[ccp4bb] Fwd: [ccp4bb] Calculation of generalised R-factor?

[Dirk Kostrewa]

Dear CCP4ers,

many thanks to all of you who replied to my request!

I wish you a Merry Christmas and a Happy New Year!

Dirk.


 Forwarded Message 
Subject:[ccp4bb] Calculation of generalised R-factor?
Date:   Tue, 20 Dec 2016 14:47:00 +0100
From:   Dirk Kostrewa 
Reply-To:   Dirk Kostrewa 
To: CCP4BB@JISCMAIL.AC.UK



Dear CCP4ers,

I want to check the validity of the refinement of anisotropic B-factors
vs. TLS + isototropic B-factors using the Hamilton R-value ratio test as
described in Ethan Merritt's paper "To B or not to B", Acta Cryst. D,
Vol 68, pp 468. This test uses the generalised R-factors (assuming unit
weights), RG=(Sum(Fo-Fc)^2/Sum(Fo)^2)^1/2. Although Hamilton wrote that
at the end of refinement, one could also use the similar ratio of the
usual R-factors, I really would like to check the ratio of the RG-values
after refinement. As far as I can see, this value is not reported by the
usual refinement programs.

Is there a program that reads an mtz file with Fo and refined Fc and
just calculates RG?

Best regards,

Dirk.

--

***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***


--

***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***

Re: [ccp4bb] Calculation of generalised R-factor?

[Ethan Merritt]

On Tuesday, 20 December 2016 10:28:44 PM Pavel Afonine wrote:
> Hi Dirk,
> 
> 
> I want to check the validity of the refinement of anisotropic B-factors vs.
> > TLS + isototropic B-factors using the Hamilton R-value ratio test as
> > described in Ethan Merritt's paper "To B or not to B", Acta Cryst. D, Vol
> > 68, pp 468. This test uses the generalised R-factors (assuming unit
> > weights), RG=(Sum(Fo-Fc)^2/Sum(Fo)^2)^1/2. Although Hamilton wrote that
> > at the end of refinement, one could also use the similar ratio of the usual
> > R-factors, I really would like to check the ratio of the RG-values after
> > refinement. As far as I can see, this value is not reported by the usual
> > refinement programs.
> 
> 
> 
> R factor is a global metric that, if considered alone, is not going to
> answer your question. Best is to consider all three:
> 
> 1) Rfree;
> 2) Rfree-Rwork;

> 3) Meaningfulness of refined TLS matrices. Note, as we discovered and
> documented recently, results of TLS refinements (TLS matrices) are
> nonsensical in 85% of PDB entries (yes, eighty-five are bad, believe it or 
> not!):

> From deep TLS validation to ensembles of atomic models built from elemental
> motions. A. Urzhumtsev, P. V. Afonine, A. H. Van Benschoten, J. S. Fraser and 
> P. D.
> Adams. Acta Cryst. (2015). D71, 1668-1683.

As you know, I disagree on this point.

The Urzhumtsev et al classification of "nonsensical" TLS matrices includes
many that make lots of sense but do not happen to describe a perfectly rigid 
body.
That's OK, because proteins are not perfectly rigid bodies.
The TLS models are useful approximations that capture 
essential features of a messy ensemble of protein atoms. 
Complaining that in practice the refined TLS values deviate from those that
would hypothetically be obtained from fitting perfectly rigid groups is beside
the point.

Of course some refinements really are bad and some models really are
unreasonable.  Validation tests can help you catch these and fix your
model or refinement.  But a validation criterion that is so strict that
it labels 85% of all protein refinements as "nonsensical" is not a very
useful test. 

> 
> I'd say if you pass "1-3)" you are more than good. If still in doubt, you
> can make an extra effort and do what's described in
> 
> Validation of crystallographic models containing TLS or other descriptions
> of anisotropy
> F. Zucker, P. C. Champ and E. A. Merritt
> Acta Cryst. (2010). D66, 889-900
> 
> which may reveal extra troubles.

Note that the primary validation test described in the Zucker paper
(we called it SKITTLS) is a check for the pairwise consistency of 
adjacent TLS groups.   It might flag as inconsistent two adjacent
groups that both pass the criteria in Urzhumtsev et al, or conversely
it might rate two groups that fail the Urzhumtsev criteria as being
nevertheless consistent in their description of atoms they jointly
apply to.

Ethan

> All the best,
> Pavel

-- 
Ethan A Merritt, Dept of Biochemistry
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

[ccp4bb] Dna model

[Anindito Sen]

Dear All, 

I want to built a 3d model of DNA to be used to show the path of genome 
transfer in a tailed phage electron density map,  during infection. 

It will be helpful if The model can be generated as an mrc  file or of a 
similar file format. 

Any suggestions? 

Thanks 

Andy

Sent from my iPhone

Re: [ccp4bb] Calculation of generalised R-factor?

[Pavel Afonine]

Hi Dirk,


I want to check the validity of the refinement of anisotropic B-factors vs.
> TLS + isototropic B-factors using the Hamilton R-value ratio test as
> described in Ethan Merritt's paper "To B or not to B", Acta Cryst. D, Vol
> 68, pp 468. This test uses the generalised R-factors (assuming unit
> weights), RG=(Sum(Fo-Fc)^2/Sum(Fo)^2)^1/2. Although Hamilton wrote that
> at the end of refinement, one could also use the similar ratio of the usual
> R-factors, I really would like to check the ratio of the RG-values after
> refinement. As far as I can see, this value is not reported by the usual
> refinement programs.



R factor is a global metric that, if considered alone, is not going to
answer your question. Best is to consider all three:

1) Rfree;
2) Rfree-Rwork;
3) Meaningfulness of refined TLS matrices. Note, as we discovered and
documented recently, results of TLS refinements (TLS matrices) are
nonsensical in 85% of PDB entries (yes, eighty-five are bad, believe it or
not!):

>From deep TLS validation to ensembles of atomic models built from elemental
motions
A. Urzhumtsev, P. V. Afonine, A. H. Van Benschoten, J. S. Fraser and P. D.
Adams
Acta Cryst. (2015). D71, 1668-1683.

I'd say if you pass "1-3)" you are more than good. If still in doubt, you
can make an extra effort and do what's described in

Validation of crystallographic models containing TLS or other descriptions
of anisotropy
F. Zucker, P. C. Champ and E. A. Merritt
Acta Cryst. (2010). D66, 889-900

which may reveal extra troubles.

All the best,
Pavel

Re: [ccp4bb] Atom clashes in active site?

[Andrew Marshall]

Hi Scott,

That would be great if you have some references handy?
Thanks very much,

Andrew Marshall
PhD Candidate
Laboratory of Protein Crystallography
Dept. of Molecular and Cellular Biology
School of Biological Sciences
The University of Adelaide

On Wed, Dec 21, 2016 at 1:48 AM, Scott Horowitz  wrote:

> Hi Andrew,
>
> Based on the atoms and distances you are mentioning, these don't sound
> like steric clashes, but like a chalcogen bond between the S and O atoms,
> and CH...O hydrogen bonds between the O and CH3. These are common and
> well-accepted interactions, but unfortunately aren't usually treated as
> such by refinement programs. Let me know if you want references for these
> interaction types.
>
> Scott
>
> On Mon, Dec 19, 2016 at 8:48 PM, Andrew Marshall <
> andrew.c.marsh...@adelaide.edu.au> wrote:
>
>> Hi all,
>>
>> Thank you for your suggestions. I tried the pdb file edit (making the
>> offending atoms of both the ligand and the protein 'B' altconf), but it
>> didn't seem to make any difference to their positions after a single round
>> of refinement..?
>> The atoms in the active site concern two acetyl groups - one from the
>> substrate, acetyl-CoA, and the other from an acetylated cysteine in the
>> protein - that I believe are poised ready for a condensation reaction. The
>> closest contacts are between S and O(carbonyl) atoms (2.9A) and O and CH3
>> (3.1A), but going off the density, I think these should be closer (more
>> like 2.8 or 2.7A). It may be that I've trapped another reaction
>> intermediate (which would be cool), but I don't think that fits the density
>> quite as well. Any thoughts/ideas?
>>
>> Thanks,
>>
>> Andrew Marshall
>> PhD Candidate
>> Laboratory of Protein Crystallography
>> Dept. of Molecular and Cellular Biology
>> School of Biological Sciences
>> The University of Adelaide
>>
>> On Tue, Dec 20, 2016 at 12:09 AM, Scott Horowitz 
>> wrote:
>>
>>> Hi Andrew,
>>>
>>> I'm curious- what are the atoms that are clashing? I worked on this sort
>>> of thing back in my Ph.D., and so I might have some useful tidbits if, for
>>> example, the S is clashing with a carbon of some sort.
>>>
>>> Thanks,
>>> Scott
>>>
>>> On Mon, Dec 19, 2016 at 12:39 AM, Andrew Marshall <
>>> andrew.c.marsh...@adelaide.edu.au> wrote:
>>>
 Hi all,

 I have a structure of a condensing enzyme with substrate bound. The
 active site is very tight, requiring some of the substrate atoms to clash
 with a catalytic cysteine. This means that although the substrate fits the
 density nicely upon manual real-space refinement, phenix recognises the
 clash, resulting in the displacement of substrate atoms so that they are
 outside the density. I can mostly fix this by using distance restraints,
 but I'd rather allow it to refine in a less biased manner, but ignore the
 clash. Is this a acceptable way forward? If so, is there a parameter I can
 edit to tell phenix to ignore clashes between these specific atoms?

 Thanks,

 Andrew Marshall
 PhD Candidate
 Laboratory of Protein Crystallography
 Dept. of Molecular and Cellular Biology
 School of Biological Sciences
 The University of Adelaide


>>>
>>>
>>> --
>>> Scott Horowitz, Ph.D.
>>> Postdoctoral Fellow
>>>
>>> University of Michigan
>>> Department of Molecular, Cellular, and Developmental Biology
>>> Bardwell lab
>>> 830 N. University Ave, Room 4007
>>> Ann Arbor, MI 48109
>>> phone: 734-647-6683
>>> fax: 734-615-4226
>>>
>>
>>
>
>
> --
> Scott Horowitz, Ph.D.
> Postdoctoral Fellow
>
> University of Michigan
> Department of Molecular, Cellular, and Developmental Biology
> Bardwell lab
> 830 N. University Ave, Room 4007
> Ann Arbor, MI 48109
> phone: 734-647-6683
> fax: 734-615-4226
>

Re: [ccp4bb] Atom clashes in active site?

[Andrew Marshall]

Hi Pavel,

That worked a treat! Thanks again for your help,

Andrew Marshall
PhD Candidate
Laboratory of Protein Crystallography
Dept. of Molecular and Cellular Biology
School of Biological Sciences
The University of Adelaide

On Tue, Dec 20, 2016 at 3:18 PM, Pavel Afonine  wrote:

> Hi Andrew,
>
> yes, exactly as you describe: set distance_ideal to a meaningful value
> (approx. distance between density peaks, doesn't have to be very accurate),
> and set sigma to some large number, say 1 or so.
>
> Pavel
>
>
> On Mon, Dec 19, 2016 at 7:40 PM, Andrew Marshall <
> andrew.c.marsh...@adelaide.edu.au> wrote:
>
>> Hi Pavel,
>>
>> To define a weak bond, would you use "geometry_restraints.edits { ...
>> bond {... " , and just set a rough distance_ideal and a very high sigma
>> (like say 5A)?
>> Or are you referring to something different?
>>
>> Andrew Marshall
>> PhD Candidate
>> Laboratory of Protein Crystallography
>> Dept. of Molecular and Cellular Biology
>> School of Biological Sciences
>> The University of Adelaide
>>
>> On Tue, Dec 20, 2016 at 1:28 PM, Pavel Afonine 
>> wrote:
>>
>>> Hi Andrew,
>>>
>>> you can define a weak bond between clashing atoms which will disable
>>> repulsion. A weak bond should not introduce any bias.
>>>
>>> Pavel
>>>
>>> On Sun, Dec 18, 2016 at 9:39 PM, Andrew Marshall <
>>> andrew.c.marsh...@adelaide.edu.au> wrote:
>>>
 Hi all,

 I have a structure of a condensing enzyme with substrate bound. The
 active site is very tight, requiring some of the substrate atoms to clash
 with a catalytic cysteine. This means that although the substrate fits the
 density nicely upon manual real-space refinement, phenix recognises the
 clash, resulting in the displacement of substrate atoms so that they are
 outside the density. I can mostly fix this by using distance restraints,
 but I'd rather allow it to refine in a less biased manner, but ignore the
 clash. Is this a acceptable way forward? If so, is there a parameter I can
 edit to tell phenix to ignore clashes between these specific atoms?

 Thanks,

 Andrew Marshall
 PhD Candidate
 Laboratory of Protein Crystallography
 Dept. of Molecular and Cellular Biology
 School of Biological Sciences
 The University of Adelaide


>>>
>>
>

Re: [ccp4bb] Ubuntu Mate for Pymol and Coot 3D

[Xiao Lei]

Thanks Nicolas and Paul!  I am using active 3D with Quadro 5000 graphics
card and Nvidia 3D kit in Fedora system (Fedora 23). Everytime I update the
kernel (dnf update), I lost the 3D in both the updated new kernel and the
old kernel, I have to reinstall the driver again, but can not make every
reinstallation to the newest kernel successful. It seems Ubuntu Mate and
Xubuntu will be very good alternatives.

On Tue, Dec 20, 2016 at 8:33 AM, Nicolas FOOS  wrote:

> Dear Paul,
>
> I am currently not working under Ubuntu OS, so I can't try your fix.
>
> But if my memory is still good, it was exactly the problem (the dynamic
> menus). And I am sure that some ccp4bb reader will be happy to find and try
> this solution.
>
> Thank you.
>
> Nicolas
>
> Nicolas Foos
> PhD
> Structural Biology Group
> European Synchrotron Radiation Facility (E.S.R.F)
> 71, avenue des Martyrs
> CS 40220
> 38043 GRENOBLE Cedex 9
> +33 (0)6 76 88 14 87
> +33 (0)4 76 88 45 19
>
> On 20/12/2016 17:26, Paul Emsley wrote:
>
>> On 20/12/16 16:21, Nicolas FOOS wrote:
>>
>>> Dear Lei,
>>>
>>> I already try :
>>>
>>> Ubuntu Mate (no problem), Xubuntu (no problem), Ubuntu (standard) (I had
>>> problem with coot due to unity desktop).
>>>
>>
>> A shot in the dark, but maybe your problem is with dynamic menus?
>>
>> If so, try this:
>>
>>
>> $ export UBUNTU_MENUPROXY=0
>>
>> before running coot.
>>
>>
>> Paul
>>
>

Re: [ccp4bb] Ubuntu Mate for Pymol and Coot 3D

[Nicolas FOOS]

Dear Paul,

I am currently not working under Ubuntu OS, so I can't try your fix.

But if my memory is still good, it was exactly the problem (the dynamic 
menus). And I am sure that some ccp4bb reader will be happy to find and 
try this solution.


Thank you.

Nicolas

Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19

On 20/12/2016 17:26, Paul Emsley wrote:

On 20/12/16 16:21, Nicolas FOOS wrote:

Dear Lei,

I already try :

Ubuntu Mate (no problem), Xubuntu (no problem), Ubuntu (standard) (I 
had problem with coot due to unity desktop).


A shot in the dark, but maybe your problem is with dynamic menus?

If so, try this:


$ export UBUNTU_MENUPROXY=0

before running coot.


Paul

Re: [ccp4bb] Ubuntu Mate for Pymol and Coot 3D

[Paul Emsley]

On 20/12/16 16:21, Nicolas FOOS wrote:

Dear Lei,

I already try :

Ubuntu Mate (no problem), Xubuntu (no problem), Ubuntu (standard) (I 
had problem with coot due to unity desktop).


A shot in the dark, but maybe your problem is with dynamic menus?

If so, try this:


$ export UBUNTU_MENUPROXY=0

before running coot.


Paul

Re: [ccp4bb] Ubuntu Mate for Pymol and Coot 3D

[Nicolas FOOS]

Dear Lei,

I already try :

Ubuntu Mate (no problem), Xubuntu (no problem), Ubuntu (standard) (I had 
problem with coot due to unity desktop).


Also alternatively : Mageia5 (no problem), Manjaro (python3 as default 
in environment create some difficulty for several Macromolecular X-ray 
soft).


In my opinion your choice is one of the more reliable.

Most of the time the problem doesn't come form the OS, but more from the 
interaction between the OS and your graphic-card.


And in your case that's precisely what is critical (since you want 3D in 
a good condition). Ubuntu works well with numbers of hardware 
configuration especially if you activate the proprietary repository in 
the packet manager.


I used for a long time Xubuntu without any issues and was very happy 
with it. CCP4 and other soft are perfectly packed for this OS.


HTH

Nicolas

Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19

On 20/12/2016 01:05, Xiao Lei wrote:

Hi All,

I am asking if anyone used Ubuntu Mate operating system and is this 
system good for Pymol and Coot 3D?

Re: [ccp4bb] Atom clashes in active site?

[Scott Horowitz]

Hi Andrew,

Based on the atoms and distances you are mentioning, these don't sound like
steric clashes, but like a chalcogen bond between the S and O atoms, and
CH...O hydrogen bonds between the O and CH3. These are common and
well-accepted interactions, but unfortunately aren't usually treated as
such by refinement programs. Let me know if you want references for these
interaction types.

Scott

On Mon, Dec 19, 2016 at 8:48 PM, Andrew Marshall <
andrew.c.marsh...@adelaide.edu.au> wrote:

> Hi all,
>
> Thank you for your suggestions. I tried the pdb file edit (making the
> offending atoms of both the ligand and the protein 'B' altconf), but it
> didn't seem to make any difference to their positions after a single round
> of refinement..?
> The atoms in the active site concern two acetyl groups - one from the
> substrate, acetyl-CoA, and the other from an acetylated cysteine in the
> protein - that I believe are poised ready for a condensation reaction. The
> closest contacts are between S and O(carbonyl) atoms (2.9A) and O and CH3
> (3.1A), but going off the density, I think these should be closer (more
> like 2.8 or 2.7A). It may be that I've trapped another reaction
> intermediate (which would be cool), but I don't think that fits the density
> quite as well. Any thoughts/ideas?
>
> Thanks,
>
> Andrew Marshall
> PhD Candidate
> Laboratory of Protein Crystallography
> Dept. of Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide
>
> On Tue, Dec 20, 2016 at 12:09 AM, Scott Horowitz 
> wrote:
>
>> Hi Andrew,
>>
>> I'm curious- what are the atoms that are clashing? I worked on this sort
>> of thing back in my Ph.D., and so I might have some useful tidbits if, for
>> example, the S is clashing with a carbon of some sort.
>>
>> Thanks,
>> Scott
>>
>> On Mon, Dec 19, 2016 at 12:39 AM, Andrew Marshall <
>> andrew.c.marsh...@adelaide.edu.au> wrote:
>>
>>> Hi all,
>>>
>>> I have a structure of a condensing enzyme with substrate bound. The
>>> active site is very tight, requiring some of the substrate atoms to clash
>>> with a catalytic cysteine. This means that although the substrate fits the
>>> density nicely upon manual real-space refinement, phenix recognises the
>>> clash, resulting in the displacement of substrate atoms so that they are
>>> outside the density. I can mostly fix this by using distance restraints,
>>> but I'd rather allow it to refine in a less biased manner, but ignore the
>>> clash. Is this a acceptable way forward? If so, is there a parameter I can
>>> edit to tell phenix to ignore clashes between these specific atoms?
>>>
>>> Thanks,
>>>
>>> Andrew Marshall
>>> PhD Candidate
>>> Laboratory of Protein Crystallography
>>> Dept. of Molecular and Cellular Biology
>>> School of Biological Sciences
>>> The University of Adelaide
>>>
>>>
>>
>>
>> --
>> Scott Horowitz, Ph.D.
>> Postdoctoral Fellow
>>
>> University of Michigan
>> Department of Molecular, Cellular, and Developmental Biology
>> Bardwell lab
>> 830 N. University Ave, Room 4007
>> Ann Arbor, MI 48109
>> phone: 734-647-6683
>> fax: 734-615-4226
>>
>
>


-- 
Scott Horowitz, Ph.D.
Postdoctoral Fellow

University of Michigan
Department of Molecular, Cellular, and Developmental Biology
Bardwell lab
830 N. University Ave, Room 4007
Ann Arbor, MI 48109
phone: 734-647-6683
fax: 734-615-4226

Re: [ccp4bb] Calculation of generalised R-factor?

[Robbie Joosten]

Hi Dirk,

You need the "Overall weighted R2 factor". The reference for the paper I
meant is
http://onlinelibrary.wiley.com/doi/10.1107/S056773947293/abstract

Cheers,
Robbie

> -Original Message-
> From: Dirk Kostrewa [mailto:kostr...@genzentrum.lmu.de]
> Sent: Tuesday, December 20, 2016 15:46
> To: Robbie Joosten ; CCP4BB
> 
> Subject: Re: [ccp4bb] Calculation of generalised R-factor?
> 
> Dear Robbie,
> 
> 
> thanks for your reply. According to the REFMAC5 manual, the weighted R-
> factor is just:
> 
> 
> weighted R factor = sum w ||Fo-|Fc||/sum w |Fo|
> 
> So, unfortunately, it is not the generalised R-factor.
> 
> Do you have a reference for that follow-up paper?
> 
> PDB_REDO does too much for my purpose ...
> 
> Cheers,
> 
> Dirk.
> 
> 
> 
> On 20.12.2016 15:37, Robbie Joosten wrote:
> 
> 
>   The value for the Hamilton test is written by Refmac as the weighted
> R-factor. There was a follow-up paper that showed that you shouldn’t use
> the normal R-factor for the Hamilton test.
> 
> 
> 
>   PDB_REDO does the Hamilton test automatically, but you can also
> feed two Refmac logfiles to the bselect program to do your own Hamilton
> test.
> 
> 
> 
>   Cheers,
> 
>   Robbie
> 
> 
> 
>   Sent from my Windows 10 phone
> 
> 
> 
>   Van: Keller, Jacob 
>   Verzonden: dinsdag 20 december 2016 14:23
>   Aan: CCP4BB@JISCMAIL.AC.UK 
>   Onderwerp: Re: [ccp4bb] Calculation of generalised R-factor?
> 
> 
> 
> 
>   I'd be interested as well.
> 
>   JPK
> 
>   -Original Message-
>   From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
> Behalf Of Dirk Kostrewa
>   Sent: Tuesday, December 20, 2016 8:47 AM
>   To: CCP4BB@JISCMAIL.AC.UK 
>   Subject: [ccp4bb] Calculation of generalised R-factor?
> 
>   Dear CCP4ers,
> 
>   I want to check the validity of the refinement of anisotropic
B-factors
> vs. TLS + isototropic B-factors using the Hamilton R-value ratio test as
> described in Ethan Merritt's paper "To B or not to B", Acta Cryst. D, Vol
68,
> pp 468. This test uses the generalised R-factors (assuming unit weights),
> RG=(Sum(Fo-Fc)^2/Sum(Fo)^2)^1/2. Although Hamilton wrote that at the
> end of refinement, one could also use the similar ratio of the usual
R-factors,
> I really would like to check the ratio of the RG-values after refinement.
As far
> as I can see, this value is not reported by the usual refinement programs.
> 
>   Is there a program that reads an mtz file with Fo and refined Fc and
> just calculates RG?
> 
>   Best regards,
> 
>   Dirk.
> 
>   --
> 
>   ***
>   Dirk Kostrewa
>   Gene Center Munich, A5.07
>   Department of Biochemistry
>   Ludwig-Maximilians-Universität München
>   Feodor-Lynen-Str. 25
>   D-81377 Munich
>   Germany
>   Phone:  +49-89-2180-76845
>   Fax:+49-89-2180-76998
>   E-mail: kostr...@genzentrum.lmu.de
> 
>   WWW:www.genzentrum.lmu.de
> 
>   ***
> 
> 
> 
> --
> 
> ***
> Dirk Kostrewa
> Gene Center Munich, A5.07
> Department of Biochemistry
> Ludwig-Maximilians-Universität München
> Feodor-Lynen-Str. 25
> D-81377 Munich
> Germany
> Phone:  +49-89-2180-76845
> Fax:+49-89-2180-76998
> E-mail: kostr...@genzentrum.lmu.de
> 
> WWW:www.genzentrum.lmu.de 
> ***

Re: [ccp4bb] Calculation of generalised R-factor?

[Dirk Kostrewa]

Dear Robbie,

thanks for your reply. According to the REFMAC5 manual, the weighted 
R-factor is just:


weighted R factor = sum w ||F_o -|F_c ||/sum w |F_o |

So, unfortunately, it is not the generalised R-factor.

Do you have a reference for that follow-up paper?

PDB_REDO does too much for my purpose ...

Cheers,

Dirk.


On 20.12.2016 15:37, Robbie Joosten wrote:


The value for the Hamilton test is written by Refmac as the weighted 
R-factor. There was a follow-up paper that showed that you shouldn’t 
use the normal R-factor for the Hamilton test.


PDB_REDO does the Hamilton test automatically, but you can also feed 
two Refmac logfiles to the bselect program to do your own Hamilton test.


Cheers,

Robbie

Sent from my Windows 10 phone

*Van: *Keller, Jacob 
*Verzonden: *dinsdag 20 december 2016 14:23
*Aan: *CCP4BB@JISCMAIL.AC.UK 
*Onderwerp: *Re: [ccp4bb] Calculation of generalised R-factor?

I'd be interested as well.

JPK

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Dirk Kostrewa

Sent: Tuesday, December 20, 2016 8:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Calculation of generalised R-factor?

Dear CCP4ers,

I want to check the validity of the refinement of anisotropic 
B-factors vs. TLS + isototropic B-factors using the Hamilton R-value 
ratio test as described in Ethan Merritt's paper "To B or not to B", 
Acta Cryst. D, Vol 68, pp 468. This test uses the generalised 
R-factors (assuming unit weights), RG=(Sum(Fo-Fc)^2/Sum(Fo)^2)^1/2. 
Although Hamilton wrote that at the end of refinement, one could also 
use the similar ratio of the usual R-factors, I really would like to 
check the ratio of the RG-values after refinement. As far as I can 
see, this value is not reported by the usual refinement programs.


Is there a program that reads an mtz file with Fo and refined Fc and 
just calculates RG?


Best regards,

Dirk.

--

***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: kostr...@genzentrum.lmu.de
WWW: www.genzentrum.lmu.de 
***


--

***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***

Re: [ccp4bb] Calculation of generalised R-factor?

[Robbie Joosten]

The value for the Hamilton test is written by Refmac as the weighted R-factor. 
There was a follow-up paper that showed that you shouldn’t use the normal 
R-factor for the Hamilton test.



PDB_REDO does the Hamilton test automatically, but you can also feed two Refmac 
logfiles to the bselect program to do your own Hamilton test.



Cheers,

Robbie



Sent from my Windows 10 phone



Van: Keller, Jacob
Verzonden: dinsdag 20 december 2016 14:23
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: Re: [ccp4bb] Calculation of generalised R-factor?



I'd be interested as well.

JPK

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk 
Kostrewa
Sent: Tuesday, December 20, 2016 8:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Calculation of generalised R-factor?

Dear CCP4ers,

I want to check the validity of the refinement of anisotropic B-factors vs. TLS 
+ isototropic B-factors using the Hamilton R-value ratio test as described in 
Ethan Merritt's paper "To B or not to B", Acta Cryst. D, Vol 68, pp 468. This 
test uses the generalised R-factors (assuming unit weights), 
RG=(Sum(Fo-Fc)^2/Sum(Fo)^2)^1/2. Although Hamilton wrote that at the end of 
refinement, one could also use the similar ratio of the usual R-factors, I 
really would like to check the ratio of the RG-values after refinement. As far 
as I can see, this value is not reported by the usual refinement programs.

Is there a program that reads an mtz file with Fo and refined Fc and just 
calculates RG?

Best regards,

Dirk.

--

***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***

Re: [ccp4bb] Calculation of generalised R-factor?

[Keller, Jacob]

I'd be interested as well.

JPK

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk 
Kostrewa
Sent: Tuesday, December 20, 2016 8:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Calculation of generalised R-factor?

Dear CCP4ers,

I want to check the validity of the refinement of anisotropic B-factors vs. TLS 
+ isototropic B-factors using the Hamilton R-value ratio test as described in 
Ethan Merritt's paper "To B or not to B", Acta Cryst. D, Vol 68, pp 468. This 
test uses the generalised R-factors (assuming unit weights), 
RG=(Sum(Fo-Fc)^2/Sum(Fo)^2)^1/2. Although Hamilton wrote that at the end of 
refinement, one could also use the similar ratio of the usual R-factors, I 
really would like to check the ratio of the RG-values after refinement. As far 
as I can see, this value is not reported by the usual refinement programs.

Is there a program that reads an mtz file with Fo and refined Fc and just 
calculates RG?

Best regards,

Dirk.

-- 

***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***

[ccp4bb] Coot crashes on starting baton mode.

[David Briggs]

Hi all,

I'm running Coot 0.8.7 (as distributed with the CCP4 package) on OSX
10.11.6.

As soon as I click to enter CA-baton mode, coot crashes (terminal output
pasted below).

All I have done prior to this is load a pdb and an mtz, build skeletons and
pick a start point.

Has anyone seen this before, and if so, how did they overcome the problem?

Thanks in advance,

Dave

Symmetry available for this molecule

INFO:: returning baton atom molecule 12

-- baton_next_ca_options

   4e-12  xyz = (-16.27,-9.644, 24.54)

   4e-13  xyz = (-21.76,-12.59,  26.3)

   4e-13  xyz = (-21.32,-13.01, 25.91)

   4e-13  xyz = (-21.21,-9.022, 20.87)

   4e-13  xyz = (-21.41,-8.895, 20.97)

   4e-13  xyz = (-20.59,-13.48, 23.92)

   4e-13  xyz = (-20.59,-13.51, 24.55)

   4e-13  xyz = (-20.68,-13.39, 25.33)

   4e-13  xyz = ( -20.6,-9.633, 20.66)

   4e-13  xyz = (-20.56,-6.015, 23.94)

   4e-13  xyz = (-19.93,-13.38, 23.31)

   4e-13  xyz = ( -16.4,-8.755,  24.6)

   4e-13  xyz = (-16.27,-9.623, 24.57)

   4e-13  xyz = (-20.62,-11.67, 21.18)

   4e-13  xyz = (-21.17,-12.03, 21.58)

   4e-14  xyz = (-20.65, -6.04, 23.86)

   4e-14  xyz = (-20.78,-6.085, 23.73)

   4e-14  xyz = ( -20.6,-10.28, 20.69)

   4e-14  xyz = (-20.67,-11.09, 20.91)

   1e-15  xyz = (-20.64,-12.43, 21.78)

   9e-16  xyz = (-19.34,-13.12, 22.81)

   4e-16  xyz = (-19.93,-12.74, 22.08)

   0  xyz = (-18.76,-10.22, 27.96)

   0  xyz = (-18.75,-9.646, 27.98)

--

Creating a molecule for Baton Atom Guide Points

!! Warning:: No symmetry available for this molecule

No Symmetry for this model

INFO:: Creating directory coot-backup

INFO:: backup file
coot-backup/Baton_Atom_Guide_Points_Tue_Dec_20_13:53:53_2016_modification_0.pdb.gz

/Applications/ccp4-7.0/bin/coot: line 284: 20534 Segmentation fault:
11  $coot_bin
"$@"

coot-exe: "/Applications/ccp4-7.0/libexec/coot-bin"

coot-version:

/Applications/ccp4-7.0/libexec/coot-bin

platform:

/usr/bin/uname

core: #f
-- 


[image: --]

David Briggs PhD
[image: https://]about.me/david_briggs

[ccp4bb] Calculation of generalised R-factor?

[Dirk Kostrewa]

Dear CCP4ers,

I want to check the validity of the refinement of anisotropic B-factors 
vs. TLS + isototropic B-factors using the Hamilton R-value ratio test as 
described in Ethan Merritt's paper "To B or not to B", Acta Cryst. D, 
Vol 68, pp 468. This test uses the generalised R-factors (assuming unit 
weights), RG=(Sum(Fo-Fc)^2/Sum(Fo)^2)^1/2. Although Hamilton wrote that 
at the end of refinement, one could also use the similar ratio of the 
usual R-factors, I really would like to check the ratio of the RG-values 
after refinement. As far as I can see, this value is not reported by the 
usual refinement programs.


Is there a program that reads an mtz file with Fo and refined Fc and 
just calculates RG?


Best regards,

Dirk.

--

***
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***

[ccp4bb] Postdoctoral position in protein crystallography available at The Institute of Cancer Research, London UK

[Rob Van Montfort]

The Institute of Cancer Research, London, is one of the world’s most 
influential cancer research institutes, with an outstanding record of 
achievement dating back more than 100 years. We provided the first convincing 
evidence that DNA damage is the basic cause of cancer, laying the foundation 
for the now universally accepted idea that cancer is a genetic disease. Today, 
The Institute of Cancer Research (ICR) leads the world at isolating 
cancer-related genes and discovering new targeted drugs for personalised cancer 
treatment. Under the leadership of our Chief Executive, Professor Paul Workman 
FMedSci, the ICR is ranked as the UK’s leading academic research centre. 
Together with our partner The Royal Marsden, we are rated in the top four 
cancer centres globally.The ICR is committed to attracting, developing and 
retaining the best minds in the world to join us in our mission – to make the 
discoveries that defeat cancer.
The Cancer Research UK Cancer Therapeutics Unit, within the Division of Cancer 
Therapeutics, is a multidisciplinary 'bench to bedside' centre, comprising 
around 160 staff dedicated to the discovery and development of novel 
therapeutics for the treatment of cancer. The Cancer Therapeutics Unit’s 
exciting goal is to discover high quality small molecule drug candidates and to 
progress these to clinical trial. All the scientific disciplines are in place 
to make this possible, including medicinal chemistry, biology, drug metabolism 
and clinical specialists who focus on new molecular targets emerging from human 
genome and ground breaking cell biology research.
A postdoctoral position is available in Dr Rob van Montfort’s Hit Discovery and 
Structural Design Team within the CTU (Ref. 1624336). The Post-doc will be 
involved in high-throughput X-ray crystallography, fragment-based screening and 
structure-based drug design and will be responsible for crystallisation, 
structure determination and structural analysis of protein-ligand complexes 
from one of the CTU’s drug discovery programmes. The successful candidate will 
also be part of the Division of Structural Biology, in which the 
crystallographers in Dr van Montfort’s team are embedded, and will have access 
to state of the art crystallisation facilities, in-house X-ray sources and 
excellent access to synchrotrons. The successful candidate will interact 
closely with the biology, computational chemistry and medicinal chemistry teams 
at the CTU, and will therefore be expected to work across the two sites in 
Chelsea, London and Sutton, Surrey. Applicants must have a PhD in a biological 
or physical science, and experience in macromolecular crystallography (to 
include protein biochemistry, protein crystallisation, & protein 
crystallography). Experience in molecular biology, structure-based drug design, 
and/or biophysics will be an advantage. Starting salary will be in the range 
£34,247 to £36,830 p.a. inclusive (based on previous experience). Appointment 
will be on a fixed-term contract for 1 year and benefits from a contributory 
defined benefit pension scheme and generous leave entitlement.
Further information about these positions can be found in the full job 
description at www.icr.ac.uk. Informal enquiries to 
rob.vanmontf...@icr.ac.uk - but applications 
must be submitted on-line (www.icr.ac.uk). Closing date 
is January 27th 2017.


Dr. Rob van Montfort
Team Leader Hit Discovery and Structural Design
Joint Interim Head of Division of Structural Biology
Divisions of Cancer Therapeutics and Structural Biology
The Institute of Cancer Research
15 Cotswold Road
Sutton SM2 5NG
UK

Tel:
+44-(0)20-8722-4364 (Sutton)
+44-(0)20-7153-5142 (Chelsea)
Email: rob.vanmontf...@icr.ac.uk







The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.

[ccp4bb] Post-doctoral position in Structural Biology of Cilia, Astbury Centre, Leeds, UK

[Joe Cockburn]

Dear All,


A post-doctoral position is available immediately in the laboratory of Dr
Joe Cockburn, at the Astbury Centre, University of Leeds, UK to perform
structure-function studies on ciliary proteins.



The position is funded by The Wellcome Trust and is available immediately
for a period of 24 months. The start date is flexible but must be before
September 2017. The deadline for applications is Monday 16th January 2017.



More information about the position and how to apply can be found here:



https://jobs.leeds.ac.uk/vacancy.aspx?ref=FBSMB1092



Thanks,

Joe



--

Dr Joe Cockburn

The Astbury Centre for Structural and Molecular Biology

University of Leeds

Leeds LS2 9JT

UK

+44 (0)113 3430758

j.j.b.cockb...@leeds.ac.uk

http://www.astbury.leeds.ac.uk/people/staff/staffpage.php?StaffID=JJBC

Re: [ccp4bb] unusual monoclinic relation?

[Randy Read]

Dear Andy,

You've mentioned that MR doesn't work in any of the space groups you've tried, 
but there are different scenarios that you might be able to recognise from 
where the MR fails.

1. You might have the wrong protein, e.g. crystallised from a contaminant.  In 
that case, I would expect to see no significant signal in either the rotation 
or translation searches.

2. You might have the right protein, but there could be some pathology 
(including some relatively obscure things like reticular merohedral twinning, 
where twin-related reflections interleave and you incorrectly infer long cell 
dimensions).  In this case, I would still expect to see a strong signal for the 
rotation search, given the nearly-perfect sequence identity, but then there 
would be no signal in the translation search (or alternatively an unrealistic 
number of strong translation peaks).

3. There might be some unexpectedly large conformational change, but you 
probably have a reasonable idea of what kinds of motions occur in your system.

Good luck, and have a happy Christmas regardless!

Randy Read

> On 19 Dec 2016, at 08:43, Andrew Lovering  wrote:
> 
> Dear All,
>  
> I have just collected data on a mutant of a protein that should be facile to 
> solve by molrep (one residue/320 changed, approx 2Ang resolution) but is 
> proving problematic. Data merging stats look good.
>  
> The spacegroup is monoclinic, P21, the cell:
>  
> a=39.47 b=157.36 c=74.9 beta=98.26
>  
> I spotted the relevant monoclinic twin laws on ccp4 twinning page and all 
> relate multiples of axes a and c with one another (na +nc etc) but in the 
> above case it would appear b~ = 4a
>  
> There are other datasets, all index in this way, some hint at issues by 
> indexing with the alternate a=74 b=157 c=79 (where a and c “swap” with a 
> doubled, and thus our b=4a turns into b=2c)
>  
> I would appreciate any advice on how to progress! Be nice to solve it 
> pre-xmas.
>  
> Best & thanks in advance,
> Andy

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

Re: [ccp4bb] Atom clashes in active site?

[Pavel Afonine]

Hi Pedro,

quick answer: no.

Longer answer:
see article "13 typical occupancy refinement scenarios and available
options in phenix.refine" here:
http://phenix-online.org/newsletter/

Pavel

On Tue, Dec 20, 2016 at 12:29 AM, Pedro Matias  wrote:

> Hi Pavel,
>
> If the occupancies are 1 does phenix still refine them? Anyway, they can
> be explicitly fixed if necessary.
>
> Pedro
>
> Às 03:00 de 20/12/2016, Pavel Afonine escreveu:
>
> Hi Perdo,
>
> technically this should work too with the caveat that non-blanc altid will
> trigger occupancy refinement for corresponding atoms which may not be
> desired.
>
> Pavel
>
>
> On Mon, Dec 19, 2016 at 12:54 AM, Pedro Matias  wrote:
>
>> Hi Andrew,
>>
>> The simplest way would be to place the "offending" atoms in separate
>> conformers as used to refine alternate conformations. This is a 1-letter
>> code that goes just before the 3-letter residue name:
>>
>> ATOM139  SG *B*CYS A  21 -20.620   4.518  34.501  0.39
>> 12.23  AS
>>
>> This trick should cause PHENIX to ignore close distances between atoms in
>> the A and B conformers.
>>
>> Hope this helps,
>>
>> Pedro Matias
>>
>>
>> Às 05:39 de 19/12/2016, Andrew Marshall escreveu:
>>
>> Hi all,
>>
>> I have a structure of a condensing enzyme with substrate bound. The
>> active site is very tight, requiring some of the substrate atoms to clash
>> with a catalytic cysteine. This means that although the substrate fits the
>> density nicely upon manual real-space refinement, phenix recognises the
>> clash, resulting in the displacement of substrate atoms so that they are
>> outside the density. I can mostly fix this by using distance restraints,
>> but I'd rather allow it to refine in a less biased manner, but ignore the
>> clash. Is this a acceptable way forward? If so, is there a parameter I can
>> edit to tell phenix to ignore clashes between these specific atoms?
>>
>> Thanks,
>>
>>

Re: [ccp4bb] Atom clashes in active site?

[Pedro Matias]

Hi Andrew,

One of the atoms should be in altconf A and the other in B. Otherwise
the problem remains.

Pedro


Às 01:48 de 20/12/2016, Andrew Marshall escreveu:
> Hi all,
>
> Thank you for your suggestions. I tried the pdb file edit (making the
> offending atoms of both the ligand and the protein 'B' altconf), but
> it didn't seem to make any difference to their positions after a
> single round of refinement..? 
> The atoms in the active site concern two acetyl groups - one from the
> substrate, acetyl-CoA, and the other from an acetylated cysteine in
> the protein - that I believe are poised ready for a condensation
> reaction. The closest contacts are between S and O(carbonyl) atoms
> (2.9A) and O and CH3 (3.1A), but going off the density, I think these
> should be closer (more like 2.8 or 2.7A). It may be that I've trapped
> another reaction intermediate (which would be cool), but I don't think
> that fits the density quite as well. Any thoughts/ideas?
>
> Thanks,
>
> Andrew Marshall
> PhD Candidate
> Laboratory of Protein Crystallography
> Dept. of Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide
>
> On Tue, Dec 20, 2016 at 12:09 AM, Scott Horowitz  > wrote:
>
> Hi Andrew,
>
> I'm curious- what are the atoms that are clashing? I worked on
> this sort of thing back in my Ph.D., and so I might have some
> useful tidbits if, for example, the S is clashing with a carbon of
> some sort.
>
> Thanks,
> Scott
>
> On Mon, Dec 19, 2016 at 12:39 AM, Andrew Marshall
>  > wrote:
>
> Hi all,
>
> I have a structure of a condensing enzyme with substrate
> bound. The active site is very tight, requiring some of the
> substrate atoms to clash with a catalytic cysteine. This means
> that although the substrate fits the density nicely upon
> manual real-space refinement, phenix recognises the clash,
> resulting in the displacement of substrate atoms so that they
> are outside the density. I can mostly fix this by using
> distance restraints, but I'd rather allow it to refine in a
> less biased manner, but ignore the clash. Is this a acceptable
> way forward? If so, is there a parameter I can edit to tell
> phenix to ignore clashes between these specific atoms?
>
> Thanks,
>
> Andrew Marshall
> PhD Candidate
> Laboratory of Protein Crystallography
> Dept. of Molecular and Cellular Biology
> School of Biological Sciences
> The University of Adelaide
>
>
>
>
> -- 
> Scott Horowitz, Ph.D.
> Postdoctoral Fellow
>
> University of Michigan
> Department of Molecular, Cellular, and Developmental Biology
> Bardwell lab
> 830 N. University Ave, Room 4007
> Ann Arbor, MI 48109
> phone: 734-647-6683
> fax: 734-615-4226
>
>

-- 

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8

Re: [ccp4bb] Atom clashes in active site?

[Pedro Matias]

Hi Pavel,

If the occupancies are 1 does phenix still refine them? Anyway, they can
be explicitly fixed if necessary.

Pedro


Às 03:00 de 20/12/2016, Pavel Afonine escreveu:
> Hi Perdo,
>
> technically this should work too with the caveat that non-blanc altid
> will trigger occupancy refinement for corresponding atoms which may
> not be desired.
>
> Pavel
>
>
> On Mon, Dec 19, 2016 at 12:54 AM, Pedro Matias  > wrote:
>
> Hi Andrew,
>
> The simplest way would be to place the "offending" atoms in
> separate conformers as used to refine alternate conformations.
> This is a 1-letter code that goes just before the 3-letter residue
> name:
>
>> ATOM139  SG *B*CYS A  21 -20.620   4.518  34.501  0.39
>> 12.23  AS  
> This trick should cause PHENIX to ignore close distances between
> atoms in the A and B conformers.
>
> Hope this helps,
>
> Pedro Matias
>
>
> Às 05:39 de 19/12/2016, Andrew Marshall escreveu:
>> Hi all,
>>
>> I have a structure of a condensing enzyme with substrate bound.
>> The active site is very tight, requiring some of the substrate
>> atoms to clash with a catalytic cysteine. This means that
>> although the substrate fits the density nicely upon manual
>> real-space refinement, phenix recognises the clash, resulting in
>> the displacement of substrate atoms so that they are outside the
>> density. I can mostly fix this by using distance restraints, but
>> I'd rather allow it to refine in a less biased manner, but ignore
>> the clash. Is this a acceptable way forward? If so, is there a
>> parameter I can edit to tell phenix to ignore clashes between
>> these specific atoms?
>>
>> Thanks,
>>
>> Andrew Marshall
>> PhD Candidate
>> Laboratory of Protein Crystallography
>> Dept. of Molecular and Cellular Biology
>> School of Biological Sciences
>> The University of Adelaide
>>
>
> -- 
>
> Industry and Medicine Applied Crystallography
> Macromolecular Crystallography Unit
> ___
> Phones : (351-21) 446-9100 Ext. 1669
>  (351-21) 446-9669 (direct)
>  Fax   : (351-21) 441-1277 or 443-3644
>
> email : mat...@itqb.unl.pt 
>
> 
> http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
> 
> 
> http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit
> 
>
> Mailing address :
> Instituto de Tecnologia Quimica e Biologica António Xavier
> Universidade Nova de Lisboa
> Av. da República
> 2780-157 Oeiras
> PORTUGAL
>
> ITQB NOVA, a great choice for your PhD
> https://youtu.be/de6j-aaTWNQ
>
> Master Programme in Biochemistry for Health
> https://youtu.be/UKstDCFjYI8
>
-- 

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8

Re: [ccp4bb] unusual monoclinic relation?

[Antony Oliver]

Dear Andrew,

If you're sub 2 Angstrom - give Archimboldo a shot. We recently solved the 
crystal structure of a unknown protein this way. You perhaps have the advantage 
of knowing what  be in there.

Antony.

--- Antony W Oliver ---
--- sent from my mobile account ---

On 20 Dec 2016, at 08:18, Andrew Lovering 
mailto:a.lover...@bham.ac.uk>> wrote:

Thanks Tim,

Yes, I may give that a go next time (the wild-type was actually solved by 
S-SAD, very nice ordered bridge)

Orperhaps time to seed / derivitize / mutate and get different packing.
Still, not before xmas!

Andy

-Original Message-
From: Tim Gruene [mailto:tim.gru...@psi.ch]
Sent: 19 December 2016 19:58
To: Andrew Lovering
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] unusual monoclinic relation?

Dear Andrew,

did you remove all cysteins, and all methionines with the mutations? Your 
resolution is about 2A, if I understand correctly. This may be suitable for S- 
SAD. I would try to get access to a modern inhouse machine to get high quality 
data at high multiplicity. Some modern synchrotron beamlines offer more than 
1-circle goniometers, but good quality data is more easily collected with a 
multi-circle instrument.

Best,
Tim

On Monday, December 19, 2016 4:42:00 PM CET Andrew Lovering wrote:
Thanks again Herman,

The protein is a two domain protein (approx 40aa, 350aa split) -
searching with either is proving fruitless.

Original, wild-type cell = 49 x 75 x 80 P212121 This painful mutant =
39 x 157 x 75 beta=98.26 P21

(so one can say that there seems to be a relationship there, wt b =
mutant c, wt c = 2x mutant a?)

We have been bitten in the past by crystallizing contaminants, but
(touch
wood) those are always small crystals one / drop, in a few conditions.
This problem set has been replicated across at least 6 differing
crystals (grown in different conditions), where there are many
crystals / drop..along with the similar cell I'm confident that we
are seeing diffraction from what we expect

I will check the diffraction images more closely, but (does anyone
agree
here?) I find this sometimes obscured by modern fine-slice/Pilatus
methodology

Might be one for 2017! p.s. no anomalous signal in there - ironically
mutant we're using knocks bound metal out!

Thanks again
Andy
From: herman.schreu...@sanofi.com 
[mailto:herman.schreu...@sanofi.com]
Sent: 19 December 2016 16:26
To: Andrew Lovering; CCP4BB@JISCMAIL.AC.UK
Subject: AW: unusual monoclinic relation?

Dear Andy,

I don't think you will solve this pre-Xmas, but here are some more
suggestions: -is there any relationship with the unit cell of the
parent, unmutated protein? This might give some ideas of the packing
of the problem crystals. -are some promising solutions being rejected
due to clashes? In that case you might try to allow for more clashes.
-can the protein be split in some separate domains? In that case you
could try MR with the separate domains. -Are you sure the crystallized
protein is the protein you think you crystallized? (see contamination
database). -Check your diffraction images to make sure there are no pathologies 
present.

Best,
Herman


Von: Andrew Lovering [mailto:a.lover...@bham.ac.uk]
Gesendet: Montag, 19. Dezember 2016 12:30
An: Schreuder, Herman R&D/DE;
CCP4BB@JISCMAIL.AC.UK
 Betreff: RE:
unusual monoclinic relation?

Thanks Herman. In short:

-no twinning suggested from xtriage etc
-P2 doesn't give a solution either
-monoclinic cell would have 2 (60% solvent) or 3 (40% solvent) copies
-I originally thought the zanuda P1 route would be the way to go, but
phaser was still churning away after running overnight and so I killed
the job thinking it was thrashing

Andy

From: 
herman.schreu...@sanofi.com
[mailto:herman.schreu...@sanofi.com] Sent: 19 December 2016 10:43
To: Andrew Lovering;
CCP4BB@JISCMAIL.AC.UK
Subject: AW: unusual monoclinic relation?

Dear Andrew,

Just a few questions:
-Do the processing/refinement programs suggest twinning?
-Are you sure your space group is P21 and not P2? Did you try MR in P2?
-How many protein molecules do you expect in the asymmetric unit?

P2(1) is a very low symmetry space group. In this case I would not try
to be clever and just reprocess the data in P1 and run MR in P1. With
Zanuda you can afterwards try to figure out what the real space group could be.

Best,
Herman


Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
Andrew Lovering Gesendet: Montag, 19. Dezember 2016 09:43
An: 
CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] unusual monoclinic relation?

Dear All,

I have just collected data on a mutant of a protein that should be
facile to solve by 

Re: [ccp4bb] unusual monoclinic relation?

[Andrew Lovering]

Thanks Tim,

Yes, I may give that a go next time (the wild-type was actually solved by 
S-SAD, very nice ordered bridge)

Orperhaps time to seed / derivitize / mutate and get different packing.
Still, not before xmas!

Andy

-Original Message-
From: Tim Gruene [mailto:tim.gru...@psi.ch] 
Sent: 19 December 2016 19:58
To: Andrew Lovering
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] unusual monoclinic relation?

Dear Andrew,

did you remove all cysteins, and all methionines with the mutations? Your 
resolution is about 2A, if I understand correctly. This may be suitable for S- 
SAD. I would try to get access to a modern inhouse machine to get high quality 
data at high multiplicity. Some modern synchrotron beamlines offer more than 
1-circle goniometers, but good quality data is more easily collected with a 
multi-circle instrument.

Best,
Tim

On Monday, December 19, 2016 4:42:00 PM CET Andrew Lovering wrote:
> Thanks again Herman,
> 
> The protein is a two domain protein (approx 40aa, 350aa split) - 
> searching with either is proving fruitless.
> 
> Original, wild-type cell = 49 x 75 x 80 P212121 This painful mutant = 
> 39 x 157 x 75 beta=98.26 P21
> 
> (so one can say that there seems to be a relationship there, wt b = 
> mutant c, wt c = 2x mutant a?)
> 
> We have been bitten in the past by crystallizing contaminants, but 
> (touch
> wood) those are always small crystals one / drop, in a few conditions. 
> This problem set has been replicated across at least 6 differing 
> crystals (grown in different conditions), where there are many 
> crystals / drop..along with the similar cell I'm confident that we 
> are seeing diffraction from what we expect
> 
> I will check the diffraction images more closely, but (does anyone 
> agree
> here?) I find this sometimes obscured by modern fine-slice/Pilatus 
> methodology
> 
> Might be one for 2017! p.s. no anomalous signal in there - ironically 
> mutant we're using knocks bound metal out!
> 
> Thanks again
> Andy
> From: herman.schreu...@sanofi.com [mailto:herman.schreu...@sanofi.com]
> Sent: 19 December 2016 16:26
> To: Andrew Lovering; CCP4BB@JISCMAIL.AC.UK
> Subject: AW: unusual monoclinic relation?
> 
> Dear Andy,
> 
> I don't think you will solve this pre-Xmas, but here are some more
> suggestions: -is there any relationship with the unit cell of the 
> parent, unmutated protein? This might give some ideas of the packing 
> of the problem crystals. -are some promising solutions being rejected 
> due to clashes? In that case you might try to allow for more clashes. 
> -can the protein be split in some separate domains? In that case you 
> could try MR with the separate domains. -Are you sure the crystallized 
> protein is the protein you think you crystallized? (see contamination 
> database). -Check your diffraction images to make sure there are no 
> pathologies present.
> 
> Best,
> Herman
> 
> 
> Von: Andrew Lovering [mailto:a.lover...@bham.ac.uk]
> Gesendet: Montag, 19. Dezember 2016 12:30
> An: Schreuder, Herman R&D/DE;
> CCP4BB@JISCMAIL.AC.UK Betreff: RE: 
> unusual monoclinic relation?
> 
> Thanks Herman. In short:
> 
> -no twinning suggested from xtriage etc
> -P2 doesn't give a solution either
> -monoclinic cell would have 2 (60% solvent) or 3 (40% solvent) copies 
> -I originally thought the zanuda P1 route would be the way to go, but 
> phaser was still churning away after running overnight and so I killed 
> the job thinking it was thrashing
> 
> Andy
> 
> From: herman.schreu...@sanofi.com
> [mailto:herman.schreu...@sanofi.com] Sent: 19 December 2016 10:43
> To: Andrew Lovering; 
> CCP4BB@JISCMAIL.AC.UK
> Subject: AW: unusual monoclinic relation?
> 
> Dear Andrew,
> 
> Just a few questions:
> -Do the processing/refinement programs suggest twinning?
> -Are you sure your space group is P21 and not P2? Did you try MR in P2?
> -How many protein molecules do you expect in the asymmetric unit?
> 
> P2(1) is a very low symmetry space group. In this case I would not try 
> to be clever and just reprocess the data in P1 and run MR in P1. With 
> Zanuda you can afterwards try to figure out what the real space group could 
> be.
> 
> Best,
> Herman
> 
> 
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
> Andrew Lovering Gesendet: Montag, 19. Dezember 2016 09:43
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [ccp4bb] unusual monoclinic relation?
> 
> Dear All,
> 
> I have just collected data on a mutant of a protein that should be 
> facile to solve by molrep (one residue/320 changed, approx 2Ang 
> resolution) but is proving problematic. Data merging stats look good.
> 
> The spacegroup is monoclinic, P21, the cell:
> 
> a=39.47 b=157.36 c=74.9 beta=98.26
> 
> I spotted the relevant monoclinic twin laws on ccp4 twinning page and 
> all relate multiples of axes a and c with one another (na +nc etc) 

[ccp4bb] Change of Email address

[Ranvir Singh]

I am in the mailing list of subscribers for ccp4bb with current yahoo mail 
account. I am going to discontinue this mail account. kindly change my email 
account to my gmail account, ranvirsin...@gmail.com
Ranvir SinghDept cum NCHGSRPanjab UniversityChandigarhINDIA.