Re: [ccp4bb] Calculating RMSD of a loop

[Jonathan Cooper]

 Sorry, I was wrong about using STDEV in Excel. Instead you would need to put 
in a formula to calculate the root mean square of your distances. On 
Tuesday, 17 September 2019, 15:14:02 BST, Jonathan Cooper 
 wrote:  
 
 I think LSQKAB can output a list of CA distances of two structures. Might be 
easier to fit them first in Coot since LSQKAB can be a pig to run and you may 
have to use the command line. You could then select the region(s) you are 
interested in and use a spreadsheet or a script to calculate the RMSD. I think 
it will only be meaningful if the loops being compared are the same length in 
both structures? If it is only one loop you could measure the CA-distances in 
Coot and plug them into Excel for a quick STDEV.

Sent from Yahoo Mail on Android 
 
  On Tue, 17 Sep 2019 at 14:42, Kyle 
Gregory<3632e92fcc15-dmarc-requ...@jiscmail.ac.uk> wrote:#yiv2001353542 
P {margin-top:0;margin-bottom:0;}Hi all, 

What is the best/easiest way to calculate RMSD of a loop for 2 c-alpha aligned 
structures?
Thought I could do this in Coot but I only see this if I align the specific 
loops, which I don't want to do.

Thanks,

Kyle 


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Re: [ccp4bb] Calculating RMSD of a loop

[Pavel Afonine]

Yet another way is:

phenix.superpose_pdbs fixed.pdb moving.pdb selection_fixed="chain A and and
resseq 1:10 and name CA" selection_moving="chain B and resseq 1:10 and name
CA"

or using the GUI.
Pavel

On Tue, Sep 17, 2019 at 8:06 AM Folmer Fredslund  wrote:

> Dear Kyle,
>
> As other non-CCP4 solutions have also been suggested, perhaps I can
> suggest using PyMOL?
> https://pymolwiki.org/index.php/Align
> Here's a nice wiki article about what you can do with the align command.
>
>
> If you're already familiar with scripting languages it's quite easy, and
> you can load your already superimposed structures and calculate on the
> selection you want.
>
>
> Hope this helps,
> Folmer Fredslund
>
>
> tir. 17. sep. 2019 15.42 skrev Kyle Gregory <
> 3632e92fcc15-dmarc-requ...@jiscmail.ac.uk>:
>
>> Hi all,
>>
>> What is the best/easiest way to calculate RMSD of a loop for 2 c-alpha
>> aligned structures?
>> Thought I could do this in Coot but I only see this if I align the
>> specific loops, which I don't want to do.
>>
>> Thanks,
>>
>> Kyle
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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>>
>
> --
>
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Re: [ccp4bb] Deliver Your Research Ideas at Crystallography Conference (fwd)

[Marjolein Thunnissen]

Yes I think I got it, along with invitations to speak at conferences on opening 
up the North Shipping route or a bit closer to home, nanotechnology. Most of 
these go almost automatic in the trash as they are just that, there is quite a 
big market out there for predatory conferences, see also 
https://www.enago.com/academy/tips-identify-avoid-predatory-conferences/

Best regards

Marjolein
[cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC]


Dr. Marjolein Thunnissen
Life Science Director
MAX IV Laboratory
Lund University
P.O. Box 118, SE-221 00 Lund, Sweden
Visiting address: Fotongatan 2, 225 94 Lund
Telephone:+46 46 2224668
Mobile:  +46 766 32 04 17
www.maxiv.lu.se


On 17 Sep 2019, at 18:46, Frances C. Bernstein 
mailto:f...@bernstein-plus-sons.com>> wrote:

I don't know if anyone else got this mailing.  The conference
is being run by an organization called Allied Academies.  It
was interesting to look up Allied Academies in wkipedia.

 Frances

=
Bernstein + Sons
*   *   Information Systems Consultants
5 Brewster Lane, Bellport, NY 11713-2803
*   * ***
 *Frances C. Bernstein
 *   ***  f...@bernstein-plus-sons.com
*** *
 *   *** 1-631-286-1339FAX: 1-631-286-1999
=

-- Forwarded message --
Date: Tue, 17 Sep 2019 12:28:30 +0530
From: crystallography2...@gmail.com
To: f...@bernstein-plus-sons.com
Subject: Deliver Your Research Ideas at Crystallography Conference


Dear Ms Frances C. ,

Greetings!

This is Cinthia Williams reaching to you informing to participate as an
Organizing Committee Member for the International Conference on
Crystallography and Structural Chemistry which is to be held on April 27-28,
2020 at Barcelona, Spain.

The gathering of international experts and investigators in Spain will leads the
conference discussion to the extent of exploring the new happenings,
investigating the case studies, and innovating the truth behind the crystals and
Crystalline Structure.

Hence, it would be really delightful if you could present at the conference
venue and witness the change in the structural science.

You can find the more details of the conference at Crystallography 2020

Waiting for your Positive Response.

Regards,
Cinthia Williams
Program Manager | Crystallography 2020
Email id: 
crystallogra...@alliedforums.org
47, Churchfield Road | London, W36AY
P: 442037691755



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[ccp4bb] One position opening at RCSB PDB/Rutgers University- BIOCHEMICAL INFORMATION & ANNOTATION SPECIALIST

[Jasmine Young]

*Curate, validate, and standardize macromolecular structures from the 
PDB community. Participate in exciting projects with significant impact 
on the scientific community.*


Data archives are critical to research and education. They provide safe 
and secure storage of valuable scientific data, and ensure that 
information is freely available to the world. Data curation is critical 
for these resources. In the case of PDB, data are carefully reviewed and 
annotated by wwPDB curators before public release. Expert curation of 
data coming into PDB is critical for ensuring findability, 
accessibility, interoperability, and reusability (FAIR). Biocurators 
communicate daily with members of the deposition community, and 
annotate, publicly release, and update entries in the PDB archive.


The RCSB PDB at Rutgers University in Piscataway, NJ has one position 
opening for a Biochemical Information & Annotation Specialist 
(Biocurator) to curate, validate, and standardize macromolecular 
structures for distribution in the PDB Core Archive.



This position offers the opportunity to participate in exciting projects 
with significant impact on the scientific community. The position is an 
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 * PhD in Biological chemistry or chemistry is required
 * Background in 3DEM or crystallography has strong advantage
 * Experience with small molecules such as organometallic complexes is
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The successful candidate should be self-motivated, pay close attention 
to detail, possess strong interpersonal, communication, and writing 
skills, with the ability to handle multiple projects, shifting 
priorities, while meeting deadlines.



Apply at Rutgers: http://jobs.rutgers.edu/postings/84303. 




--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===




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[ccp4bb] Deliver Your Research Ideas at Crystallography Conference (fwd)

[Frances C. Bernstein]

I don't know if anyone else got this mailing.  The conference
is being run by an organization called Allied Academies.  It
was interesting to look up Allied Academies in wkipedia.

  Frances

=
Bernstein + Sons
*   *   Information Systems Consultants
5 Brewster Lane, Bellport, NY 11713-2803
*   * ***
 *Frances C. Bernstein
  *   ***  f...@bernstein-plus-sons.com
 *** *
  *   *** 1-631-286-1339FAX: 1-631-286-1999
=

-- Forwarded message --
Date: Tue, 17 Sep 2019 12:28:30 +0530
From: crystallography2...@gmail.com
To: f...@bernstein-plus-sons.com
Subject: Deliver Your Research Ideas at Crystallography Conference


Dear Ms Frances C. ,

Greetings!

This is Cinthia Williams reaching to you informing to participate as an
Organizing Committee Member for the International Conference on
Crystallography and Structural Chemistry which is to be held on April 27-28,
2020 at Barcelona, Spain.

The gathering of international experts and investigators in Spain will leads the
conference discussion to the extent of exploring the new happenings,
investigating the case studies, and innovating the truth behind the crystals and
Crystalline Structure.

Hence, it would be really delightful if you could present at the conference
venue and witness the change in the structural science.

You can find the more details of the conference at Crystallography 2020

Waiting for your Positive Response.

Regards,
Cinthia Williams
Program Manager | Crystallography 2020
Email id: crystallogra...@alliedforums.org
47, Churchfield Road | London, W36AY
P: 442037691755



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[ccp4bb] Postdoc position at USU, Bethesda, MD

[Pazgier, Marzena]

HJF is seeking a Postdoctoral Fellow to support the Infectious Disease program 
of Dr. Marzena Pazgier 
(https://www.usuhs.edu/national/faculty/marzena-pazgier-phd) of the Department 
of Medicine of Uniformed Services University of the Health Science (USU) in 
Bethesda, MD.

We are looking for a highly motivated candidate with a strong experience in 
structural biology methods that include X-ray crystallography, electron and/or 
cryo-electron microscopy. Central to our laboratory mission is an in-depth 
exploration of the basic mechanisms in innate and adaptive responses to 
infectious disease with the goal of the development of protein-based 
therapeutics and novel vaccine concepts. Candidates are expected to work on 
ongoing research projects in the structural biology of infectious disease, 
primarily HIV-1. Qualifications for the position include: strong hands-on 
experience in structural techniques related to X-ray crystallography and/or 
electron and cryo-electron microscopy, molecular cloning, protein expression in 
various systems, and molecular interaction and structure-function analyses. A 
background in structural biology of viruses or immunology will be considered a 
strong plus. Qualified candidates should have a doctorate in areas related to 
structural biology and should have had at least three years of postdoctoral 
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self-motivation and record of publication are required. Experience in writing 
grant proposals will be a plus.

USU is in Bethesda, MD, directly across the street from the NIH, and is thus 
part of an extraordinarily vibrant local biomedical research community. Our 
research projects take advantage of excellent USU Core facilities that include 
a Structural Biology Core equipped with crystallization robots and a robotic 
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to USU.

Candidates should apply to the Henry M. Jackson Foundation: 
http://careers.hjf.org, by submitting a CV plus names and contact information 
for 3 references.

Note: Candidates may also directly contact Dr. Pazgier at 
marzena.pazg...@usuhs.edu.



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Re: [ccp4bb] Calculating RMSD of a loop

[Eleanor Dodson]

Well LSQKAB is set up to do this.
You ask (not sure of the key words - always use gui or coot..)

FIT CA 7 15 chain A
match CA 21 29 CHAIN B

then you can add more spans as required ..

You can do it in COOT
Calculate
LSQKAB  - then select which residues to fit

or from GUI1

However both LSQKAB LSQMAN will try to optimise the fit for the selected
span.
Do you want to fit 50 residues then get the error for just a few?

LSQKAB will print out a table of all the fit distances, and give an overall
RMSD, but you would have to select and average the span you want by some
other means..
I think the same is true for LSQMAN

Eleanor



On Tue, 17 Sep 2019 at 16:07, Martyn Winn - UKRI STFC <
martyn.w...@stfc.ac.uk> wrote:

> This is probably a good opportunity to say that the USF has moved to
> https://github.com/martynwinn/Uppsala-Software-Factory
>
> Gerard asked for this so that they wouldn't be lost. I haven't put any
> effort into checking the binaries or compilation, but I will do what I can
> on a best effort basis ...
>
> Others are welcome to contribute ...
>
> cheers
> m
>
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Degano Massimo
> Sent: 17 September 2019 15:35
> To: ccp4bb
> Subject: Re: [ccp4bb] Calculating RMSD of a loop
>
> Hi,
>
> (good old) LSQMAN from the Uppsala Software Facotry will do this for you.
> First you align the structures based on the subset of atoms you want to
> match, then use the RMSD command to calculate the rmsd for the subset of
> atoms you are interested in.
> Best wishes,
>
> Massimo
>
> --
> Dr. Massimo Degano
> Biocrystallography Unit
> Dept. of Immunology, Transplantation, and Infectious Diseases
> IRCCS Scientific Institute San Raffaele
> via Olgettina 58
> 20132 Milan - Italy
> email: degano.mass...@hsr.it
> phone: +39-0226437152
> fax: +39-0226434153
> skype: maxdegano
> ORCID: -0002-0787-1883
>
> http://research.hsr.it/en/divisions/immunology-transplantation-and-infectious-diseases/biocrystallography.html
> <
> http://research.hsr.it/en/divisions/immunology-transplantation-and-infectious-diseases/biocrystallography.html
> >
>
>
> On 17 Sep 2019, at 15:31, Kyle Gregory <
> 3632e92fcc15-dmarc-requ...@jiscmail.ac.uk 3632e92fcc15-dmarc-requ...@jiscmail.ac.uk>> wrote:
>
> Hi all,
>
> What is the best/easiest way to calculate RMSD of a loop for 2 c-alpha
> aligned structures?
> Thought I could do this in Coot but I only see this if I align the
> specific loops, which I don't want to do.
>
> Thanks,
>
> Kyle
>
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
> [5xmille]<
> http://www.5xmille.org/?utm_source=mail&utm_medium=web_link&utm_campaign=5xmille_2018
> >
>
> 5xmille. INSIEME POSSIAMO continuare a scoprire nuove cure.
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> Rispetta l'ambiente: non stampare questa mail se non è necessario.
> Respect the environment: print this email only if necessary.
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Re: [ccp4bb] Rfree from another mtz file

[Mariana Ajalla]

Hi,

Thanks everyone for the answers!
I was able to identify my R free sets and they are the same =D

Best regards

Mariana


De: CCP4 bulletin board  em nome de Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Enviado: terça-feira, 17 de setembro de 2019 11:29
Para: CCP4BB@JISCMAIL.AC.UK 
Assunto: Re: [ccp4bb] Rfree from another mtz file

If you use either GUI2 or GUI you simply name the old file you want to take the 
FreeR flags from..

The pipeline then initiates the steps catalogued by Robbie..

Eleanor
As Tim, and others say, you can assign new FreeR flags, but dont get upset when 
starting refinement with the prevuis model you see the Free R steadily 
increasing with refinement for several cycles!
Eleanor

On Tue, 17 Sep 2019 at 06:15, Robbie Joosten 
mailto:robbie_joos...@hotmail.com>> wrote:
I totally agree. And because the new dataset is of higher resolution, there 
will be new reflections in the test set anyway.

Now if you want to use the same testset always for series of isomorphous 
datasets (even though you do not need to), you can do this:
- Use unique to make a full set of reflections given your space group and cell 
dimensions
- Assign a testset to that file using the program freerflag
Foreach dataset:
- Copy over the testset from you master file
End

Note that the testsets in the datasets will be super/subsets of each other but 
assuming the data are complete they will be the same if you use the same 
resolution cut-offs.

Cheers,
Robbie

On 17 Sep 2019 02:17, Tim Gruene 
mailto:tim.gru...@univie.ac.at>> wrote:

Dear Mariana,

you can simply create a new set for Rfree, independently of the previous one.
It will be as good as the copied one, and there is no reason why you would
need to maintain the same flags. As Ian Tickle explained only briefly ago,
your new data set will have new, independent errors.

Best regards,
Tim

On Tuesday, September 17, 2019 12:29:19 AM CEST Mariana Ajalla wrote:
> Dear all,
>
> We tried to use the Rfree set from a lower resolution data with a higher
> resolution from the same Crystal. To do so We used aimless at ccp4i with
> the option use free flag from another mtz file and extend the data.
>
> I think it worked, but now we don't know how to be sure we have the same
> Rfree set. Does anyone have a way to prove it?
> Thank you in advance,
> Best,
> Mariana
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [ccp4bb] [EXTERNAL] [ccp4bb] Rfree from another mtz file

[Edward A. Berry]

On 09/16/2019 06:29 PM, Mariana Ajalla wrote:

Dear all,

We tried to use the Rfree set from a lower resolution data with a higher 
resolution from the same Crystal. To do so We used aimless at ccp4i with the 
option use free flag from another mtz file and extend the data.

I think it worked, but now we don't know how to be sure we have the same Rfree 
set.
  Does anyone have a way to prove it?
Thank you in advance,
Best,
Mariana



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Mariana,
 If you solve a new dataset with a structure previously refined in an isomorphous crystal, and use 
the same free set as was used for that refinement, you will generally notice that the initial Rfree 
is higher than initial Rwork, as it was with the old dataset. If you start with a new free set, 
Rfree and Rwork will initially be the same, and diverge with refinement. This implies that there is 
some correlation between Fo-Fc calculated with the new data and Fo-Fc from the old dataset. This 
would lead some to say your Rfree is "corrupted" if you choose a new set, and it will 
only be valid after many cycles of refinement to "shake out" the bias. Note that Ian 
Tickle qualified his results by saying it is necessary to refine to convergence for his conclusions 
to hold.

How can the old and new Fo-Fc be correlated, if the errors in the new data are independent from the errors in the old dataset? Well, the errors in measurement  contribute only a small fraction to the Fo-Fc differences, as evidenced by the fact that Rpim is much smaller than either Rfree or Rwork. Thinking in terms of "fitting the noise", if we define the noise to be the differences between Fo and Fc, there are two sources for that noise. One is error in measurement, and as noted these should be completely independent. The other "noise" is the difference between our best-refined structure and the actual structure- modeling solvent, fitting disorder with isotropic or even anisotropic B factors when in fact it is more complicated, single or few alternate conformations when in fact there is a range of positions, etc. If the new data actually represents the same structure, or even a new structure of the same protein in an isomorphous crystal, these errors are likely to be the same in the 
n


ew dataset, and could account for the fact that the fit is better for the 
working reflections which the structure has been refined to minimize against 
the old dataset, when refined against the new dataset.

Again thinking of "fitting the noise", we clearly do not want to fit the noise that comes 
from errors in measurement. But these are uncorrelated between the datasets, so choosing the same 
free set has no effect on this. As for fitting the "noise" that is the difference between 
our model and the real structure, this is a gray area. I tend to think fitting this noise (making 
our structure more like the true structure) would be a good thing, and if it can be biased by using 
all the reflections it would be a good thing. But the fact is it is going to make the R-free lower, 
at least initially, and give you an unfair advantage over the purist who insists on using the same 
free set for isomorphous structures. Until there is a general consensus on this it might be a good 
idea to keep the old free set, if only because your reviewer might be one of those purists!



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Re: [ccp4bb] Rfree from another mtz file

[Eleanor Dodson]

If you use either GUI2 or GUI you simply name the old file you want to take
the FreeR flags from..

The pipeline then initiates the steps catalogued by Robbie..

Eleanor
As Tim, and others say, you can assign new FreeR flags, but dont get upset
when starting refinement with the prevuis model you see the Free R steadily
increasing with refinement for several cycles!
Eleanor

On Tue, 17 Sep 2019 at 06:15, Robbie Joosten 
wrote:

> I totally agree. And because the new dataset is of higher resolution,
> there will be new reflections in the test set anyway.
>
> Now if you want to use the same testset always for series of isomorphous
> datasets (even though you do not need to), you can do this:
> - Use unique to make a full set of reflections given your space group and
> cell dimensions
> - Assign a testset to that file using the program freerflag
> Foreach dataset:
> - Copy over the testset from you master file
> End
>
> Note that the testsets in the datasets will be super/subsets of each other
> but assuming the data are complete they will be the same if you use the
> same resolution cut-offs.
>
> Cheers,
> Robbie
>
> On 17 Sep 2019 02:17, Tim Gruene  wrote:
>
> Dear Mariana,
>
> you can simply create a new set for Rfree, independently of the previous
> one.
> It will be as good as the copied one, and there is no reason why you would
> need to maintain the same flags. As Ian Tickle explained only briefly ago,
> your new data set will have new, independent errors.
>
> Best regards,
> Tim
>
> On Tuesday, September 17, 2019 12:29:19 AM CEST Mariana Ajalla wrote:
> > Dear all,
> >
> > We tried to use the Rfree set from a lower resolution data with a higher
> > resolution from the same Crystal. To do so We used aimless at ccp4i with
> > the option use free flag from another mtz file and extend the data.
> >
> > I think it worked, but now we don't know how to be sure we have the same
> > Rfree set. Does anyone have a way to prove it?
> > Thank you in advance,
> > Best,
> > Mariana
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
>
>
> --
>
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Re: [ccp4bb] Calculating RMSD of a loop

[Martyn Winn - UKRI STFC]

This is probably a good opportunity to say that the USF has moved to 
https://github.com/martynwinn/Uppsala-Software-Factory

Gerard asked for this so that they wouldn't be lost. I haven't put any effort 
into checking the binaries or compilation, but I will do what I can on a best 
effort basis ...

Others are welcome to contribute ...

cheers
m

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Degano 
Massimo
Sent: 17 September 2019 15:35
To: ccp4bb
Subject: Re: [ccp4bb] Calculating RMSD of a loop

Hi,

(good old) LSQMAN from the Uppsala Software Facotry will do this for you. First 
you align the structures based on the subset of atoms you want to match, then 
use the RMSD command to calculate the rmsd for the subset of atoms you are 
interested in.
Best wishes,

Massimo

--
Dr. Massimo Degano
Biocrystallography Unit
Dept. of Immunology, Transplantation, and Infectious Diseases
IRCCS Scientific Institute San Raffaele
via Olgettina 58
20132 Milan - Italy
email: degano.mass...@hsr.it
phone: +39-0226437152
fax: +39-0226434153
skype: maxdegano
ORCID: -0002-0787-1883
http://research.hsr.it/en/divisions/immunology-transplantation-and-infectious-diseases/biocrystallography.html


On 17 Sep 2019, at 15:31, Kyle Gregory 
<3632e92fcc15-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Hi all,

What is the best/easiest way to calculate RMSD of a loop for 2 c-alpha aligned 
structures?
Thought I could do this in Coot but I only see this if I align the specific 
loops, which I don't want to do.

Thanks,

Kyle


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[5xmille]

5xmille. INSIEME POSSIAMO continuare a scoprire nuove cure.

CODICE FISCALE 07636600962


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Re: [ccp4bb] Calculating RMSD of a loop

[Folmer Fredslund]

Dear Kyle,

As other non-CCP4 solutions have also been suggested, perhaps I can suggest
using PyMOL?
https://pymolwiki.org/index.php/Align
Here's a nice wiki article about what you can do with the align command.


If you're already familiar with scripting languages it's quite easy, and
you can load your already superimposed structures and calculate on the
selection you want.


Hope this helps,
Folmer Fredslund


tir. 17. sep. 2019 15.42 skrev Kyle Gregory <
3632e92fcc15-dmarc-requ...@jiscmail.ac.uk>:

> Hi all,
>
> What is the best/easiest way to calculate RMSD of a loop for 2 c-alpha
> aligned structures?
> Thought I could do this in Coot but I only see this if I align the
> specific loops, which I don't want to do.
>
> Thanks,
>
> Kyle
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
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Re: [ccp4bb] Calculating RMSD of a loop

[Degano Massimo]

Hi,

(good old) LSQMAN from the Uppsala Software Facotry will do this for you. First 
you align the structures based on the subset of atoms you want to match, then 
use the RMSD command to calculate the rmsd for the subset of atoms you are 
interested in.
Best wishes,

Massimo

--
Dr. Massimo Degano
Biocrystallography Unit
Dept. of Immunology, Transplantation, and Infectious Diseases
IRCCS Scientific Institute San Raffaele
via Olgettina 58
20132 Milan - Italy
email: degano.mass...@hsr.it
phone: +39-0226437152
fax: +39-0226434153
skype: maxdegano
ORCID: -0002-0787-1883
http://research.hsr.it/en/divisions/immunology-transplantation-and-infectious-diseases/biocrystallography.html

On 17 Sep 2019, at 15:31, Kyle Gregory 
<3632e92fcc15-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Hi all,

What is the best/easiest way to calculate RMSD of a loop for 2 c-alpha aligned 
structures?
Thought I could do this in Coot but I only see this if I align the specific 
loops, which I don't want to do.

Thanks,

Kyle


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[5xmille]

5xmille. INSIEME POSSIAMO continuare a scoprire nuove cure.
CODICE FISCALE 07636600962


Rispetta l'ambiente: non stampare questa mail se non ? necessario.
Respect the environment: print this email only if necessary.



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Re: [ccp4bb] Calculating RMSD of a loop

[Jonathan Cooper]

I think LSQKAB can output a list of CA distances of two structures. Might be 
easier to fit them first in Coot since LSQKAB can be a pig to run and you may 
have to use the command line. You could then select the region(s) you are 
interested in and use a spreadsheet or a script to calculate the RMSD. I think 
it will only be meaningful if the loops being compared are the same length in 
both structures? If it is only one loop you could measure the CA-distances in 
Coot and plug them into Excel for a quick STDEV.

Sent from Yahoo Mail on Android 
 
  On Tue, 17 Sep 2019 at 14:42, Kyle 
Gregory<3632e92fcc15-dmarc-requ...@jiscmail.ac.uk> wrote:#yiv2516608606 
P {margin-top:0;margin-bottom:0;}Hi all, 

What is the best/easiest way to calculate RMSD of a loop for 2 c-alpha aligned 
structures?
Thought I could do this in Coot but I only see this if I align the specific 
loops, which I don't want to do.

Thanks,

Kyle 


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Re: [ccp4bb] Calculating RMSD of a loop

[Wim Burmeister]

  
  
Hello,
I admit that I only found the solution to import the pdb's after
alignment of the body of the protein into a spreadsheet (LibreOffice
Calc) and then to calculate the rms of the atoms of the loop (or of
the CA atoms of the loop).
Best wishes
Wim

On 17/09/2019 15:31, Kyle Gregory
  wrote:


  
  
   Hi all, 

What is the best/easiest way to calculate RMSD of a loop for 2
c-alpha aligned structures?
Thought I could do this in Coot but I only see this if I align
the specific loops, which I don't want to do. 

Thanks,

Kyle 
  
  
  
  To unsubscribe from the CCP4BB list, click the
following link:
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-- 
  
  
  




  Changement climatique : «Les autres
combats n’ont aucun sens si celui-là est perdu» (Aurélien
  Barrau)
  

  

  



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[ccp4bb] Calculating RMSD of a loop

[Kyle Gregory]

Hi all,

What is the best/easiest way to calculate RMSD of a loop for 2 c-alpha aligned 
structures?
Thought I could do this in Coot but I only see this if I align the specific 
loops, which I don't want to do.

Thanks,

Kyle



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[ccp4bb] Faculty position at Case Western Reserve University: Tenure Track Assistant or Associate Professor of Biochemistry

[Focco Van den Akker]

Dear all,

Case Western Reserve University, Department of Biochemistry invites
applications for tenure-track faculty or tenured faculty positions.  While
applications from individuals with interests in any area of biochemistry
are requested, areas of specific interest include metabolism/metabolomics,
RNA biology, stress response signaling, and chromatin biology as they
pertain to fundamental aspects of human diseases such as cancer biology.

More details are here in the ad posted on the ASBMB website:
http://www.asbmb.org/Careers/Jobs/81363/

Thank you,
Focco

-- 
Focco van den Akker, Ph.D.
Associate Professor
Department of Biochemistry RT500
School of Medicine
Case Western Reserve University
10900 Euclid Avenue
Cleveland, OH 44106-4935
phone:  (216) 368-8511
fax:(216) 368-8845
E-mail: focco.vandenak...@case.edu
Faculty webpage:
http://www.cwru.edu/med/biochemistry/faculty/vandenakker.html
Lab webpage:
http://www.cwru.edu/med/biochemistry/vandenAkker_lab/index.html



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[ccp4bb] New vacancy at MAX IV : Research engineer - Instrument scientist at BioMAX

[Uwe Müller]

Lunds universitet, MAX IV, MX group

Lund University was founded in 1666 and is repeatedly ranked among the world’s 
top 100 universities. The University has 40 000 students and 7 600 staff based 
in Lund, Helsingborg and Malmö. We are united in our efforts to understand, 
explain and improve our world and the human condition.MAX IV is a Swedish 
national large-scale research laboratory hosted by Lund University. It provides 
scientists from Sweden as well as internationally, with state-of-the-art 
instrumentation for research in areas such as engineering, physics, structural 
biology, chemistry and nanotechnology. Fully developed it will receive more 
than 2 000 scientists annually, conducting ground-breaking experiments in 
materials and life sciences using the brilliant X-ray light. As a national 
laboratory, MAX IV is operated in agreement with governmental regulations, and 
in compliance with major funders such as the Swedish Research Council (VR) and 
the Wallenberg Foundation. 250 people are currently employed at MAX IV 
Laboratory, and 16 beamlines are funded. The facility is in a ramp-up phase 
with 3 beamlines now receiving users and 13 more scheduled to be commissioned 
and built to receive users within the next few years. The facility is 
dimensioned for 25-28 beamlines.

BioMAX is the first operational beamline for macromolecular crystallography at 
MAX IV, which runs for the last 3 years within the MAX IV user program. The 
beamline comprises a state-of-the-art instrumentation with high performance 
x-ray transport and control systems, goniometry, x-ray detectors and a 
cryogenic sample changer (see also: http://www.maxiv.se/biomax).

The beamline is operated by the interdisciplinary BioMAX-team which is part of 
the MX-group. Within this group we are also jointly developing a new beamlines 
project: MicroMAX, a serial crystallography beamline for studying protein 
dynamics.

The MX-group is now looking for an expert, with a strong interest in 
developing, operating and maintaining complex scientific instrumentation of the 
BioMAX beamline.

This position offers ample possibilities to work with and to develop scientific 
instrumentation and methodologies, which can be used later together with the 
BioMAX users for basic and applied research tasks. Due to the broad spectrum of 
activities, this position is ideal to develop a related portfolio of expertise 
and knowledge by the candidate.

Tasks

  *   Operation and maintenance of the beam line technical infrastructure, in 
close cooperation with the team of scientists and engineers of the MX-group and 
MAX IV
  *   If applicable, develop own in house research activities which are related 
to BioMAX & MicroMAX
  *   Shared tasks and responsibilities within the constant beamline 
development and upgrade
  *   Regular beamline commissioning tasks
  *   Develop strategies and methods for diagnostics and control of the BioMAX 
technical infrastructure and implement those
  *   Contribute to the design, purchase and installation of new beamline and 
experimental station components to ensure availability of an internationally 
competitive and reliable beamline environment
  *   Shared responsibilities for the scientific/technical support of external 
users during their beamtime
  *   Cooperation with the MicroMAX team on the design, construction and future 
operation of this new beamline

Required Qualifications

  *   University degree in engineering or natural sciences in subjects of 
relevance for BioMAX
  *   Proven ability to cooperate well within a team
  *   Excellent command in written and spoken English
  *   A demonstrated ability to work independently
  *   Demonstrated experiences with synchrotron radiation instrumentation
  *   Significant experiences in managing complex instrumentation projects at 
all stages

Additional desirable qualifications

  *   Experience of X-ray optics and its integration into setups such as 
synchrotron radiation beamlines
  *   Demonstrated experiences in mechanical engineering including 3D-CAD/CAM
  *   Demonstrated experiences in mechatronics
  *   Solid knowledge in software development
  *   Experience of microfluidic design, development and use
  *   Experience of nano-positioning systems
  *   Interest and experience in scientific use of techniques of interest for 
BioMAX (i.e. experiments, data analysis, publication and presentation of 
results)

MAX IV operates 24/7 and you will be part in on-call service of the MX-group 
for user support, including weekends and bank holidays in accordance to the 
working hour regulation.

You will be invited to visit partner facilities, attend workshops and 
conferences to disseminate the acquired knowledge. This means that you must be 
willing to travel occasionally.

Probationary period may apply.

On call services may apply in the future.

Lund University welcomes applicants with diverse backgrounds and experiences. 
We regard gender equality and diversity as a s

[ccp4bb] SAXS workshop at BioCAT

[Thomas Irving]

BioCAT is offering its fifth intensive HOW-TO course in BioSAXS. Students
will have two days of lectures and hands-on software tutorials on the
basics of BioSAXS data collection and processing from expert practitioners
in the field. This will be followed by data collection on the BioCAT
beamline (Sector 18 at the APS) and data analysis help. Students are
encouraged to bring 1-2 research samples for the data collection.

Also, for the first time ever, BioCAT is offering this course for remote
participants. Remote participants will get a live-stream of the lectures,
and all of the tutorial materials. They will not be able to collect data.

The course will take place from 11/5/19-11/7/19 at the APS. Registration
for on-site participants is first come, first served, and limited to the
first 15 registrants due to time constraints on how many users can collect
data during the course.

Full information, a link for registration, and the tentative schedule can
be found on our website:
https://www.bio.aps.anl.gov/news/everything-biosaxs-5.html

Thanks,
Tom Irving



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