Re: [ccp4bb] Structure solution - hexapeptide

[Diana Tomchick]

I’ll second the use of ACORN. I was able to solve an RNA duplex structure with 
1.4 Å data using the program, and it only took about 20 minutes of CPU time on 
an old (~5 years) Mac Pro.

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu>
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Aug 2, 2018, at 9:00 AM, Mark J. van Raaij 
mailto:mjvanra...@cnb.csic.es>> wrote:


When I was at Santiago de Composrela Univ., we have had success with the CCP4 
program ACORN even at around 1.2 Å resolution. Also peptides, no heavy atoms.
Didn't do this myself though I have to admit, but could put you in contact with 
the people who did.

Mark J van Raaij
CNB-CSIC
wwwuser.csic.es/~mjvanraaij<http://wwwuser.csic.es/~mjvanraaij>


Mark J van Raaij
CNB-CSIC
wwwuser.csic.es/~mjvanraaij<http://wwwuser.csic.es/~mjvanraaij>

 Original message 
From: Kristof Van Hecke 
mailto:kristofrg.vanhe...@gmail.com>>
Date: 02/08/2018 14:53 (GMT+01:00)
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] Structure solution - hexapeptide

Dear all,

I’m trying to solve a structure of a (modified) hexapeptide:
- inhouse (very decent) data up to 0.8 Angstrom
- average redundancy = 10
- according to the Matthews coefficient of 1.88 with 34.77 %solvent, there 
should be 3 Nmol/asym
- ‘large’ unit cell of about a=54, b=54, c=12
- SG = P3(1)12 or P3(2)12

As there’s (presumably) only C, H, N and O in the structure, I’m not able to 
solve this via Direct Methods, Charge Flipping etc,.
Trying MR (with Phaser) doesn’t give any results either, as there’s hardly any 
homologous models


Has anyone encountered a similar problem please, and could provide any possible 
solutions?
(building in heavy atoms isn’t my first option at the moment,. )


Thank you very much

Regards

Kristof


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Medical Center



The future of medicine, today.




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Re: [ccp4bb] Structure solution - hexapeptide

[George Sheldrick]

A particularly useful command line option in SHELXT for such cases is 
-L15 to try all trigonal and hexagonal space groups. SHELXT is included 
in recent CCP4 distributions and is also available with documentation 
from shelx.uni-goettingen.de


George

On 02.08.2018 15:53, Aaron Finke wrote:

Hi Kristof,

Direct methods/charge flipping won’t work if your data quality is poor 
below ~1Å. Take a look at your Rmerge, as Jeffrey mentioned. Small 
molecule crystals have more stringent standards for data quality. If 
your Rmerge is 50% or more, it’s probably just noise and not useful 
for direct methods.


If SHELXT doesn’t work on the full data set, try cutting the data down 
to 0.9 Å or even 1 Å. I have had limited success doing that on some 
particularly bad data sets.  Alternatively, run SHELXD at full 
resolution indefinitely (NTRY 0) until it finds a solution. It could 
take days, but you may get something.


As a last resort, if you think this hexapeptide may have any secondary 
structure, you may want to try ab initio MR with ARCIMBOLDO.


Aaron

--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu 

On Aug 2, 2018, at 8:53 AM, Kristof Van Hecke 
mailto:kristofrg.vanhe...@gmail.com>> 
wrote:


Dear all,

I’m trying to solve a structure of a (modified) hexapeptide:
- inhouse (very decent) data up to 0.8 Angstrom
- average redundancy = 10
- according to the Matthews coefficient of 1.88 with 34.77 %solvent, 
there should be 3 Nmol/asym

- ‘large’ unit cell of about a=54, b=54, c=12
- SG = P3(1)12 or P3(2)12

As there’s (presumably) only C, H, N and O in the structure, I’m not 
able to solve this via Direct Methods, Charge Flipping etc,.
Trying MR (with Phaser) doesn’t give any results either, as there’s 
hardly any homologous models



Has anyone encountered a similar problem please, and could provide 
any possible solutions?

(building in heavy atoms isn’t my first option at the moment,. )


Thank you very much

Regards

Kristof


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--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry
University of Goettingen
Tammannstr.  4
D37077 Goettingen
Germany
Tel: +49 551 3933021 or +49 5594 227312




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Re: [ccp4bb] Structure solution - hexapeptide

[Mark J. van Raaij]

When I was at Santiago de Composrela Univ., we have had success with the CCP4 
program ACORN even at around 1.2 Å resolution. Also peptides, no heavy 
atoms.Didn't do this myself though I have to admit, but could put you in 
contact with the people who did.
Mark J van RaaijCNB-CSICwwwuser.csic.es/~mjvanraaij

Mark J van RaaijCNB-CSICwwwuser.csic.es/~mjvanraaij
 Original message From: Kristof Van Hecke 
 Date: 02/08/2018  14:53  (GMT+01:00) To: 
CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Structure solution - hexapeptide 
Dear all, 

I’m trying to solve a structure of a (modified) hexapeptide:
- inhouse (very decent) data up to 0.8 Angstrom
- average redundancy = 10 
- according to the Matthews coefficient of 1.88 with 34.77 %solvent, there 
should be 3 Nmol/asym
- ‘large’ unit cell of about a=54, b=54, c=12 
- SG = P3(1)12 or P3(2)12 

As there’s (presumably) only C, H, N and O in the structure, I’m not able to 
solve this via Direct Methods, Charge Flipping etc,. 
Trying MR (with Phaser) doesn’t give any results either, as there’s hardly any 
homologous models


Has anyone encountered a similar problem please, and could provide any possible 
solutions? 
(building in heavy atoms isn’t my first option at the moment,. )


Thank you very much

Regards

Kristof 


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1




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Re: [ccp4bb] Structure solution - hexapeptide

[Aaron Finke]

Hi Kristof,

Direct methods/charge flipping won’t work if your data quality is poor below 
~1Å. Take a look at your Rmerge, as Jeffrey mentioned. Small molecule crystals 
have more stringent standards for data quality. If your Rmerge is 50% or more, 
it’s probably just noise and not useful for direct methods.

If SHELXT doesn’t work on the full data set, try cutting the data down to 0.9 Å 
or even 1 Å. I have had limited success doing that on some particularly bad 
data sets.  Alternatively, run SHELXD at full resolution indefinitely (NTRY 0) 
until it finds a solution. It could take days, but you may get something.

As a last resort, if you think this hexapeptide may have any secondary 
structure, you may want to try ab initio MR with ARCIMBOLDO.

Aaron

--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu

On Aug 2, 2018, at 8:53 AM, Kristof Van Hecke 
mailto:kristofrg.vanhe...@gmail.com>> wrote:

Dear all,

I’m trying to solve a structure of a (modified) hexapeptide:
- inhouse (very decent) data up to 0.8 Angstrom
- average redundancy = 10
- according to the Matthews coefficient of 1.88 with 34.77 %solvent, there 
should be 3 Nmol/asym
- ‘large’ unit cell of about a=54, b=54, c=12
- SG = P3(1)12 or P3(2)12

As there’s (presumably) only C, H, N and O in the structure, I’m not able to 
solve this via Direct Methods, Charge Flipping etc,.
Trying MR (with Phaser) doesn’t give any results either, as there’s hardly any 
homologous models


Has anyone encountered a similar problem please, and could provide any possible 
solutions?
(building in heavy atoms isn’t my first option at the moment,. )


Thank you very much

Regards

Kristof


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Re: [ccp4bb] Structure solution - hexapeptide

[Jeffrey, Philip D.]

"Very decent" means different things to different people.  Is your Rmerge < 20% 
in the 0.84 Å shell ?  If so that's a small molecule quality data set and 
something like that should solve relatively straightforwardly with e.g. SHELXT. 
 However the classical program would be SHELXD and perhaps a CPU day or three 
(speaking from recent experience with data that did not go quite as far).

If it doesn't solve, then there's probably something interesting about the 
data.  P3x 1 2 is a rare space group in both protein world and small molecule 
world.  I would suggest checking for signs of twinning and dropping back to 
point group 3.

You should not be surprised  if your bulk solvent content is almost 
non-existent and you have 5 molecules in the asymmetric unit.

Cheers
Phil Jeffrey
Princeton

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kristof Van 
Hecke [kristofrg.vanhe...@gmail.com]
Sent: Thursday, August 02, 2018 8:53 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Structure solution - hexapeptide

Dear all,

I’m trying to solve a structure of a (modified) hexapeptide:
- inhouse (very decent) data up to 0.8 Angstrom
- average redundancy = 10
- according to the Matthews coefficient of 1.88 with 34.77 %solvent, there 
should be 3 Nmol/asym
- ‘large’ unit cell of about a=54, b=54, c=12
- SG = P3(1)12 or P3(2)12

As there’s (presumably) only C, H, N and O in the structure, I’m not able to 
solve this via Direct Methods, Charge Flipping etc,.
Trying MR (with Phaser) doesn’t give any results either, as there’s hardly any 
homologous models


Has anyone encountered a similar problem please, and could provide any possible 
solutions?
(building in heavy atoms isn’t my first option at the moment,. )


Thank you very much

Regards

Kristof


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1



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Re: [ccp4bb] Structure solution - hexapeptide

[Christopher Squire]

Hi agree,

Try SHELXT. I have just solved several tetrapeptides, linear and cyclic, and 
with up to 5 molecules per au. Shelxt solved them exceptionally easily at 
0.77-0.89 angstrom resolution. Most of the oxygens and nitrogens were picked by 
the software correctly. You know you have the right solution if you have the 
correct form of the amino acids, D- or L-form - assuming you know the sequence! 
Does a really good job of picking the space group too.

Good luck!

Chris.


From: CCP4 bulletin board  on behalf of 
graeme.win...@diamond.ac.uk 
Sent: 03 August 2018 1:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Structure solution - hexapeptide

Kristof,

Just checking - have you tried SHELXT? Feeding in umerged HKL file

I appreciate that this is direct methods but the tool is pretty powerful

Also: you could find processing the data with different tools helps…

Best wishes Graeme (who dabbles in “small" molecule stuff, too)

> On 2 Aug 2018, at 08:53, Kristof Van Hecke  
> wrote:
>
> Dear all,
>
> I’m trying to solve a structure of a (modified) hexapeptide:
> - inhouse (very decent) data up to 0.8 Angstrom
> - average redundancy = 10
> - according to the Matthews coefficient of 1.88 with 34.77 %solvent, there 
> should be 3 Nmol/asym
> - ‘large’ unit cell of about a=54, b=54, c=12
> - SG = P3(1)12 or P3(2)12
>
> As there’s (presumably) only C, H, N and O in the structure, I’m not able to 
> solve this via Direct Methods, Charge Flipping etc,.
> Trying MR (with Phaser) doesn’t give any results either, as there’s hardly 
> any homologous models
>
>
> Has anyone encountered a similar problem please, and could provide any 
> possible solutions?
> (building in heavy atoms isn’t my first option at the moment,. )
>
>
> Thank you very much
>
> Regards
>
> Kristof
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1


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Re: [ccp4bb] Structure solution - hexapeptide

[graeme.win...@diamond.ac.uk]

Kristof,

Just checking - have you tried SHELXT? Feeding in umerged HKL file

I appreciate that this is direct methods but the tool is pretty powerful

Also: you could find processing the data with different tools helps… 

Best wishes Graeme (who dabbles in “small" molecule stuff, too) 

> On 2 Aug 2018, at 08:53, Kristof Van Hecke  
> wrote:
> 
> Dear all, 
> 
> I’m trying to solve a structure of a (modified) hexapeptide:
> - inhouse (very decent) data up to 0.8 Angstrom
> - average redundancy = 10 
> - according to the Matthews coefficient of 1.88 with 34.77 %solvent, there 
> should be 3 Nmol/asym
> - ‘large’ unit cell of about a=54, b=54, c=12 
> - SG = P3(1)12 or P3(2)12 
> 
> As there’s (presumably) only C, H, N and O in the structure, I’m not able to 
> solve this via Direct Methods, Charge Flipping etc,. 
> Trying MR (with Phaser) doesn’t give any results either, as there’s hardly 
> any homologous models
> 
> 
> Has anyone encountered a similar problem please, and could provide any 
> possible solutions? 
> (building in heavy atoms isn’t my first option at the moment,. )
> 
> 
> Thank you very much
> 
> Regards
> 
> Kristof 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1


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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 
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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[ccp4bb] Structure solution - hexapeptide

[Kristof Van Hecke]

Dear all, 

I’m trying to solve a structure of a (modified) hexapeptide:
- inhouse (very decent) data up to 0.8 Angstrom
- average redundancy = 10 
- according to the Matthews coefficient of 1.88 with 34.77 %solvent, there 
should be 3 Nmol/asym
- ‘large’ unit cell of about a=54, b=54, c=12 
- SG = P3(1)12 or P3(2)12 

As there’s (presumably) only C, H, N and O in the structure, I’m not able to 
solve this via Direct Methods, Charge Flipping etc,. 
Trying MR (with Phaser) doesn’t give any results either, as there’s hardly any 
homologous models


Has anyone encountered a similar problem please, and could provide any possible 
solutions? 
(building in heavy atoms isn’t my first option at the moment,. )


Thank you very much

Regards

Kristof 


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