[ccp4bb] Open Beamline Scientist Position at XAIRA beamline-Alba Synchrotron

[J Juanhuix Gibert]

Dear colleagues,

A position of Beamline Scientist for the new BL06-XAIRA microfocus 
Macromolecular Crystallography beamline at the Alba Synchrotron 
(Barcelona) is currently open. We are seeking a positive, motivated 
scientist, proficient in macromolecular crystallography methods, 
computer/programming oriented, preferably with experience in beamline 
operation and/or the design of MX end station elements, and keen to join 
the beamline team in an exciting environment.


BL06-XAIRA beamline, which will join the existing XALOC beamline 
at Alba to cater the 
worldwide MX community, is now in the design phase and is planned to be 
operational late 2020. The beamline aims at producing a 4-15 keV X-ray 
beam with a focal spot size of ~3x1 um2 FWHM optimized to /standard 
/microfocus MX experiments  at an energy of ~12 keV, as well as to 
native phasing experiments at 4 keV or higher energies.


The successful candidate will be encouraged to develop his/her 
scientific research while making it compatible with the construction and 
commissioning of the beamline, as well as with the research lines in 
structural biology already ongoing at Alba.


Deadline for applications is _14 July 2017_. To have information on the 
profile and to apply to the position please refer to:

https://intranet.cells.es/Jobs/JobOffers/ViewJob?job_id=257

Best regards,


*Jordi Juanhuix *

BL06-XAIRA Beamline Responsible

*ALBA SYNCHROTRON LIGHT SOURCE*

_Carrer__de la llum, 2-26 | 08290 | Cerdanyola del Vallès| Barcelona | 
Spain _ 

(+34) 935924322



*_www.albasynchrotron.es_ **| 
**_juanh...@cells.es _ *


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Re: [ccp4bb] RMSD between unaligned structures

[James Holton]

James,

I wrote a jiffy script for doing this ages ago.

http://bl831.als.lbl.gov/~jamesh/pickup/rmsd

Please feel free to copy/edit/port and use in whatever you like. It's 
only a few dozen lines.  Reports RMS deviations for all pairs of atoms 
with the same "name" (columns 12-27 in the PDB file), no matter how far 
apart they are.


I had not noticed Compar before!  But it does give me the same result as 
my jiffy script if I give it large distance and B cutoffs.  Compar might 
be faster if that's important.


On a similar subject, reforigin, csymmatch and 
phenix.find_alt_orig_sym_mate can do hand flips as well as origin 
shifts, but I don't see anything out there except perhaps zanuda that 
can hop over alternative indexing choices.  For example, if you blindly 
solve the same structure from two different data sets and then want to 
compare the PDB files, you will get into trouble if your space group is, 
say, P31, where there are four different and mutually-incompatible ways 
to have indexed the data.  Unless you used a reference data set, your 
automated data processing program probably chose one of the four 
possible indexing conventions at random.  Neither Phenix nor CCP4 seem 
to have a tool for resolving such cases.  Not from PDB files alone.  
Yes, you can always go back and re-process your data with a reference, 
or you can be more cleverer and use Pointless to re-index the merged 
data using a PDB file as a reference, but then you are stuck as to what 
real-space operator to apply to the PDB file that has already been 
carefully refined against the data that Pointless just re-indexed.  What 
real-space operator "follows" a given re-indexing operation in 
reciprocal space?  It's not as trivial as you might think.  Yes, you can 
always run a Phaser job to avoid thinking about symmetry, but that is a 
lot of CPU to burn up just to find a symmetry operator.  Zanuda does 
this internally, but doesn't seem to have a way of generating 
symmetry-allowed alignments without re-refining everything.  Or am I 
missing something?


-James Holton
MAD Scientist


On 7/3/2017 6:43 AM, R.D. Oeffner wrote:


Hi James

If you have access to a Phenix installation then 
phenix.find_alt_orig_sym_mate does what you want in one go. It tries 
to position the two MR structures on the same origin and symmetry site 
like Csymmatch. Besides computing a score value indicating the quality 
of the match it also computes the RMSD between the two structures. 
This RMSD is computed with the sequence alignment generated by the SSM 
superpose program. So if one MR solution is wrong it would yield a 
rather large RMSD value.


Robert

On 03/07/2017 13:16, James Foadi wrote:


Hi Eleanor.
You do the alignment if you are looking to measure the similarity of 
two molecules after refinement or the similarity of two molecules in 
general. When you do this, like you say, you have to carry out some 
sort of alignment, i.e. you move one of the two structures so to have 
the highest degree of overlapping with the other , without any 
constraint. This is what most of the programs do (and after having 
done that they compute the RMSD). But I'm looking for a program to 
measure the RMSD of two fixed (un-moved) structures; the structures 
have already been moved (with the symmetry and unit cell origin 
constrain) by CSYMMATCH. Does it make sense to you?

James
Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell 
Science and Innovation Campus Didcot Oxfordshire OX11 0DE United 
Kingdom office email: james.fo...@diamond.ac.uk alternative email: 
j.fo...@imperial.ac.uk personal web page: http://www.jfoadi.me.uk



On Monday, 3 July 2017, 11:59, Eleanor Dodson 
 wrote:



Dont understand your Q James..
You have to make sort of alignment to get the RMSD surely?
And csymmatch will just apply the symmetry and origin shifts needed 
for any comparisonn?

E

On 3 July 2017 at 11:32, Stéphane Duquerroy 
mailto:stephane.duquer...@u-psud.fr>> 
wrote:


Hi James
LSQMAN can calculate the current RMSD between the 2 models
(RMsd_calc mol1 range1 mol2 range2 [Ltarget])
Be careful it renames the chain names
Stephane
-- -
Duquerroy Stéphane
Structural Virology Unit - PASTEUR INSTITUTE
25 rue du Dr Roux, 75015 Paris, France
lab: +33 (0)1 45 68 82 66
fax: +33 (0)1 45 68 89 93
email: sduq...@pasteur.fr 
-- --



*De: *"James Foadi" <09daa8ec3774-dmarc-
requ...@jiscmail.ac.uk
>
*À: *
*Envoyé: *Lundi 3 Juillet 2017 11:47:00
*Objet: *[ccp4bb] RMSD between unaligned structures

Dear ccp4 tribe,
this might have been asked before, but I haven't paid enough
attention.
I'd like to measure the RMSD between two models 

Re: [ccp4bb] to fix angle between ligand and residue atoms

[Robbie Joosten]

Hi Markus,



You can add  plenarity restraint to your LINK. You can model it after one of 
the peptide LINKs in the mon_lib_list.cif file from CCP4.



Cheers,

Robbie





Sent from my Windows 10 phone



Van: Markus Heckmann
Verzonden: maandag 3 juli 2017 16:46
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] to fix angle between ligand and residue atoms



Dear ccp4-ers,
I have a data set at 2.8 A. There is clear *continuous*  density for a
ligand + residue. I used the LINK record to connect the S-gamma-atom
from Cys to C1-atom of ligand OCA. My biochemistry collaborator says
that CB-SG-C1-O1 should be approximately planar. However, during
refinement with REFMAC5, the connecting region does lose planarity.
The ligand and residue does indeed stay properly inside the density. I
assume this is due to the low(er) resolution. Should I fix the
planarity or should I leave it to the refinement?
Thank you all,
Markus

Re: [ccp4bb] RMSD between unaligned structures

[Edward A. Berry]

I second the use of LSQMAN.
The command for calculating wo aligning appears to be:
rmsd_calc (abbreviated rm).
   http://xray.bmc.uu.se/usf/lsqman_man.html#S59

If you have multiple chains, use the option "chain_mode original"
before loading the pdb's to avoid renaming chains:
   http://xray.bmc.uu.se/usf/lsqman_man.html#S25

On 07/03/2017 06:32 AM, Stéphane Duquerroy wrote:

Hi James
LSQMAN can calculate the current RMSD between the 2 models (RMsd_calc mol1 
range1 mol2 range2 [Ltarget])
Be careful it renames the chain names

Stephane

---
Duquerroy Stéphane
Structural Virology Unit - PASTEUR INSTITUTE
25 rue du Dr Roux, 75015 Paris, France
lab: +33 (0)1 45 68 82 66
fax: +33 (0)1 45 68 89 93
email: sduq...@pasteur.fr




--
*De: *"James Foadi" <09daa8ec3774-dmarc-requ...@jiscmail.ac.uk>
*À: *
*Envoyé: *Lundi 3 Juillet 2017 11:47:00
*Objet: *[ccp4bb] RMSD between unaligned structures

Dear ccp4 tribe,
this might have been asked before, but I haven't paid enough attention.

I'd like to measure the RMSD between two models after molecular replacement. I 
can force the two models to overlap as much as possible within the symmetry and 
origin-shift constraints (using CSYMMATCH). But I don't want the program that 
compute RMSD to align the two structures. Can you suggest what I should use? 
And, perhaps, what keywords I should adopt?

Many thanks, in advance.

James
Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science and 
Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: 
james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk personal 
web page: http://www.jfoadi.me.uk

[ccp4bb] to fix angle between ligand and residue atoms

[Markus Heckmann]

Dear ccp4-ers,
I have a data set at 2.8 A. There is clear *continuous*  density for a
ligand + residue. I used the LINK record to connect the S-gamma-atom
from Cys to C1-atom of ligand OCA. My biochemistry collaborator says
that CB-SG-C1-O1 should be approximately planar. However, during
refinement with REFMAC5, the connecting region does lose planarity.
The ligand and residue does indeed stay properly inside the density. I
assume this is due to the low(er) resolution. Should I fix the
planarity or should I leave it to the refinement?
Thank you all,
Markus

Re: [ccp4bb] RMSD between unaligned structures

[R.D. Oeffner]

 

Hi James 

If you have access to a Phenix installation then
phenix.find_alt_orig_sym_mate does what you want in one go. It tries to
position the two MR structures on the same origin and symmetry site like
Csymmatch. Besides computing a score value indicating the quality of the
match it also computes the RMSD between the two structures. This RMSD is
computed with the sequence alignment generated by the SSM superpose
program. So if one MR solution is wrong it would yield a rather large
RMSD value. 

Robert 

On 03/07/2017 13:16, James Foadi wrote: 

> Hi Eleanor. 
> You do the alignment if you are looking to measure the similarity of two 
> molecules after refinement or the similarity of two molecules in general. 
> When you do this, like you say, you have to carry out some sort of alignment, 
> i.e. you move one of the two structures so to have the highest degree of 
> overlapping with the other , without any constraint. This is what most of the 
> programs do (and after having done that they compute the RMSD). But I'm 
> looking for a program to measure the RMSD of two fixed (un-moved) structures; 
> the structures have already been moved (with the symmetry and unit cell 
> origin constrain) by CSYMMATCH. Does it make sense to you? 
> 
> James 
> 
> Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science 
> and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office 
> email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk 
> personal web page: http://www.jfoadi.me.uk 
> 
> On Monday, 3 July 2017, 11:59, Eleanor Dodson  
> wrote:
> 
> Dont understand your Q James.. You have to make sort of alignment to get the 
> RMSD surely? And csymmatch will just apply the symmetry and origin shifts 
> needed for any comparisonn? E 
> 
> On 3 July 2017 at 11:32, Stéphane Duquerroy  
> wrote:
> 
>> Hi James 
>> LSQMAN can calculate the current RMSD between the 2 models (RMsd_calc mol1 
>> range1 mol2 range2 [Ltarget]) 
>> Be careful it renames the chain names 
>> 
>> Stephane 
>> 
>> -- -
>> Duquerroy Stéphane
>> Structural Virology Unit - PASTEUR INSTITUTE
>> 25 rue du Dr Roux, 75015 Paris, France
>> lab: +33 (0)1 45 68 82 66
>> fax: +33 (0)1 45 68 89 93
>> email: sduq...@pasteur.fr
>> -- --
>> 
>> -
>> 
>> DE: "James Foadi" <09daa8ec3774-dmarc- requ...@jiscmail.ac.uk>
>> À: 
>> ENVOYÉ: Lundi 3 Juillet 2017 11:47:00
>> OBJET: [ccp4bb] RMSD between unaligned structures 
>> 
>> Dear ccp4 tribe, 
>> this might have been asked before, but I haven't paid enough attention.
>> 
>> I'd like to measure the RMSD between two models after molecular replacement. 
>> I can force the two models to overlap as much as possible within the 
>> symmetry and origin-shift constraints (using CSYMMATCH). But I don't want 
>> the program that compute RMSD to align the two structures. Can you suggest 
>> what I should use? And, perhaps, what keywords I should adopt? 
>> 
>> Many thanks, in advance. 
>> 
>> James 
>> 
>> Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science 
>> and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office 
>> email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk 
>> personal web page: http://www.jfoadi.me.uk [1]

-- 
Robert Oeffner, Ph.D.
Research Associate, The Read Group
Department of Haematology, 
Cambridge Institute for Medical Research 
University of Cambridge 
Cambridge Biomedical Campus 
Wellcome Trust/MRC Building 
Hills Road 
Cambridge CB2 0XY

www.cimr.cam.ac.uk/investigators/read/index.html
tel: +44(0)1223 763234

 

Links:
--
[1] http://www.jfoadi.me.uk/

Re: [ccp4bb] RMSD between unaligned structures

[Eleanor Dodson]

Yes - I wrote something long long ago called compar. It is still there..



you give it XYZIN1 and XYZIN2 and I think it lists all distances somewhere
E


[ed1@setsuko ~]$ compar

 





 ###
 ###
 ###
 ### CCP4 7.0.042: COMPAR   version 7.0.042 : ##
 ###
 User: ed1  Run date:  3/ 7/2017 Run time: 13:36:49


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67,
235-242.
 as well as any specific reference in the program write-up.



FORMATTED  SCRATCH file opened on unit   7

Logical name: CMPTMP, Filename: /tmp/ed1/compar_TMP.30038


  unknown-format file is being opened on unit 1 for INPUT.


 *** RWBROOK error: point code unitfunction
 ***1   -41MMDB_F_Open
 *** file   : XYZIN1
 *** reason : cannot open a file
 *** continue running, may crash ...


 COMPAR:   XYZOPEN: Error opening logical name XYZIN1
 COMPAR:   XYZOPEN: Error opening logical name XYZIN1
Times: User:   0.0s System:0.0s Elapsed: 0:00





you give it XYZIN1 and XYZIN2 and I think it lists all distances..
E

On 3 July 2017 at 13:16, James Foadi  wrote:

> Hi Eleanor.
> You do the alignment if you are looking to measure the similarity of two
> molecules after refinement or the similarity of two molecules in general.
> When you do this, like you say, you have to carry out some sort of
> alignment, i.e. you move one of the two structures so to have the highest
> degree of overlapping with the other , without any constraint. This is what
> most of the programs do (and after having done that they compute the RMSD).
> But I'm looking for a program to measure the RMSD of two fixed (un-moved)
> structures; the structures have already been moved (with the symmetry and
> unit cell origin constrain) by CSYMMATCH. Does it make sense to you?
>
> James
>
> Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science
> and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office
> email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk
> personal web page: http://www.jfoadi.me.uk
>
>
> On Monday, 3 July 2017, 11:59, Eleanor Dodson 
> wrote:
>
>
> Dont understand your Q James..
> You have to make sort of alignment to get the RMSD surely?
> And csymmatch will just apply the symmetry and origin shifts needed for
> any comparisonn?
> E
>
> On 3 July 2017 at 11:32, Stéphane Duquerroy 
> wrote:
>
> Hi James
> LSQMAN can calculate the current RMSD between the 2 models (RMsd_calc mol1
> range1 mol2 range2 [Ltarget])
> Be careful it renames the chain names
>
> Stephane
>
> -- -
> Duquerroy Stéphane
> Structural Virology Unit - PASTEUR INSTITUTE
> 25 rue du Dr Roux, 75015 Paris, France
> lab: +33 (0)1 45 68 82 66
> fax: +33 (0)1 45 68 89 93
> email: sduq...@pasteur.fr
> -- --
>
>
>
> --
> *De: *"James Foadi" <09daa8ec3774-dmarc- requ...@jiscmail.ac.uk
> <09daa8ec3774-dmarc-requ...@jiscmail.ac.uk>>
> *À: *
> *Envoyé: *Lundi 3 Juillet 2017 11:47:00
> *Objet: *[ccp4bb] RMSD between unaligned structures
>
>
> Dear ccp4 tribe,
> this might have been asked before, but I haven't paid enough attention.
>
> I'd like to measure the RMSD between two models after molecular
> replacement. I can force the two models to overlap as much as possible
> within the symmetry and origin-shift constraints (using CSYMMATCH). But I
> don't want the program that compute RMSD to align the two structures. Can
> you suggest what I should use? And, perhaps, what keywords I should adopt?
>
> Many thanks, in advance.
>
> James
>
> Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science
> and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office
> email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk
> personal web page: http://www.jfoadi.me.uk
>
>
>
>
>

Re: [ccp4bb] RMSD between unaligned structures

[James Foadi]

Hi Eleanor.You do the alignment if you are looking to measure the similarity of 
two molecules after refinement or the similarity of two molecules in general. 
When you do this, like you say, you have to carry out some sort of alignment, 
i.e. you move one of the two structures so to have the highest degree of 
overlapping with the other , without any constraint. This is what most of the 
programs do (and after having done that they compute the RMSD). But I'm looking 
for a program to measure the RMSD of two fixed (un-moved) structures; the 
structures have already been moved (with the symmetry and unit cell origin 
constrain) by CSYMMATCH. Does it make sense to you?
James
 Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science and 
Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: 
james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk personal 
web page: http://www.jfoadi.me.uk 

On Monday, 3 July 2017, 11:59, Eleanor Dodson  
wrote:
 

 Dont understand your Q James..
You have to make sort of alignment to get the RMSD surely?
And csymmatch will just apply the symmetry and origin shifts needed for any 
comparisonn?
E

On 3 July 2017 at 11:32, Stéphane Duquerroy  
wrote:

Hi James
LSQMAN can calculate the current RMSD between the 2 models (RMsd_calc mol1 
range1 mol2 range2 [Ltarget])
Be careful it renames the chain names

Stephane

-- -
Duquerroy Stéphane
Structural Virology Unit - PASTEUR INSTITUTE
25 rue du Dr Roux, 75015 Paris, France
lab: +33 (0)1 45 68 82 66
fax: +33 (0)1 45 68 89 93
email: sduq...@pasteur.fr
-- --



De: "James Foadi" <09daa8ec3774-dmarc- requ...@jiscmail.ac.uk>
À: 
Envoyé: Lundi 3 Juillet 2017 11:47:00
Objet: [ccp4bb] RMSD between unaligned structures

Dear ccp4 tribe,this might have been asked before, but I haven't paid enough 
attention.

I'd like to measure the RMSD between two models after molecular replacement. I 
can force the two models to overlap as much as possible within the symmetry and 
origin-shift constraints (using CSYMMATCH). But I don't want the program that 
compute RMSD to align the two structures. Can you suggest what I should use? 
And, perhaps, what keywords I should adopt?
Many thanks, in advance.
James Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell 
Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office 
email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk 
personal web page: http://www.jfoadi.me.uk




   

[ccp4bb] Cryo-EM Research Scientist position at Imperial College London & MRC LMS

[Speck, Christian]

The MRC LMS & Imperial College is looking for a Cryo-EM research Scientist.

Your main role will be to manage the EM requirements of the institute. Electron 
microscopy has been identified as a key technology at the ICL/LMS to support 
investigation into epigenetic mechanisms, large molecular machines involved in 
DNA transactions and chromosome structure. You will support research groups in 
structurally characterising proteins using cryo-EM, particularly by single 
particle analysis. This is an ideal opportunity to apply cutting edge imaging 
technologies to investigate mechanisms in chromosome biology, to develop new 
technological capabilities and work together with leading research groups.

New EM capacity is currently being developed at the Institute, with a view to 
enhance and expand this significantly over the next few years. Currently, the 
LMS is equipped with a CM200 FEG transmission cryo-electron microscope, a fast 
Tietz 2k camera and a sample preparation suite including a Vitrobot Mark IV. 
Presently, access to high end microscopes is available through the national 
facility, an established collaboration with the LMB and the Wellcome Trust 
funded LonCEM consortium.

This is a full-time, three-year position (HM2017109).

Informal enquiries may be made to Prof. Christian Speck 
(chris.sp...@imperial.ac.uk)

For more details and instructions for application, please visit:

Job advert: Nature 
Website
Application link and job description at Imperial College London: IC 
Website

Best wishes,

Christian


__

Professor Christian Speck, PhD, FRSB
Chair in Genome Biochemistry & Molecular Biology
Wellcome Trust Investigator

Imperial College London
Faculty of Medicine
Institute of Clinical Sciences (CRB room 3006)
Hammersmith Hospital Campus
Du Cane Road
London W12 0NN

Tel: 0044 20 8383 3387
Mobile: 0044 796 181 5557
Skype ID: dna_rep

email: christian.sp...@imperial.ac.uk
website: www.specklab.com
Imperial College website: 
www.imperial.ac.uk/people/chris.speck

[http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/wtvm050463.jpg][Athena
 Swan Bronze Award Logo]

Re: [ccp4bb] RMSD between unaligned structures

[Eleanor Dodson]

Dont understand your Q James..
You have to make sort of alignment to get the RMSD surely?
And csymmatch will just apply the symmetry and origin shifts needed for any
comparisonn?
E

On 3 July 2017 at 11:32, Stéphane Duquerroy 
wrote:

> Hi James
> LSQMAN can calculate the current RMSD between the 2 models (RMsd_calc mol1
> range1 mol2 range2 [Ltarget])
> Be careful it renames the chain names
>
> Stephane
>
> ---
> Duquerroy Stéphane
> Structural Virology Unit - PASTEUR INSTITUTE
> 25 rue du Dr Roux, 75015 Paris, France
> lab: +33 (0)1 45 68 82 66 <+33%201%2045%2068%2082%2066>
> fax: +33 (0)1 45 68 89 93 <+33%201%2045%2068%2089%2093>
> email: sduq...@pasteur.fr
> 
>
>
>
> --
> *De: *"James Foadi" <09daa8ec3774-dmarc-requ...@jiscmail.ac.uk>
> *À: *
> *Envoyé: *Lundi 3 Juillet 2017 11:47:00
> *Objet: *[ccp4bb] RMSD between unaligned structures
>
>
> Dear ccp4 tribe,
> this might have been asked before, but I haven't paid enough attention.
>
> I'd like to measure the RMSD between two models after molecular
> replacement. I can force the two models to overlap as much as possible
> within the symmetry and origin-shift constraints (using CSYMMATCH). But I
> don't want the program that compute RMSD to align the two structures. Can
> you suggest what I should use? And, perhaps, what keywords I should adopt?
>
> Many thanks, in advance.
>
> James
>
> Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science
> and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office
> email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk
> personal web page: http://www.jfoadi.me.uk
>
>

Re: [ccp4bb] RMSD between unaligned structures

[Stéphane Duquerroy]

Hi James 
LSQMAN can calculate the current RMSD between the 2 models (RMsd_calc mol1 
range1 mol2 range2 [Ltarget]) 
Be careful it renames the chain names 

Stephane 

--- 
Duquerroy Stéphane 
Structural Virology Unit - PASTEUR INSTITUTE 
25 rue du Dr Roux, 75015 Paris, France 
lab: +33 (0)1 45 68 82 66 
fax: +33 (0)1 45 68 89 93 
email: sduq...@pasteur.fr 
 



- Mail original -

De: "James Foadi" <09daa8ec3774-dmarc-requ...@jiscmail.ac.uk> 
À: 
Envoyé: Lundi 3 Juillet 2017 11:47:00 
Objet: [ccp4bb] RMSD between unaligned structures 

Dear ccp4 tribe, 
this might have been asked before, but I haven't paid enough attention. 

I'd like to measure the RMSD between two models after molecular replacement. I 
can force the two models to overlap as much as possible within the symmetry and 
origin-shift constraints (using CSYMMATCH). But I don't want the program that 
compute RMSD to align the two structures. Can you suggest what I should use? 
And, perhaps, what keywords I should adopt? 

Many thanks, in advance. 

James 
Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science and 
Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: 
james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk personal 
web page: http://www.jfoadi.me.uk 

[ccp4bb] RMSD between unaligned structures

[James Foadi]

Dear ccp4 tribe,this might have been asked before, but I haven't paid enough 
attention.

I'd like to measure the RMSD between two models after molecular replacement. I 
can force the two models to overlap as much as possible within the symmetry and 
origin-shift constraints (using CSYMMATCH). But I don't want the program that 
compute RMSD to align the two structures. Can you suggest what I should use? 
And, perhaps, what keywords I should adopt?
Many thanks, in advance.
James Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell 
Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office 
email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk 
personal web page: http://www.jfoadi.me.uk