Re: [ccp4bb] sfall bug?

2015-07-07 Thread Kay Diederichs
Just a few observations:

I ran 
echo MODE SFCALC XYZIN\\n SYMM P21\\n RESO 30 3 | sfall xyzin a.pdb hklout 
temp.mtz > a.log
and
echo MODE SFCALC XYZIN\\n SYMM P21\\n RESO 30 3 | sfall xyzin b.pdb hklout 
temp.mtz > b.log
and looked at a.log and b.log

They differ only as follows: a.log has
  First 10 atoms of atsort - orthog coordinates
 16204FE1  ICS  6496 10.0180 -7.5680 56.1090 1.005.976
   fractional coordinates  0.38411-0.05791 0.55929


  First 10 atoms of atsort - orthog coordinates
 16289FE1  ICS  7496 35.7530  7.5810-12.1820 1.005.916
   fractional coordinates  0.38376 0.05800-0.12143
  First 10 atoms of sorted file in asym unit -  
   20.61588   0.44071   0.44209105.97 1.00 6  ***ZZZ  END 
   10.38376   0.87857   0.05800205.91 1.00 6  ***ZZZ  END 

  First atom of sorted file in atsort 
   20.61588   0.44071   0.44209105.97131.00  ***ZZZ  END 

whereas b.log has
  First 10 atoms of atsort - orthog coordinates
 16204FE1  ICS  6496 35.7530  7.5810-12.1820 1.005.916
   fractional coordinates  0.38376 0.05800-0.12143


  First 10 atoms of atsort - orthog coordinates
 16289FE1  ICS  7496 10.0180 -7.5680 56.1090 1.005.976
   fractional coordinates  0.38411-0.05791 0.55929
  First 10 atoms of sorted file in asym unit -  
   10.38376   0.87857   0.05800105.91 1.00 6  ***ZZZ  END 
   20.61588   0.44071   0.44209205.97 1.00 6  ***ZZZ  END 

  First atom of sorted file in atsort 
   10.38376   0.87857   0.05800105.91131.00  ***ZZZ  END 

What I don't understand is why the sorted lists are different? Sorting should 
make the resulting lists look the same, to my limited understanding. What is 
peculiar about the coordinates of these atoms is that there x coordinate in 
fractional units is almost the same, and their y coordinate is mirrored at the 
origin.Maybe that could play a role.

Kay


Re: [ccp4bb] sfall bug?

2015-07-07 Thread Clemens Vonrhein
Hi Jens,

I do get the same results when running

  sfall xyzin a.pdb hklout a.mtz mapout a.map 

[ccp4bb] Post-doctoral research position at the Biozentrum, University of Basel

2015-07-07 Thread Sebastian Hiller
*Post-doctoral position: Structure and function of a large membrane protein
insertase complex*


A postdoctoral research position is available in the group of Sebastian
Hiller at the Biozentrum, University Basel. In this project, we want to
unravel the mechanism for insertion of beta-barrel membrane proteins into
mitochondrial and bacterial outer membranes at atomic resolution. This
process is mediated by large insertase complexes including Omp85 proteins.
The project characterizes structure, function, and dynamics of such a
complex using solution NMR spectroscopy and complementary techniques, in
combination with suitable biochemical preparations.

The project is ideally suited for a competitive researcher with experience
in membrane protein biochemistry and solution NMR spectroscopy. Motivated
individuals with a different background in structural biology are also
strongly encouraged to apply. The Biozentrum offers an international and
enthusiastic work environment with excellent infrastructure in all areas of
life science. Our facilities for structural biology include 600-900 MHz
Bruker NMR spectrometers, high-throughput crystallization screening,
state-of-the-art cryo-electron microscopy, and a biophysics core facility. The
position is available for a duration of at least two years and with a
starting date within the next 6 months.

Applicants should submit a CV, list of publications, a letter of
motivation, and contact information for at least two reference persons.

Prof. Sebastian Hiller
Focal Area Structural Biology and Biophysics
Biozentrum, University of Basel
Klingelbergstrasse 70, 4056 Basel, Switzerland

sebastian.hil...@unibas.ch
http://www.biozentrum.unibas.ch/hiller/

phone: +41 61 267 20 82
fax: +41 61 267 21 09


Re: [ccp4bb] Post-doctoral research position at the Biozentrum, University of Basel

2015-07-07 Thread André Hoelz
  Sent from my BlackBerry 10 smartphone.From: Sebastian HillerSent: Tuesday, July 7, 2015 2:47 AMTo: CCP4BB@JISCMAIL.AC.UKReply To: Sebastian HillerSubject: [ccp4bb] Post-doctoral research position at the Biozentrum, University of BaselPost-doctoral position: Structure and function of a large membrane protein insertase complex A
postdoctoral research position is available in the group of Sebastian Hiller at
the Biozentrum, University Basel. In this project, we want to unravel
the mechanism for insertion of beta-barrel membrane proteins into
mitochondrial and bacterial outer membranes at atomic resolution. This process is mediated by large insertase complexes including Omp85
proteins. The project characterizes structure, function,
and dynamics of such a complex using solution NMR spectroscopy and complementary techniques,
in combination with suitable biochemical preparations.

The
project
 is ideally suited for a competitive researcher with experience in
membrane protein biochemistry and solution NMR spectroscopy. Motivated 
individuals with a different background in structural biology are also 
strongly encouraged to apply. The Biozentrum offers an international and 
enthusiastic work environment with excellent infrastructure in all areas
 of life science. Our facilities for structural biology include 600-900 
MHz Bruker NMR spectrometers, high-throughput crystallization screening,
 state-of-the-art cryo-electron microscopy, and a biophysics core 
facility. The position
is available for a duration of at least two years and with a starting date within the next
6 months.

Applicants
should submit a CV, list of publications, a letter of motivation, and contact
information for at least two reference persons. Prof. Sebastian HillerFocal Area Structural Biology and BiophysicsBiozentrum, University of BaselKlingelbergstrasse 70, 4056 Basel, Switzerlandsebastian.hil...@unibas.chhttp://www.biozentrum.unibas.ch/hiller/phone: +41 61 267 20 82fax: +41 61 267 21 09



Re: [ccp4bb] DNA RNA annealing problem

2015-07-07 Thread Hargreaves, David
Hi Weifei,

When I was looking at Holliday junction annealing I found that the salt 
concentration was important. NaCl around 300-500mM improved yield as did MgCl2 
at lower (100-200mM) concentrations. So, it might be worth trying higher salt.

Dave

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ChenWeiFei
Sent: 03 July 2015 16:14
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] DNA RNA annealing problem

Dear all,
I want to get a complex of DNA-RNA-protein. But I have a big problem of 
annealing DNA-RNA.
The length of DNA is 19nt and RNA is 17nt.
Annealing protocol:
2uM DNA
2uM RNA
10mM Tris-Hcl
100mMNaCl
1mMEDTA

Heated to 95 for 5min, cooling down slowly for nearly 2h to room temperature.

I can just get a result of two single strand DNA/RNA. PAGE analysis.

No double helix was founded.

Does anyone have the same problem or know how to fix it.

Thank you for your answering.

Best regards,
Weifei



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Re: [ccp4bb] DNA RNA annealing problem

2015-07-07 Thread Almudena Ponce Salvatierra
Hi Weifei,

so... what I do is to mix them in a 1:1ish ratio, then I check that ratio
on the HPLC in case I can adjust it to 1:1. I.e. Instead of mixing 30 nmol
of RNA with 30 of DNA if I want a 1:1 ratio complex, I mix 30 of RNA and 25
of DNA. I calculate their molar extinction coefficient (epsilon) and check
what is the ratio between the one of RNA and the one of DNA. Out of the
HPLC I calculate the area of the peaks, divide one by the other one and
check whether this ratio matches the one between the epsilons. If it
doesn't then you calculate how much you still need to add to achieve this
1:1 ratio.

Depending on your desired final concentrartion you probably have to
concentrate this RNA-DNA mixture before adding the buffer. I concentrate in
viva spin colum and then add the buffer (mine is 10mM HEPES pH 8.0, 150 mM
NaCl, and 2mM KCl. I anneal it at 95° for 3 minutes and then let it cool to
room temperature for about 20'. After it cools down I add 20 mM MgCl2.

I'm not sure this helps a lot or not... this is what I do... I don't know
if it gives you any idea of what can be not working in your case.

Good luck.

Best,

ALmudena

2015-07-03 17:14 GMT+02:00 ChenWeiFei :

> Dear all,
> I want to get a complex of DNA-RNA-protein. But I have a big problem of
> annealing DNA-RNA.
> The length of DNA is 19nt and RNA is 17nt.
> Annealing protocol:
> 2uM DNA
> 2uM RNA
> 10mM Tris-Hcl
> 100mMNaCl
> 1mMEDTA
>
> Heated to 95 for 5min, cooling down slowly for nearly 2h to room
> temperature.
>
> I can just get a result of two single strand DNA/RNA. PAGE analysis.
>
> No double helix was founded.
>
> Does anyone have the same problem or know how to fix it.
>
> Thank you for your answering.
>
> Best regards,
> Weifei




-- 
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany


Re: [ccp4bb] determine NCS operators from PDB coordinates

2015-07-07 Thread Tobias Beck
Dear all,

Thanks for your helpful emails.

Here is a short summary:

I followed Edward Berry's suggestions. Unfortunately I could not use any
superposition to the new structure, as suggested by some, since the
structures are too different.
I used lsqman and mama to obtain the sperical polars for my twofold as
pointed out by Ed. After this, I rotated my structure in two steps based on
these angles, but using rotation matrixes in the form

cos_theta   -sin_theta0

sin_thetacos_theta0

0   0  1

as pointed out by Ed, to align the twofold axis in my structure to a
twofold axis in the new space group. That was done in pdbset (I did not
need to consider translation in my case).

Thanks again for helping me!

Best wishes, Tobias.

On Fri, Jun 19, 2015 at 4:54 PM, Edward A. Berry  wrote:

> A number of superposition programs allow to superimpose specified atoms
> (such as CA).
> Once you get the operator, comparing two different operators is not a job
> for a conventional superposition program, since you are superimposing a
> line on a line which has the extra degree of freedom- rotation about the
> line.
> If you express the operator in spherical polar coordinates, which the
> superposition
> program may provide or you can get from the matrix using ccp4 "rotmat",
> you should be able to work out the relation between the axes.
>
> Using the Uppsala sofware factory programs:
>
> #This is superimposing parts of chains C, A, B on P, N, O (and vice versa
> - it's proper 2-fold)
> lsqman -b < chain_mode original
> re m1  cbc596.pdb
> exp m1
> C20-370  P20-370 A20-200 A250-400 B30-200 B250-400 N20-200 N250-400
> O30-200 O250-400
> m1
> P20  C20 N20 N250 O30 O250 A20 A250 B30 B250
> save m1 m1 ncsasc01.odb
> quit
> eof
>
> This prints the operator and saves it in ncsasc01.odb*
> 
> - The   2010 atoms have an RMS distance of0.130 A
> - RMS delta B  =   15.367 A2
> - Corr. coeff. =  0.6601
> - Rotation:  -0.834671 -0.550747 -0.001321
> --0.550747  0.834660 0.004400
> --0.001321  0.004400 -0.89
> - Translation :129.38438.428   171.594
> ---
>
> Now use mama in an off-label way to convert to polar coordinates:
> mama
> overlap ncs  ncsasc01.odb
> gives:
> ---
> - RT-OP  1 =-0.8346710   -0.5507473   -0.0013208
> 129.384
> -   -0.55074730.83466040.0044000
>  38.428
> -   -0.00132080.0044000   -0.894
> 171.594
> - Determinant of rotation matrix 1.00
> - Column-vector products (12,13,23)  0.000.000.00
> - Crowther Alpha Beta Gamma   106.709 179.736  73.291
> - ***Spherical polars Omega Phi Chi   90.132 -73.291
>  180.000***
> - Direction cosines of rotation axis 0.287514   -0.957774 -0.002303
> - X-PLOR polars Phi Psi Kappa *undefined* *undefined* 180.000
> - Lattmann Theta+ Theta2 Theta-  -180.000 179.736-146.582
> - Rotation angle 180.000
> -
>  * if you use the .odb file outside of the USF software, be aware the
> matrix is the transpose
> (or more accurately it is written by columns). In ccp4 this is taken care
> of withthe keyword "odb".
>
>
> On 06/19/2015 09:07 AM, Tobias Beck wrote:
>
>> Dear all,
>>
>> I have a PDB file that contains NCS in the asymmetric unit, probably
>> point group D3.
>>
>> 1.) What program is recommended for determining the symmetry operators
>> from PDB coordinates? I found findncs, but this uses only heavy atom
>> coordinates (I could probably use just the sulfurs from the PDB as a work
>> around).
>>
>> 2.) Then I would like to compare the PDB file to a related structure.
>> Here I would like to align the symmetry operators determined above with
>> symmetry elements found in a different space group, for example align the
>> twofold axis from NCS with a twofold axis in found in a particular space
>> group.
>> What is a good way to go about this?
>>
>> I am aware that NCS is used in programs as restraints during refinement,
>> but here I am interested in obtaining the NCS symmetry operators and
>> aligning them to symmetry elements present in a new space group. Maybe I am
>> overlooking an obvious solution.
>>
>> Any help is greatly appreciated.
>>
>> Thanks and best wishes, Tobias.
>> --
>> ___
>>
>> Dr. Tobias Beck
>> - independent group leader -
>> RWTH Aachen University
>> Institute of Inorganic Chemistry
>> Landoltweg 1, office: 304N
>> 52056 Aachen, Germany
>> phone:  +49-241-80-90057
>> fax:   +49-241-80-99003
>> web: http://www.ac.rwth-aachen.de/extern/beck/
>> ___
>>
>>


-- 
___

Dr. Tobias Beck
- independent group leader -
RWTH Aachen University
Institute of Inorganic Chemistry
Landoltweg 1, office: 304N
52056 Aachen, Germany
phon

[ccp4bb] Scientist position at Zymeworks, Vancouver, Canada

2015-07-07 Thread Yang-Chieh Chou
Dear CCP4 members,

Please allow me to introduce you to Zymeworks, a fast-growing biotechnology
company with offices in Canada and the US, dedicated to the research,
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to the design of experiments and data analysis, as well as engaging itself
to understand their needs and plan for new technology developments. Beyond
strong analytical skills, the ideal candidate will have a good
understanding of protein engineering and drug design using *in silico*
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*Roles and Responsibilities**:*


   -  Ensure the correct functionality and optimal fit-for-purpose of our
   computational tools.
   - Provide support in the applications of our computational platform.
   - Work with our team of protein engineers and therapeutics R&D
   scientists to create requirements and specifications for new tools to be
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   - Plan, implement, and report validations of state-of-the-art
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   - Maintain and create Standard Operating Procedures for the tools and
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   - Experience in utilizing Molecular Dynamics or Protein Design methods
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   is required.
   - Strong skills in Data Analysis with experience in data visualization
   and informatics.
   - Experience in protein purification, characterization and other aspects
   of protein science is required.
   - Experience with protein assays including UPLC/SEC, DSC, SPR, LC-MS,
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Scientist, Technology Integration in the subject line. Due to the high
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1320-Scientist-Technology_Integration.pdf
Description: Adobe PDF document


Re: [ccp4bb] DNA RNA annealing problem

2015-07-07 Thread DUMAS Philippe (VIE)

Le Mardi 7 Juillet 2015 14:03 CEST, Almudena Ponce Salvatierra 
 a écrit:

Hello
Do you have full complementarity of DNA and RNA  ?
Does the difference in lenght (17 nt/19 nt) mean that you have a bulge on the 
DNA when the duplex is formed ?
In short, what is the Tm of this duplex at these strand and salt concentrations?
If the Tm is 35 °C, then "room temperature" may be a bit hot depending on where 
you are in this month of July.
Also, what was the temperature of the gel during migration ?

Do you have access to ITC ?
If yes, we have found that this is a perfect technique (1) to check that you 
have formation of the duplex (basepair formation generates a lot of heat), (2) 
that you are using 100 % of each strand (or may be less...), (3) that you can 
stop injecting the second strand when the stoichiomertic ratio is 1/1 (no 
strand in excess: perfect for crystallization) and, finally, (4) that you can 
retrieve the sample from the cell, concentrate it and make crystallization 
drops.

See: Da Veiga C., Mezher J., Dumas P., and Eric Ennifar (2015).Isothermal 
Titration Calorimetry: Assisted Crystallization of RNA-Ligand Complexes. In 
Nucleic Acid Crystallography : Methods and Protocols. (Ennifar E., ed..) in 
press. Humana Press. NY. Abstract

I hope this can be useful.

Philippe Dumas


>
> 2015-07-03 17:14 GMT+02:00 ChenWeiFei :
>
> > Dear all,
> > I want to get a complex of DNA-RNA-protein. But I have a big problem of
> > annealing DNA-RNA.
> > The length of DNA is 19nt and RNA is 17nt.
> > Annealing protocol:
> > 2uM DNA
> > 2uM RNA
> > 10mM Tris-Hcl
> > 100mMNaCl
> > 1mMEDTA
> >
> > Heated to 95 for 5min, cooling down slowly for nearly 2h to room
> > temperature.
> >
> > I can just get a result of two single strand DNA/RNA. PAGE analysis.
> >
> > No double helix was founded.
> >
> > Does anyone have the same problem or know how to fix it.
> >
> > Thank you for your answering.
> >
> > Best regards,
> > Weifei
>
>
>
>
> --
> Almudena Ponce-Salvatierra
> Macromolecular crystallography and Nucleic acid chemistry
> Max Planck Institute for Biophysical Chemistry
> Am Fassberg 11 37077 Göttingen
> Germany






[ccp4bb] OT: mapping PDB to mmCIF data quantities

2015-07-07 Thread Phil Jeffrey
I'm updating some code to have limited mmCIF/PDB format interoperability 
and have hit a snag.  While I can infer the connection between some data 
items in the PDB header REMARK and the items in mmCIF I can't 
definitively deduce some others.  In particular the mapping of

REMARK  2  RESOLUTION
seems a little ambiguous and the dictionary documentation doesn't help 
in this regard.


Does anyone know where to find an explicit mapping of one data field to 
another between the two formats ?  (I don't expect there to be a data 
field in the PDB header for everything in mmCIF but I do for the reverse 
case).



Thanks
Phil Jeffrey
Princeton


Re: [ccp4bb] determine NCS operators from PDB coordinates

2015-07-07 Thread Edward A. Berry

Well done.
Sorry for the many typos, but they don't seem to have slowed you down any!
eab

On 07/07/2015 11:25 AM, Tobias Beck wrote:

Dear all,

Thanks for your helpful emails.

Here is a short summary:

I followed Edward Berry's suggestions. Unfortunately I could not use any 
superposition to the new structure, as suggested by some, since the structures 
are too different.
I used lsqman and mama to obtain the sperical polars for my twofold as pointed 
out by Ed. After this, I rotated my structure in two steps based on these 
angles, but using rotation matrixes in the form

cos_theta   -sin_theta0

sin_thetacos_theta0

0   0  1

as pointed out by Ed, to align the twofold axis in my structure to a twofold 
axis in the new space group. That was done in pdbset (I did not need to 
consider translation in my case).

Thanks again for helping me!

Best wishes, Tobias.

On Fri, Jun 19, 2015 at 4:54 PM, Edward A. Berry mailto:ber...@upstate.edu>> wrote:

A number of superposition programs allow to superimpose specified atoms 
(such as CA).
Once you get the operator, comparing two different operators is not a job
for a conventional superposition program, since you are superimposing a
line on a line which has the extra degree of freedom- rotation about the 
line.
If you express the operator in spherical polar coordinates, which the 
superposition
program may provide or you can get from the matrix using ccp4 "rotmat",
you should be able to work out the relation between the axes.

Using the Uppsala sofware factory programs:

#This is superimposing parts of chains C, A, B on P, N, O (and vice versa - 
it's proper 2-fold)
lsqman -b < -0.550747 -0.001321 

--0.550747  0.834660 0.004400 

--0.001321  0.004400 -0.89 
- Translation :129.38438.428   171.594
---

Now use mama in an off-label way to convert to polar coordinates:
mama
overlap ncs  ncsasc01.odb
gives:
---
- RT-OP  1 =-0.8346710-0.5507473
-0.0013208129.384
-   -0.5507473  0.8346604 
0.0044000 38.428
-   -0.00132080.0044000   -0.894 
171.594
- Determinant of rotation matrix 1.00
- Column-vector products (12,13,23)  0.000.000.00
- Crowther Alpha Beta Gamma   106.709 179.736  73.291
- ***Spherical polars Omega Phi Chi   90.132 -73.291 
180.000***
- Direction cosines of rotation axis 0.287514-0.957774 
-0.002303 
- X-PLOR polars Phi Psi Kappa *undefined* *undefined* 180.000
- Lattmann Theta+ Theta2 Theta-  -180.000 179.736-146.582
- Rotation angle 180.000
-
  * if you use the .odb file outside of the USF software, be aware the 
matrix is the transpose
(or more accurately it is written by columns). In ccp4 this is taken care of withthe 
keyword "odb".


On 06/19/2015 09:07 AM, Tobias Beck wrote:

Dear all,

I have a PDB file that contains NCS in the asymmetric unit, probably 
point group D3.

1.) What program is recommended for determining the symmetry operators 
from PDB coordinates? I found findncs, but this uses only heavy atom 
coordinates (I could probably use just the sulfurs from the PDB as a work 
around).

2.) Then I would like to compare the PDB file to a related structure. 
Here I would like to align the symmetry operators determined above with 
symmetry elements found in a different space group, for example align the 
twofold axis from NCS with a twofold axis in found in a particular space group.
What is a good way to go about this?

I am aware that NCS is used in programs as restraints during 
refinement, but here I am interested in obtaining the NCS symmetry operators 
and aligning them to symmetry elements present in a new space group. Maybe I am 
overlooking an obvious solution.

Any help is greatly appreciated.

Thanks and best wishes, Tobias.
--
___

Dr. Tobias Beck
- independent group leader -
RWTH Aachen University
Institute of Inorganic Chemistry
Landoltweg 1, office: 304N
52056 Aachen, Germany
phone: +49-241-80-90057 
fax: +49-241-80-99003 
web: http://www.ac.rwth-aachen.de/extern/beck/
___




--
___

Dr. Tobias Beck
- independent group leader -
RWTH Aachen University
Institute of Inorganic Chemistry
Landoltweg 1, office: 304N
52056 Aachen, Germany
phone:  +49-241-80-90057
fax:   +49-241-80-99003
web: http://www.ac.rwth-aachen.de/extern/beck/
_

Re: [ccp4bb] OT: mapping PDB to mmCIF data quantities

2015-07-07 Thread Ethan A Merritt
On Tuesday, 07 July, 2015 13:05:55 Phil Jeffrey wrote:
> I'm updating some code to have limited mmCIF/PDB format interoperability 
> and have hit a snag.  While I can infer the connection between some data 
> items in the PDB header REMARK and the items in mmCIF I can't 
> definitively deduce some others.  In particular the mapping of
> REMARK  2  RESOLUTION
> seems a little ambiguous and the dictionary documentation doesn't help 
> in this regard.

So far as I know, anything that begins with "REMARK" is not guaranteed
to follow any standardized convention.  Different programs fill in 
different things here, and depositors can add new stuff.
The current PDB documentation states:

  REMARK 2 states the highest resolution, in Angstroms, that was used in 
  building the model. As with all the remarks, the first REMARK 2 record 
  is empty and is used as a spacer.

"Used in building the model" is nicely ambiguous, so I doubt that 
you can map it uniquely to any single value reported by some particular
program.

Ethan



> 
> Does anyone know where to find an explicit mapping of one data field to 
> another between the two formats ?  (I don't expect there to be a data 
> field in the PDB header for everything in mmCIF but I do for the reverse 
> case).
> 
> 
> Thanks
> Phil Jeffrey
> Princeton
-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742


Re: [ccp4bb] paired refinement

2015-07-07 Thread Shane Caldwell
Chiming in late with a follow-up question:

>On the other hand in paired refinement, if adding the data improves the
structure
>as measured by Rfree in a zone excluding the added data, then it is hard
to deny
>that that data are worth including.

Is it correct to think that model geometry would also be valuable at this
point? If adding reflections lead to a model with more reasonable average
bond angles, reduced clashes, etc., that would indicate that the added
reflections have improved the refinement, no? The geometry stats should
also be completely independent from the crystallographic stats.

Shane Caldwell
McGill University



On Fri, Jul 3, 2015 at 2:56 AM, Kay Diederichs <
kay.diederi...@uni-konstanz.de> wrote:

> On Thu, 2 Jul 2015 13:25:07 -0400, Edward A. Berry 
> wrote:
>
> >My take on this-
> >No one has been willing to specify a cutoff (and probably there is no
> rigorous way to
> >mathematically define the cutoff) and say "If CC* (or CCfree or whatever)
> is below X
> >then it will not improve your structure, if above X then it will".
>
> the electron microscopy community uses a similar measure ("FSC", Fourier
> Shell Correlation) as CC1/2. They follow their "Gold Standard" if they cut
> their data at FSC=0.143 . Mathematically, CC1/2=0.143 is equivalent to
> CC*=0.5 . So researchers of that community _do_ specify a cutoff, and by
> calling it "Gold Standard" they cast it in stone. Very helpful because
> probably no reviewer ever calls a "Gold Standard" into question.
>
> > Probably depends
> >among other things on how strong the lower resolution data is, how good
> the
> >structure is without the added data.
>
> the latter point is crucial: a structure that is good can "make use of"
> higher-resolution data than a structure that is not properly refined. That
> is different from the situation in electron microscopy, where the phases
> are obtained experimentally. This is why an X-ray structure at an early
> stage of iterative refinement/fitting may possibly not be improved by the
> weak high-resolution data , and why the paired refinement should be done
> during the "end game" of refinement. But as long as CC1/2 is statistically
> significant it may improve a very good model even if CC*<0.5 (see Bublitz
> et al IUCrJ 2, 409-420 (2015) for an example).
>
> To find out how close the structure to the data is, it helps to compare
> CCwork and CC*.
>
> An arbitrary cutoff (like CC*=0.5) is thus not sensible in all situations;
> it may serve as a rule of thumb though since the difference in resolution
> limit is not large anyway: CC*=0.5 and CC*=0.3 usually differ by (say) 0.1A
> only.
>
> >On the other hand in paired refinement, if adding the data improves the
> structure
> >as measured by Rfree in a zone excluding the added data, then it is hard
> to deny
> >that that data are worth including.
>
> Absolutely. Much better than to believe in rules of thumb.
>
> best,
>
> Kay
>
> >
> >eab
> >
> >On 07/02/2015 12:52 PM, Keller, Jacob wrote:
> >> Wasn’t all of this put to bed through the implementation of CC measures?
> >>
> >> JPK
> >>
> >> *From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf
> Of *Robbie Joosten
> >> *Sent:* Thursday, July 02, 2015 12:46 PM
> >> *To:* CCP4BB@JISCMAIL.AC.UK
> >> *Subject:* Re: [ccp4bb] paired refinement
> >>
> >> But it is not the R-free of the shell here. In paired refinement you
> take the R-free of the reflections outside the shell.
> >>
> >> Cheers,
> >> Robbie
> >>
> >> Sent with my Windows Phone
> >>
> >>
> --
> >>
> >> *Van: *Edward A. Berry 
> >> *Verzonden: *‎2-‎7-‎2015 18:43
> >> *Aan: *CCP4BB@JISCMAIL.AC.UK 
> >> *Onderwerp: *Re: [ccp4bb] paired refinement
> >>
> >> Another criterion for cutoff, also requiring the structure to be solved,
> >> is the agreement between data and structure, e.g. Rfree or CCfree.
> >> I think it is very unlikely that you could get Rfree =.2493 in a shell
> >> which contains only noise. So

Re: [ccp4bb] paired refinement

2015-07-07 Thread Dale Tronrud
   Comparing stats on geometry as well as R values is confounded by the
problem of choosing weights.  Should you hold the weights fixed or
perform an individualized weight optimization at each step?

   More importantly, our geometry libraries are imperfect.  We know from
surveys that the fit of models to Engh & Huber gets worst as the
resolution of their X-ray data gets higher.  This is because there are
real (and to a good extent conformationally dependent) variations in
bond angles that are brought to light by the high resolution (better
than about 1.6A) data.

   If I add quality high resolution data I would expect the geometry
stats to get worst.

Dale Tronrud

On 7/7/2015 11:17 AM, Shane Caldwell wrote:
> Chiming in late with a follow-up question:
> 
>>On the other hand in paired refinement, if adding the data improves the
> structure
>>as measured by Rfree in a zone excluding the added data, then it is
> hard to deny
>>that that data are worth including.
> 
> Is it correct to think that model geometry would also be valuable at
> this point? If adding reflections lead to a model with more reasonable
> average bond angles, reduced clashes, etc., that would indicate that the
> added reflections have improved the refinement, no? The geometry stats
> should also be completely independent from the crystallographic stats.
> 
> Shane Caldwell
> McGill University
> 
> 
> 
> On Fri, Jul 3, 2015 at 2:56 AM, Kay Diederichs
> mailto:kay.diederi...@uni-konstanz.de>>
> wrote:
> 
> On Thu, 2 Jul 2015 13:25:07 -0400, Edward A. Berry
> mailto:ber...@upstate.edu>> wrote:
> 
> >My take on this-
> >No one has been willing to specify a cutoff (and probably there is no 
> rigorous way to
> >mathematically define the cutoff) and say "If CC* (or CCfree or 
> whatever) is below X
> >then it will not improve your structure, if above X then it will".
> 
> the electron microscopy community uses a similar measure ("FSC",
> Fourier Shell Correlation) as CC1/2. They follow their "Gold
> Standard" if they cut their data at FSC=0.143 . Mathematically,
> CC1/2=0.143 is equivalent to CC*=0.5 . So researchers of that
> community _do_ specify a cutoff, and by calling it "Gold Standard"
> they cast it in stone. Very helpful because probably no reviewer
> ever calls a "Gold Standard" into question.
> 
> > Probably depends
> >among other things on how strong the lower resolution data is, how good 
> the
> >structure is without the added data.
> 
> the latter point is crucial: a structure that is good can "make use
> of" higher-resolution data than a structure that is not properly
> refined. That is different from the situation in electron
> microscopy, where the phases are obtained experimentally. This is
> why an X-ray structure at an early stage of iterative
> refinement/fitting may possibly not be improved by the weak
> high-resolution data , and why the paired refinement should be done
> during the "end game" of refinement. But as long as CC1/2 is
> statistically significant it may improve a very good model even if
> CC*<0.5 (see Bublitz et al IUCrJ 2, 409-420 (2015) for an example).
> 
> To find out how close the structure to the data is, it helps to
> compare CCwork and CC*.
> 
> An arbitrary cutoff (like CC*=0.5) is thus not sensible in all
> situations; it may serve as a rule of thumb though since the
> difference in resolution limit is not large anyway: CC*=0.5 and
> CC*=0.3 usually differ by (say) 0.1A only.
> 
> >On the other hand in paired refinement, if adding the data improves the 
> structure
> >as measured by Rfree in a zone excluding the added data, then it is hard 
> to deny
> >that that data are worth including.
> 
> Absolutely. Much better than to believe in rules of thumb.
> 
> best,
> 
> Kay
> 
> >
> >eab
> >
> >On 07/02/2015 12:52 PM, Keller, Jacob wrote:
> >> Wasn’t all of this put to bed through the implementation of CC
> measures?
> >>
> >> JPK
> >>
> >> *From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
> ] *On Behalf Of *Robbie Joosten
> >> *Sent:* Thursday, July 02, 2015 12:46 PM
> >> *To:* CCP4BB@JISCMAIL.AC.UK 
> >> *Subject:* Re: [ccp4bb] paired refinement
> >>
> >> But it is not the R-free of the shell here. In paired refinement
> you take the R-free of the reflections outside the shell.
> >>
> >> Cheers,
> >> Robbie
> >>
> >> Sent with my Windows Phone
> >>
> >>
> 
> -

[ccp4bb] Classifying Diverse Conformations of Many Structures of a Protein

2015-07-07 Thread Keller, Jacob
Is anyone aware of a way to classify large numbers (100s) of 
conformationally-diverse crystal structures of a single protein (here 
calmodulin)? Pairwise RMSD matrixes seem possible, but may be complicated since 
there are two somewhat stable lobes, and the flexible linker in the middle. 
What I am imagining is a sort of multidimensional tree depicting the 
relationships in conformation space of the various structures.

I remember something for this called esct or similar, but can't seem to google 
it.

Any thoughts?

Jacob

***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***


Re: [ccp4bb] Classifying Diverse Conformations of Many Structures of a Protein

2015-07-07 Thread Tristan Croll
Sounds like a perfect application for principal components analysis. Check out 
Bio3D: http://thegrantlab.org/bio3d/index.php.

Cheers,

Tristan

 
 
Tristan Croll
Lecturer
Faculty of Health
School of Biomedical Sciences
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443
 
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> On 8 Jul 2015, at 11:06 am, Keller, Jacob  wrote:
> 
> Is anyone aware of a way to classify large numbers (100s) of 
> conformationally-diverse crystal structures of a single protein (here 
> calmodulin)? Pairwise RMSD matrixes seem possible, but may be complicated 
> since there are two somewhat stable lobes, and the flexible linker in the 
> middle. What I am imagining is a sort of multidimensional tree depicting the 
> relationships in conformation space of the various structures.
> 
> I remember something for this called esct or similar, but can't seem to 
> google it.
> 
> Any thoughts?
> 
> Jacob
> 
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: kell...@janelia.hhmi.org
> ***


[ccp4bb] [Job] Postdoctoral Position in Structural Biology at Mayo Clinic, Rochester, USA

2015-07-07 Thread Mer, Georges, Ph.D.
Postdoctoral Position in Structural Biology at Mayo Clinic, Rochester, USA

A Postdoctoral position is available to a highly motivated individual trained 
in structural biology. The project will involve the structural and dynamic 
characterization of large protein complexes broadly involved in chromatin 
remodeling and the DNA damage response.

Funding for this position is secured for up to 5 years.

Please email a CV and a letter of motivation to Georges Mer:  
mer.geor...@mayo.edu

A Postdoctoral Research Fellow at Mayo Clinic is a temporary position supported 
by a competitive salary and benefits package. Qualified individuals will 
demonstrate potential for research as evidenced by their training and 
peer-reviewed publications.

Re: [ccp4bb] Classifying Diverse Conformations of Many Structures of a Protein

2015-07-07 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Jacob,

information about Thomas Schneider's program 'escet' that you remember
can be found at
http://www.embl-hamburg.de/~tschneider/escet/index.html

Best,
Tim

On 07/08/2015 03:03 AM, Keller, Jacob wrote:
> Is anyone aware of a way to classify large numbers (100s) of
> conformationally-diverse crystal structures of a single protein
> (here calmodulin)? Pairwise RMSD matrixes seem possible, but may be
> complicated since there are two somewhat stable lobes, and the
> flexible linker in the middle. What I am imagining is a sort of
> multidimensional tree depicting the relationships in conformation
> space of the various structures.
> 
> I remember something for this called esct or similar, but can't
> seem to google it.
> 
> Any thoughts?
> 
> Jacob
> 
> *** Jacob Pearson Keller,
> PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr,
> Ashburn, VA 20147 email: kell...@janelia.hhmi.org 
> ***
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149

GPG Key ID = A46BEE1A

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