers,

-James Holton
MAD Scientist


On 1/26/2022 9:25 AM, Guenter Fritz wrote:

Dear Dom,

thanks a lot. Yes, this might work sending a combipuck alongside with 
a good bottle for the local contact.

I was wondering whether the grippers can handle a block of propane?

Best wishes,
guenter

Dear Guenter,

Would the use of vials inside combi-pucks 
(https://www.mitegen.com/product/combipuck-system/) and some 
arrangements with your local contact at the other end, perhaps help 
with using propane remotely?


BW,

D

On 26/01/2022 16:53, Guenter Fritz wrote:

Dear all,

we have some  delicate crystals which might benefit from freezing in 
propane. In former times (when I was still travelling to the 
beamlines) we waited until the propane was solid in the vial and 
then let the propane thaw in the cryo stream at the beamline.


But how can we  do this in these days with unipucks and no manual 
mounting?


I was thinking about freezing in ethane and then transfer the loops 
to liquid nitrogen, similarly we handle grids for cryo EM. Does 
somebody has tried that? Any experience, tips & tricks would be very 
welcome! Thanks in advance and best regards,


Guenter

 



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Re: [ccp4bb] freezing in ethane / propane - unipucks ?

[Guenter Fritz]

Dear Dom,

thanks a lot. Yes, this might work sending a combipuck alongside with a 
good bottle for the local contact.

I was wondering whether the grippers can handle a block of propane?

Best wishes,
guenter

Dear Guenter,

Would the use of vials inside combi-pucks 
(https://www.mitegen.com/product/combipuck-system/) and some 
arrangements with your local contact at the other end, perhaps help 
with using propane remotely?


BW,

D

On 26/01/2022 16:53, Guenter Fritz wrote:

Dear all,

we have some  delicate crystals which might benefit from freezing in 
propane. In former times (when I was still travelling to the 
beamlines) we waited until the propane was solid in the vial and then 
let the propane thaw in the cryo stream at the beamline.


But how can we  do this in these days with unipucks and no manual 
mounting?


I was thinking about freezing in ethane and then transfer the loops 
to liquid nitrogen, similarly we handle grids for cryo EM. Does 
somebody has tried that? Any experience, tips &  tricks would be very 
welcome! Thanks in advance and best regards,


Guenter



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Re: [ccp4bb] freezing in ethane / propane - unipucks ?

[Dom Bellini - MRC LMB]

Dear Guenter,

Would the use of vials inside combi-pucks 
(https://www.mitegen.com/product/combipuck-system/) and some 
arrangements with your local contact at the other end, perhaps help with 
using propane remotely?


BW,

D

On 26/01/2022 16:53, Guenter Fritz wrote:

Dear all,

we have some  delicate crystals which might benefit from freezing in 
propane. In former times (when I was still travelling to the 
beamlines) we waited until the propane was solid in the vial and then 
let the propane thaw in the cryo stream at the beamline.


But how can we  do this in these days with unipucks and no manual 
mounting?


I was thinking about freezing in ethane and then transfer the loops to 
liquid nitrogen, similarly we handle grids for cryo EM. Does somebody 
has tried that? Any experience, tips &  tricks would be very welcome! 
Thanks in advance and best regards,


Guenter



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--
Dom Bellini, Xray Crystallography Facility (1S205)
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH
Phone 01223 267839



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[ccp4bb] freezing in ethane / propane - unipucks ?

[Guenter Fritz]

Dear all,

we have some  delicate crystals which might benefit from freezing in 
propane. In former times (when I was still travelling to the beamlines) 
we waited until the propane was solid in the vial and then let the 
propane thaw in the cryo stream at the beamline.


But how can we  do this in these days with unipucks and no manual mounting?

I was thinking about freezing in ethane and then transfer the loops to 
liquid nitrogen, similarly we handle grids for cryo EM. Does somebody 
has tried that? Any experience, tips &  tricks would be very welcome! 
Thanks in advance and best regards,


Guenter



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