Re: [ccp4bb] Per-residue RMSD for multiple structures?

[Stephen Graham]

I am pretty sure you can do this using LSQMAN from Gerard (BluRay?) Kleywegt.

The pertinent commands are MCENTRAL to determine the 'most
representative structure' (i.e. the one to align upon and show in the
figure), MALIGN to do the alignment and then MPLOT to calculate a
'multi-RMSD' for each residue (see manual for details - set the
'cut-off for printing' to 0 to get all values).

Regards depiction, I think pymol can also represent structures as
sausages based on their B values:
cartoon putty
show cartoon

HTH,

Stephen

On 23 February 2010 01:31, Ethan Merritt  wrote:
> Hi all,
>
> I am comparing 4 very similar (<1.5A rmsd) large (750 residues) structures,
> but struggling to find a way to generate a figure that conveys where they
> are most alike and where they diverge.
>
> Simply drawing a superimposed set of backbone traces results in what looks
> like colored spaghetti.  I don't think that's going to work.
>
> So I had the idea of drawing a single backbone trace, or ribbon diagram,
> and coloring by the RMSD of the four C-alphas at each residue position.
> But I can't find a program that will output this as a table of numbers
> I can use.  All of the multiple structure superposition programs must
> have this information internally.  After all, that's what they are minimizing.
> But do any of the programs provide an option to write it out?
>
> I can get pairwise per-residue deviations by doing SSM superposition in Coot,
> but that doesn't get me to an RMSD for all four structures jointly.
>
>        Ethan
>
>
> --
> Ethan A Merritt
> Biomolecular Structure Center
> University of Washington, Seattle 98195-7742
>



-- 
Dr Stephen Graham
1851 Research Fellow
Cambridge Institute for Medical Research
Wellcome Trust/MRC Building
Addenbrooke's Hospital, Hills Road
Cambridge, CB2 0XY, UK
Phone: +44 1223 762 638

Re: [ccp4bb] Per-residue RMSD for multiple structures?

[Mensur Dlakic]

One possible representation is the "sausage" produced by MOLMOL. It is 
meant for NMR ensembles - the thickness of sausage is directly proportional 
to local RMSD. Take a look at this image:


http://www.msg.ucsf.edu/local/programs/molmol/images/tutorial_ex3.gif

MOLMOL can be downloaded from 
http://www.mol.biol.ethz.ch/groups/wuthrich_group/software


At 06:31 PM 2/22/2010, Ethan Merritt wrote:

Hi all,

I am comparing 4 very similar (<1.5A rmsd) large (750 residues) structures,
but struggling to find a way to generate a figure that conveys where they
are most alike and where they diverge.

Simply drawing a superimposed set of backbone traces results in what looks
like colored spaghetti.  I don't think that's going to work.

So I had the idea of drawing a single backbone trace, or ribbon diagram,
and coloring by the RMSD of the four C-alphas at each residue position.
But I can't find a program that will output this as a table of numbers
I can use.  All of the multiple structure superposition programs must
have this information internally.  After all, that's what they are minimizing.
But do any of the programs provide an option to write it out?

I can get pairwise per-residue deviations by doing SSM superposition in Coot,
but that doesn't get me to an RMSD for all four structures jointly.

Ethan


--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742


==
| Mensur Dlakic, PhD| Tel: (406) 994-6576|
| Department of Microbiology| Fax: (406) 994-4926|
| Montana State University  | Lab: (406) 994-6237|
| 109 Lewis Hall, P.O. Box 173520   | http://myprofile.cos.com/mensur|
| Bozeman, MT 59717-3520| E-mail: mdla...@montana.edu|
==

[ccp4bb] Postdoctoral position available in structural virology

[Frank Lee]

Applications are invited for a postdoctoral position in Dr. Fang Li's
lab at the Department of Pharmacology, University of Minnesota Twin
Cities. Research involves biochemical and structural studies on
proteins that guide invasion and replication of important viral
pathogens.

Strong background in molecular biology and protein
biochemistry is required. Experience in insect cell culture and protein 
crystallography is preferred. Candidates must have completed PhD at
the time of the appointment. Salary commensurates with experience. The
position starts immediately. For more information about Dr. Li's lab,
visit http://www.msi.umn.edu/~lifang/



Interested applicants should send (1) a resume, (2) a one-page summary
of previous research experience, and (3) arrange three letters of
recommendation to Dr. Fang Li via emai: lif...@umn.edu



  

[ccp4bb] Per-residue RMSD for multiple structures?

[Ethan Merritt]

Hi all,

I am comparing 4 very similar (<1.5A rmsd) large (750 residues) structures, 
but struggling to find a way to generate a figure that conveys where they 
are most alike and where they diverge.  

Simply drawing a superimposed set of backbone traces results in what looks
like colored spaghetti.  I don't think that's going to work.

So I had the idea of drawing a single backbone trace, or ribbon diagram,
and coloring by the RMSD of the four C-alphas at each residue position.
But I can't find a program that will output this as a table of numbers
I can use.  All of the multiple structure superposition programs must
have this information internally.  After all, that's what they are minimizing.
But do any of the programs provide an option to write it out?

I can get pairwise per-residue deviations by doing SSM superposition in Coot,
but that doesn't get me to an RMSD for all four structures jointly.

Ethan


-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] crystal contacts

[Parthasarathy Sampathkumar]

Dear Amit,

You might want to take a look at NOXclass webserver:
http://noxclass.bioinf.mpi-inf.mpg.de/help.php

Relevant paper is available at:
http://www.biomedcentral.com/1471-2105/7/27

Goold Luck,
Partha Sampathkumar
NYSGXRC

On Mon, Feb 22, 2010 at 6:49 AM, amit sharma <3112a...@gmail.com> wrote:

> Dear All,
>
> Apologies for a non-CCP4question. I have a structure of a dimeric molecule,
> where the interfaces between monomers is held by a couple of tyrosine
> residues (per monomer)  juxtaposed with each other. The molecule exists as a
> dimer in solution. Are there ways/programs to show that the interaction
> between the tyrosine residues is not a consequence of crystal contacts. I
> guess the fact that the molecule occurs as a dimer in solution strongly
> suggests so. Also, any directions towards literature showing similar cases
> would be of great help.
>
> Many thanks in advance
> --
> Amit Sharma
> Postdoctoral Fellow,
> Department of Biophysics,
> Johns Hopkins University,
> Baltimore,
> MD21218
>

Re: [ccp4bb] short step

[Edward A. Berry]

Edward A. Berry wrote:

Try grepping "crystal" your .x files (or whatever you called the
denzo output files). Also grep for "start".

By default denzo updates start-phi to the end
of the previous oscillation. Since 0,5 degree is within radius of
convergence, it re-refines crystal rotx to be compatible with this
assumption and the oscillation photograph, which means crystal rotx
will be moving backwards 0.5 degrees for each frame. Scalepack
in postrefinement sees this as a serious case of "slippage" and is
unable to postrefine a value of crystal rotx that is compatible with
all the frames.

(and dies trying)



It may be possible to turn of post-refinement with "POSTREFINE 0"
or some such.

Or keep post-refinement but "fit batch rotx" instead of "fit crystal rotx".
This allows it to refine a separate value of rotx for every frame.


Ed B

Ed Pozharski wrote:

I want to process bunch of frames with extremely short step - i.e. these
are 0.5degree oscillations but crystal only rotates by 1 degree over
1000 frames (I would have kept it at the same orientation if Rigaku
control software would allow zero step). Denzo can process the frames
all right, but scalepack chokes on it saying "Floating Exception". I
don't have much experience with mosflm, and it failed also.

What I wonder is if this happens because both programs have some bug in
these unusual conditions or there is something fundamental that prevents
scaling such data?

Cheers,

Ed.

Re: [ccp4bb] short step

[Edward A. Berry]

Try grepping "crystal" your .x files (or whatever you called the
denzo output files). Also grep for "start".

By default denzo updates start-phi to the end
of the previous oscillation.  Since 0,5 degree is within radius of
convergence, it re-refines crystal rotx to be compatible with this
assumption and the oscillation photograph, which means crystal rotx
will be moving backwards 0.5 degrees for each frame. Scalepack
in postrefinement sees this as a serious case of "slippage" and is
unable to postrefine a value of crystal rotx that is compatible with
all the frames.

It may be possible to turn of post-refinement with "POSTREFINE 0"
or some such.

Ed

Ed Pozharski wrote:

I want to process bunch of frames with extremely short step - i.e. these
are 0.5degree oscillations but crystal only rotates by 1 degree over
1000 frames (I would have kept it at the same orientation if Rigaku
control software would allow zero step).  Denzo can process the frames
all right, but scalepack chokes on it saying "Floating Exception".  I
don't have much experience with mosflm, and it failed also.

What I wonder is if this happens because both programs have some bug in
these unusual conditions or there is something fundamental that prevents
scaling such data?

Cheers,

Ed.

Re: [ccp4bb] short step

[Ethan Merritt]

On Monday 22 February 2010 15:23:35 Ed Pozharski wrote:
> I want to process bunch of frames with extremely short step - i.e. these
> are 0.5degree oscillations but crystal only rotates by 1 degree over
> 1000 frames (I would have kept it at the same orientation if Rigaku
> control software would allow zero step).  Denzo can process the frames
> all right, but scalepack chokes on it saying "Floating Exception".  I
> don't have much experience with mosflm, and it failed also.  

I would not expect any program to deal successfully with this, because
the reflection profile along the rotation axis (successive frames) is
essentially infinite.

Perhaps there is some way you can turn off all scaling of partials?  

Or maybe you can set the mosaicity to 0, and hope that no reflections
are treated as being partials?

I suppose what you really want is the change in intensity for a 
given integration box on the surface of the detector over time?
But that is not what the normal scaling programs are designed for.

somewhat puzzled,

Ethan


> What I wonder is if this happens because both programs have some bug in
> these unusual conditions or there is something fundamental that prevents
> scaling such data? 
> 
> Cheers,
> 
> Ed.
> 
> -- 
> Edwin Pozharski, PhD, Assistant Professor
> University of Maryland, Baltimore
> --
> When the Way is forgotten duty and justice appear;
> Then knowledge and wisdom are born along with hypocrisy.
> When harmonious relationships dissolve then respect and devotion arise;
> When a nation falls to chaos then loyalty and patriotism are born.
> --   / Lao Tse /
> 



-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] crystal contacts

[Bostjan Kobe]

Dear Amit

As Paul suggests, you can get some idea if the interaction is consistent
with biologically relevant protein-protein interfaces through looking at the
the size of the interface and the nature of the contacts in the interface.
There is substantial literature on this topic, see
http://www.ncbi.nlm.nih.gov/pubmed/19021571?itool=EntrezSystem2.PEntrez.Pubm
ed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=11
for example for a review.

The better way of course to test the relevance of this interface is
experimentally, by mutating the tyrosines and seeing the effect on the
oligomeric state in solution.

Best wishes

Bostjan


On 23/02/10 12:57 AM, "Paul Emsley"  wrote:

> amit sharma wrote:
>> 
>> Apologies for a non-CCP4question.
> 
> Aggh!  Stop! Stop it! Stop apologising for using CCP4BB in the way
> it is supposed to be used!
> 
> And not only that, this is not a non-CCP4 question.
> 
>> I have a structure of a dimeric molecule, where the interfaces between
>> monomers is held by a couple of tyrosine residues (per monomer)
>> juxtaposed with each other. The molecule exists as a dimer in
>> solution. Are there ways/programs to show that the interaction between
>> the tyrosine residues is not a consequence of crystal contacts. I
>> guess the fact that the molecule occurs as a dimer in solution
>> strongly suggests so. Also, any directions towards literature showing
>> similar cases would be of great help.
> 
> PISA tries to distinguish between assemblies that occur only as a result
> of crystal contacts and those that are intrinsic molecular interactions.
> 
> 
> Paul.

---
Bostjan Kobe
ARC Federation Fellow
Professor of Structural Biology
School of Chemistry and Molecular Biosciences
  and Institute for Molecular Bioscience (Division of Chemistry and
Structural Biology)
Cooper Road
University of Queensland
Brisbane, Queensland 4072
Australia
Phone: +61 7 3365 2132
Fax: +61 7 3365 4699
E-mail: b.k...@uq.edu.au
URL: http://profiles.bacs.uq.edu.au/Bostjan.Kobe.html
Office: Building 76 Room 329
Notice: If you receive this e-mail by mistake, please notify me, and do not
make any use of its contents. I do not waive any privilege, confidentiality
or copyright associated with it. Unless stated otherwise, this e-mail
represents only the views of the Sender and not the views of The University
of Queensland.

[ccp4bb] short step

[Ed Pozharski]

I want to process bunch of frames with extremely short step - i.e. these
are 0.5degree oscillations but crystal only rotates by 1 degree over
1000 frames (I would have kept it at the same orientation if Rigaku
control software would allow zero step).  Denzo can process the frames
all right, but scalepack chokes on it saying "Floating Exception".  I
don't have much experience with mosflm, and it failed also.  

What I wonder is if this happens because both programs have some bug in
these unusual conditions or there is something fundamental that prevents
scaling such data? 

Cheers,

Ed.

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
--   / Lao Tse /

[ccp4bb] XDS Data Processing webinar

[Angela Criswell]

Dear colleagues,

I would like to draw your attention to an upcoming educational webinar 
that will cover data processing with XDS. This webinar is the 2nd in the 
previously posted webinar series to cover X-ray diffraction data 
processing packages.

This week's webinar, presented by Kay Diederichs, is titled "Practical 
Approaches to Data Processing with XDS" and will take place on February 
25, 2010 at  9:00 AM EST (2:00 GMT). You can find more information 
including a registration link at the following site: 
http://www.rigaku.com/protein/webinars.html

Best regards,
Angela



--
Angela R. Criswell, Ph. D.
VP, Life Sciences
Rigaku Americas Corporation
9009 New Trails Drive
The Woodlands, TX  77381
Ph: +1 281 362 2300 ext. 216
Fax: +1 281 364 3628
Email: angela.crisw...@rigaku.com
URL: http://www.Rigaku.com

Re: [ccp4bb] crystal contacts

[Paul Emsley]

amit sharma wrote:


Apologies for a non-CCP4question. 


Aggh!  Stop! Stop it! Stop apologising for using CCP4BB in the way 
it is supposed to be used!


And not only that, this is not a non-CCP4 question.

I have a structure of a dimeric molecule, where the interfaces between 
monomers is held by a couple of tyrosine residues (per monomer)  
juxtaposed with each other. The molecule exists as a dimer in 
solution. Are there ways/programs to show that the interaction between 
the tyrosine residues is not a consequence of crystal contacts. I 
guess the fact that the molecule occurs as a dimer in solution 
strongly suggests so. Also, any directions towards literature showing 
similar cases would be of great help.


PISA tries to distinguish between assemblies that occur only as a result 
of crystal contacts and those that are intrinsic molecular interactions.



Paul.

[ccp4bb] crystal contacts

[amit sharma]

Dear All,

Apologies for a non-CCP4question. I have a structure of a dimeric molecule,
where the interfaces between monomers is held by a couple of tyrosine
residues (per monomer)  juxtaposed with each other. The molecule exists as a
dimer in solution. Are there ways/programs to show that the interaction
between the tyrosine residues is not a consequence of crystal contacts. I
guess the fact that the molecule occurs as a dimer in solution strongly
suggests so. Also, any directions towards literature showing similar cases
would be of great help.

Many thanks in advance
-- 
Amit Sharma
Postdoctoral Fellow,
Department of Biophysics,
Johns Hopkins University,
Baltimore,
MD21218

Re: [ccp4bb] domain contact surface

[Rafael Fernández Leiro]

Dear Jane, 

If you rename one of domains with a different chain ID (in the PDB) you can 
submit the structure to PISA 
(http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html) and it will do the job.
Regards
Rafa
===
Rafael Fernández Leiro
Departamento de Biología Celular y Molecular
Facultad de Ciencias
Universidade da Coruña
Campus de A Zapateira s/n
E-15071 La Coruña (Spain)
Phone: +34 981 167 000 / 2136 (Lab.)
   +34 666 003 613(Home)
===
El 19/02/2010, a las 16:42, Jane Bailey escribió:

> Dear all,
> 
> I am trying to calculate the domain-domain contact surface from one chain. I 
> see AREAIMOL to only tell you the accessible surface area/residue. Could any 
> other software/webserve could specify residues in the contact surface and 
> calculate the total contact area?
> 
> Thanks
> 
> J.

[ccp4bb] Postdoc in Protein Crystallisation at the Swiss Light Source

[Rouven Bingel-Erlenmeyer]

/The Paul Scherrer Institute is with 1300 employees the largest research 
centre for natural and engineering sciences in Switzerland and a 
worldwide leading user laboratory. Its research activities are 
concentrated on the three main topics of solid-state physics, energy and 
environmental research as well as human health.


The Swiss Light Source (SLS) is one of the most advanced synchrotron 
radiation sources worldwide. The SLS operates two state-of-the-art 
undulator beam lines for protein crystallography, and a third, highly 
automated beam line located at a superbend magnet (X06DA). At beam line 
X06DA a crystallisation facility which is integrated with the beam line 
in order to allow for in situ X-ray diffraction screening is being 
implemented. The Macromolecular Crystallography Group (MX-Group) is 
involved in several aspects of protein crystallography including the 
design and construction of new beam line components as well as various 
structural biology projects, especially in collaboration with the 
Biomolecular Research Group at our institute under the guidance of Prof. 
Dr Gebhard Schertler.


We are looking for a /


 Postdoctoral Fellow

*in protein crystallisation *


 Your tasks

You will coordinate and ultimately lead our efforts to further establish 
the high-throughput crystallisation facility and its integration with 
beam line X06DA at the Swiss Light Source. In collaboration with the 
scientists and engineers of the SLS MX-Group as well as the PSI 
structural biology unit you will additionally further develop the in 
situ X-ray diffraction screening capabilities of the facility and 
coordinate its integration with the sample data base. In addition, there 
are excellent opportunities to pursue your own research projects in 
protein crystallography.



 Your profile

You hold a PhD degree in biology or (bio-)chemistry, and have experience 
in either protein crystallography or high-throughput methods in 
crystallisation. Experience in synchrotron related research or with data 
bases is a plus. If you are self-motivated and a good team player this 
position will offer great opportunities to start your research career in 
an exciting and highly multidisciplinary environment.


For further information please contact: Dr Rouven Bingel-Erlenmeyer, 
phone +41 56 310 58 23, rouven.bingel-erlenme...@psi.ch 
 or Dr Clemens Schulze-Briese, 
phone +41 56 310 45 33, clemens.schu...@psi.ch 



Please submit your application to: Paul Scherrer Institut, Human 
Resources, Ref. code 6112, Elke Baumann, 5232 Villigen PSI, Switzerland 
or to: elke.baum...@psi.ch 


--
**
Paul Scherrer Institute
Dr. Rouven Bingel-Erlenmeyer
Swiss Light Source
WSLA 222
5232 Villigen
SWITZERLAND

rouven.bingel-erlenme...@psi.ch
http://sls.web.psi.ch

+41 56 310 5823 phone
+41 56 310 5292 fax
**