Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

[chenzhonghao...@163.com]

Dear Prof. Dr. Dodson and all CCP4 community,
 
  Thanks for your reply.
 
 Just now, I used baverage. I found that it can average the B factor but not 
refine it.
  This function does not fit my requirement, because my resolution is low as 3 
A. 
 Many people said that Refmac5 overrefines the structure if I used isotropic 
temperature refinement.
 
Did refmac5 or other programs in CCP4 have similar functions like 
one_adp_group_per_residue or two_adp_groups_per_residue in Phenix?
 
 Any help would be highly appreciated!
 



chenzhonghao...@163.com
 
From: Eleanor Dodson
Date: 2024-01-05 23:48
To: CCP4BB
Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?
Hmmm -  I am not sure about the value of this - one expects the longer floppier 
side chains to have very different B values for the CB than the OE2..
The program BAVERAGE gives you a plot of mean B value residue by residue..


baverage - averages B over main and side chain atoms
SYNOPSIS¶
baverage XYZIN foo_in.pdb RMSTAB foo_out1.tab XYZOUT foo_out2.pdb
[Keyworded input]
DESCRIPTION¶
A very simple minded program to read a PDB file, tabulate to RMSTAB the average 
B values residue by residue (main chain and side chain separately) and the RMS 
deviation of the B values from this mean. It also outputs a PDB file with 
outlying B factors reset to lie within the given range.

On Fri, 5 Jan 2024 at 03:08, chenzhonghao...@163.com  
wrote:
Dear CCP4 community, 

 I found that Refmac5 refined the temperature factor only by four modes (see 
the bottom of the attached figure). However, no
grouped B-factor (one or two per residue instead of one per atom) was found.

 Actually, PHENIX and CNS can do it. But we are not familiar with both 
software. I want to know whether Refmac5 refines one or
two group B per residue (for side and main chains) grouped temperature factor?

 Any help would be highly appreciated

 Thanks in advance.

best,


 Zhonghao Chen










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Re: [ccp4bb] How to make GDP.BeF3 solution ?

[Bernhard Rupp]

Some blast from the past: Facility management came in full hazmat suits to 
decommission the old multiwire detectors with the large Be windows.

https://www.ruppweb.org/Garland/gallery/Ch8/pages/Biomolecular_Crystallography_Fig_8-07.htm

 

Anyhow, got one on the DOE Beryllium worker’s list. Free lung X-rays

 

--

Bernhard Rupp, Psilosopher

  https://psilosophy.org/

  https://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Don’t lick it and don’t breathe it. 

--

 

From: CCP4 bulletin board  On Behalf Of Diana Tomchick
Sent: Friday, January 5, 2024 13:14
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] How to make GDP.BeF3 solution ?

 

Be aware that beryllium is also quite toxic.

 

https://en.wikipedia.org/wiki/Acute_beryllium_poisoning

 

Diana

 

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu  
(214) 645-6383 (phone)
(214) 645-6353 (fax)

  _  

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of Dr. Kevin M Jude mailto:kj...@stanford.edu> 
>
Sent: Friday, January 5, 2024 1:51 PM
To: CCP4BB@JISCMAIL.AC.UK   
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] How to make GDP.BeF3 solution ? 

 

EXTERNAL MAIL

Nb, dissolution of BeCl2 in water is quite exothermic and releases HCl vapor, 
you will want to prepare that stock in a fume hood.

 

Best wishes

Kevin

 

From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of Matthew BOWLER mailto:mbow...@embl.fr> >
Date: Thursday, January 4, 2024 at 2:19 AM
To: CCP4BB@JISCMAIL.AC.UK   
mailto:CCP4BB@JISCMAIL.AC.UK> >
Subject: Re: [ccp4bb] How to make GDP.BeF3 solution ?

Dear Firdous,

beryllium fluoride is actually a ground state analogue of GTP as 
trifluoroberyllate is tetrahedral. To get a transition sate analogue you need 
either AlF4- or MgF3-. Preparation of these complexes is very easy. The great 
advantage of metal fluoride transition state analogue and ground state analogue 
complexes is the fact that all components are present in solution and readily 
self-assemble in the active site forming stable enzyme complexes that are 
relevant to the catalytic cycle. The inorganic metal fluoride salts (AlF3, and 
MgF2) are too insoluble to use; therefore, the fluoride anion and metal cation 
components must be added from separate stock solutions. Both ammonium fluoride 
and sodium fluoride are suitable as the source of fluoride and are readily 
soluble in water. Metal chlorides can be easily dissolved in water at high 
concentration (0.5 M) and the solutions conserved at -20°C. One of the critical 
aspects in preparing metal fluoride enzyme complexes is the pH of the resulting 
solution. In particular, solutions of AlCl3 and BeCl2 are highly acidic (pH 2) 
samples should be prepared in 100 mM unbuffered Tris base. The optimized 
sequence of component addition is to add fluoride to the prepared buffer first, 
then the metal chloride stock.

Hope this helps, Matt

 

 

 

 

 

On 02/01/2024 18:53, Firdous Tarique wrote:

Hi 

 

I would appreciate it if someone could share with me a step by step protocol 
for making a stable GDP.BeF3 solution which is often used as a transition state 
analogue for structural studies of a protein complex ? 

 

Or a vendor from where it can be purchased directly.

 

Regards

 

Firdous

 


  _  


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 =1 

-- 
Matthew Bowler
Project Leader MASSIF1@ESRF
European Molecular Biology Laboratory
71 avenue des Martyrs 
CS 90181 F-38042 Grenoble
France
===
Tel: +33 (0) 4.76.20.76.37
Fax: +33 (0) 4.76.20.71.99
 
http://www.embl.fr/ 

 
http://www.esrf.eu/MASSIF1 

 
https://twitter.com/id30_massif1 

Re: [ccp4bb] How to make GDP.BeF3 solution ?

[Pius Padayatti]

Hi Firdous
Can you ask Trilink biotechnologies
if they can make it
for you
very good experience many speciality materials made
Disclaim: i do not work with them or have any financial connections with
them
I think jena discontinued this item but they used to sell this as well
When you get an answer can everyone know here as well
best

*Pius Padayatti*




On Tue, Jan 2, 2024 at 9:54 AM Firdous Tarique 
wrote:

> Hi
>
> I would appreciate it if someone could share with me a step by step
> protocol for making a stable GDP.BeF3 solution which is often used as a
> transition state analogue for structural studies of a protein complex ?
>
> Or a vendor from where it can be purchased directly.
>
> Regards
>
> Firdous
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] How to make GDP.BeF3 solution ?

[Diana Tomchick]

Be aware that beryllium is also quite toxic.

https://en.wikipedia.org/wiki/Acute_beryllium_poisoning

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

From: CCP4 bulletin board  on behalf of Dr. Kevin M Jude 

Sent: Friday, January 5, 2024 1:51 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] How to make GDP.BeF3 solution ?


EXTERNAL MAIL

Nb, dissolution of BeCl2 in water is quite exothermic and releases HCl vapor, 
you will want to prepare that stock in a fume hood.



Best wishes

Kevin



From: CCP4 bulletin board  on behalf of Matthew BOWLER 

Date: Thursday, January 4, 2024 at 2:19 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] How to make GDP.BeF3 solution ?

Dear Firdous,

beryllium fluoride is actually a ground state analogue of GTP as 
trifluoroberyllate is tetrahedral. To get a transition sate analogue you need 
either AlF4- or MgF3-. Preparation of these complexes is very easy. The great 
advantage of metal fluoride transition state analogue and ground state analogue 
complexes is the fact that all components are present in solution and readily 
self-assemble in the active site forming stable enzyme complexes that are 
relevant to the catalytic cycle. The inorganic metal fluoride salts (AlF3, and 
MgF2) are too insoluble to use; therefore, the fluoride anion and metal cation 
components must be added from separate stock solutions. Both ammonium fluoride 
and sodium fluoride are suitable as the source of fluoride and are readily 
soluble in water. Metal chlorides can be easily dissolved in water at high 
concentration (0.5 M) and the solutions conserved at -20°C. One of the critical 
aspects in preparing metal fluoride enzyme complexes is the pH of the resulting 
solution. In particular, solutions of AlCl3 and BeCl2 are highly acidic (pH 2) 
samples should be prepared in 100 mM unbuffered Tris base. The optimized 
sequence of component addition is to add fluoride to the prepared buffer first, 
then the metal chloride stock.

Hope this helps, Matt











On 02/01/2024 18:53, Firdous Tarique wrote:

Hi



I would appreciate it if someone could share with me a step by step protocol 
for making a stable GDP.BeF3 solution which is often used as a transition state 
analogue for structural studies of a protein complex ?



Or a vendor from where it can be purchased directly.



Regards



Firdous





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--

Matthew Bowler

Project Leader MASSIF1@ESRF

European Molecular Biology Laboratory

71 avenue des Martyrs

CS 90181 F-38042 Grenoble

France

===

Tel: +33 (0) 4.76.20.76.37

Fax: +33 (0) 4.76.20.71.99



http://www.embl.fr/

http://www.esrf.eu/MASSIF1

https://twitter.com/id30_massif1

https://www.embl.org/people/person/mbowler/

===





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CAUTION: This email originated from outside UTSW. Please be cautious of links 
or attachments, and 

Re: [ccp4bb] How to make GDP.BeF3 solution ?

[Dr. Kevin M Jude]

Nb, dissolution of BeCl2 in water is quite exothermic and releases HCl vapor, 
you will want to prepare that stock in a fume hood.

Best wishes
Kevin

From: CCP4 bulletin board  on behalf of Matthew BOWLER 

Date: Thursday, January 4, 2024 at 2:19 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] How to make GDP.BeF3 solution ?

Dear Firdous,

beryllium fluoride is actually a ground state analogue of GTP as 
trifluoroberyllate is tetrahedral. To get a transition sate analogue you need 
either AlF4- or MgF3-. Preparation of these complexes is very easy. The great 
advantage of metal fluoride transition state analogue and ground state analogue 
complexes is the fact that all components are present in solution and readily 
self-assemble in the active site forming stable enzyme complexes that are 
relevant to the catalytic cycle. The inorganic metal fluoride salts (AlF3, and 
MgF2) are too insoluble to use; therefore, the fluoride anion and metal cation 
components must be added from separate stock solutions. Both ammonium fluoride 
and sodium fluoride are suitable as the source of fluoride and are readily 
soluble in water. Metal chlorides can be easily dissolved in water at high 
concentration (0.5 M) and the solutions conserved at -20°C. One of the critical 
aspects in preparing metal fluoride enzyme complexes is the pH of the resulting 
solution. In particular, solutions of AlCl3 and BeCl2 are highly acidic (pH 2) 
samples should be prepared in 100 mM unbuffered Tris base. The optimized 
sequence of component addition is to add fluoride to the prepared buffer first, 
then the metal chloride stock.

Hope this helps, Matt










On 02/01/2024 18:53, Firdous Tarique wrote:
Hi

I would appreciate it if someone could share with me a step by step protocol 
for making a stable GDP.BeF3 solution which is often used as a transition state 
analogue for structural studies of a protein complex ?

Or a vendor from where it can be purchased directly.

Regards

Firdous



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

--

Matthew Bowler

Project Leader MASSIF1@ESRF

European Molecular Biology Laboratory

71 avenue des Martyrs

CS 90181 F-38042 Grenoble

France

===

Tel: +33 (0) 4.76.20.76.37

Fax: +33 (0) 4.76.20.71.99



http://www.embl.fr/

http://www.esrf.eu/MASSIF1

https://twitter.com/id30_massif1

https://www.embl.org/people/person/mbowler/

===



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Re: [ccp4bb] [External] Re: [ccp4bb] alternatives to Consurf server

[Schnicker, Nicholas J]

Hi Andre,

I don't know if anyone mentioned Conservation-Colab, although it maps the 
conservation onto an AF model.
https://zenodo.org/records/10062829

Cheers,
Nick

Nicholas Schnicker, PhD
Director, Protein & Crystallography Facility
Adjunct Assistant Professor, Molecular Physiology & Biophysics
University of Iowa
51 Newton Rd, 4-611 BSB
Iowa City, IA 52242
319-335-7671

From: CCP4 bulletin board  on behalf of Andrew Gnann 

Sent: Thursday, January 4, 2024 8:29 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [External] Re: [ccp4bb] alternatives to Consurf server

Hi Andre,
I recently prepared a Consurf-like figure using conservation scores pulled from 
alignments in JalView. You would follow instructions for running 
data2bfactor.py in PyMOL, feeding the conservation scores to replace your 
model's B factor column. Then set up a color ramp like you would use to display 
B factors. Please let me know if you go this route and run into issues.

Here is a link to a copy of data2bfactor.py: 
https://gist.github.com/Croydon-Brixton/ca916769c285faed69740d384b5daf23

Best,
Andrew

On Thu, Jan 4, 2024, 9:07 AM Andre Godoy 
<0b9d7671a1b6-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Dear CCP4ers,

Wishing you all a Happy New Year!

You may have noticed that the Consurf server has been down since the conflicts 
in the Middle East began. Does anyone know of alternative tools that can 
provide similar results?

Best regards.


Andre S. Godoy, PhD

Universidade de São Paulo
Instituto de Física de São Carlos
Av. João Dagnone, 1100, Jd. Santa Angelina
13563-120 - São Carlos, SP, Brazil



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Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

[Eleanor Dodson]

Hmmm -  I am not sure about the value of this - one expects the longer
floppier side chains to have very different B values for the CB than the
OE2..

The program BAVERAGE gives you a plot of mean B value residue by residue..



*baverage* - averages B over main and side chain atoms
SYNOPSIS¶ 
*baverage XYZIN* *foo_in.pdb* *RMSTAB* *foo_out1.tab* *XYZOUT*
*foo_out2.pdb*
[Keyworded input ]
DESCRIPTION¶ 

A very simple minded program to read a PDB file, tabulate to RMSTAB the
average B values residue by residue (main chain and side chain separately)
and the RMS deviation of the B values from this mean. It also outputs a PDB
file with outlying B factors reset to lie within the given range.

On Fri, 5 Jan 2024 at 03:08, chenzhonghao...@163.com <
chenzhonghao...@163.com> wrote:

> Dear CCP4 community,
>
>  I found that Refmac5 refined the temperature factor only by four modes
> (see the bottom of the attached figure). However, no
> grouped B-factor (one or two per residue instead of one per atom) was
> found.
>
>  Actually, PHENIX and CNS can do it. But we are not familiar with both
> software. I want to know whether Refmac5 refines one or
> two group B per residue (for side and main chains) grouped temperature
> factor?
>
>  Any help would be highly appreciated
>
>  Thanks in advance.
>
> best,
>
>
>  Zhonghao Chen
>
>
>
>
>
>
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
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[ccp4bb] Attractive job opportunity in Berlin - HZB and Humboldt University advertise a postdoc position

[Manfred Weiss]

The Helmholtz Zentrum Berlin für Materialien und Energie (HZB), the
Max-Delbrück-Center for Molecular Medicine (MDC), the Leibniz-Institute

for Molecular Pharmacology (FMP)the Freie Universität Berlin, the Charite,

the Max-Planck-Institute for Colloids and Interfaces and the Humboldt

Universität zu Berlin jointly operate three experimental stations for bio-

macromolecular crystallography at BESSY II, Berlin's modern synchrotron

radiation source, located in the lovely Southeast of Berlin.


The Humboldt University zu Berlin is seeking a Post Doctoral Research

Assistant to work on and support research topics in the field of structural

enzymology (e.g. control of chemical reactions in macromolecular crystals,

combination of UV/Vis absorption spectroscopy and crystallography, etc.)

originating from the group of Prof. Dr. Holger Dobbek. The successful candidate

will also be involved in the development of high-throughput crystallography

(fragment-screening), and in the operation of the BESSY II bio-macromolecular

crystallography beamlines (headed by Dr. Manfred S. Weiss) including supporting

external users at the beamlines and will take part in graduate student
education.

Initially, a contract lasting until 31.12.2026 will be offered to the
successful candidate

with the possibility for an extension. The salary will be based on German
Federal TVöD.

The position is available immediately. Applicants should hold a Ph.D. in the
biological,

chemical or physical sciences and have a solid background in biochemical
methods, in
bio-macromolecular crystallography and/or related fields. The position also
requires the

documented ability to conduct independent research as well as excellent
communication

and interpersonal skills.


Please send applications (CV, list of publications, references, .pdf-file
format) citing the

reference number AN/423/23 in electronic form until 26.01.2023 to:

Dr. Manfred Weiss (manfred.we...@helmholtz-berlin.de)

Here is the link to the job advertisement (in German):

https://haushalt-und-personal.hu-berlin.de/de/personal/stellenausschreibungen/
wissenschaftliche-r-mitarbeiter-in-m-w-d-befristet-fuer-vorauss-3-jahre-e-13-tv-l-hu-teilzeitbeschaeftigung-ggf-moeglich


Best wishes,

Manfred Weiss, on behalf of PS-GMX and the Joint Berlin MX-Laboratory





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[ccp4bb] Postdoctoral positions at Karolinska Institutet, Stockholm

[Luca Jovine]

Fertilization is a fundamental event in the life cycle of all 
sexually-reproducing organisms, and our laboratory at Karolinska Institutet 
(http://jovinelab.org) investigates the molecular basis of egg-sperm 
interaction by integrating biochemistry, X-ray crystallography, cryo-EM and 
deep learning-based protein structure prediction.

We are looking for highly motivated postdoctoral fellows who'd like to focus on 
a topic that is both highly important from a basic science point of view and 
directly relevant for human reproductive medicine.

For more information and to submit an application, please visit:

https://ki.varbi.com/en/what:job/jobID:687262

You are of course always welcome to also contact me directly for informal 
queries.

With best wishes for a successful and inspiring start to the new year, we look 
forward to receiving your application!

Luca

--

Luca Jovine, Ph.D.
Professor of Structural Biology, Member of EMBO and the Nobel Assembly
Karolinska Institutet
Department of Biosciences and Nutrition
Medicinaren 25 Neo
Blickagången 16, SE-141 83 Huddinge, Sweden
E-mail: luca.jov...@ki.se
W3: http://jovinelab.org




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[ccp4bb] Staff scientist and technician positions available

[Alexandra Deaconescu]

STAFF SCIENTIST AND TECHNICIAN POSITIONS AVAILABLE

at Brown University, USA

The Deaconescu Lab at Brown University has one immediate opening for a staff 
scientist and one technician. The laboratory’s interests lie primarily in 
stress responses, with particular emphasis on responses to DNA damage and the 
mechanochemistry of DNA-based motors. We utilize a combination of biochemical, 
biophysical and structural techniques. (e.g. X-ray crystallography, electron 
microscopy). Examples of recent work are: Brugger et al, JBC (2023, 2024), 
Schwartz et al, Protein Science (2021), Brugger et al, Nature Communications 
(2020), Dorich et al, Genes & Development (2019), Vemu et al. Science (2018), 
Le TT et al. Cell (2018).

Successful candidates would have solid experience with protein biochemistry 
(including their purification, functional characterization and assay 
development). We have a variety of projects available at different stages of 
development, including some that involve drug design. Prior knowledge of 
crystallography and/or single-particle electron microscopy is highly desirable, 
but not required.  Generous compensation, benefits and vacation time are 
available to those qualified.

A successful technician candidate should preferably have a degree in 
chemistry/biological sciences and more than two years experience at the bench, 
at the minimum with molecular biology, and ideally, also with protein 
purification and crystallization.

Interested candidates should send a CV, a one page research experience summary 
and contact information for three references to 
alexandra_deaconescu[at]brown.edu. Please use “staff scientist” or “technician 
candidate” as a subject.

Brown University, an Ivy League school ranked as 5th best in the US by the Wall 
Street Journal, is located in Providence, Rhode Island less than one hour away 
by train from Boston. Rhode Island provides plenty of opportunities for outdoor 
recreation with beautiful beaches and sailing.

Lab webpage: https://deaconesculab.com

Alexandra Deaconescu, B.E., Ph.D.
Assistant Professor
Brown University

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Re: [ccp4bb] RMSD per residue graph for multiple aligned PDB files

[Harry Powell]

AFAIK the CCP4 tools “superpose” and “gesamt” both give tables of per-residue 
RMSD

Harry

> On 5 Jan 2024, at 10:49, Tomas Malinauskas  
> wrote:
> 
> Dear All,
> 
> I apologize for asking a somewhat off-topic question.
> 
> I have multiple aligned PDB files loaded in PyMOL, each representing
> different conformations of the same protein. I'm interested in
> creating a graph displaying RMSD per residue, similar to those shown
> at 
> https://www.ks.uiuc.edu/Training/Tutorials/science/aars/aars_html.bak/node22.html
> or 
> https://www.compchems.com/how-to-compute-the-rmsf-using-gromacs/#the-gmx-rmsf-command.
> 
> I'm wondering if anyone has a script available that can calculate RMSD
> per residue and write the data to a text file for graph generation. If
> so, would they be able to share it with everyone?
> 
> Thank you for your help.
> 
> Best wishes,
> Tomas
> 
> 
> 
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Re: [ccp4bb] RMSD per residue graph for multiple aligned PDB files

[Prof. Dr. Arne Skerra]

Dear Thomas,

Just have a look at this paper where we have made three-dimensional 
sketches of both backbone and side chain RMSDs:

https://pubmed.ncbi.nlm.nih.gov/34988429

The illustrations were done with Chimera, but "B-factor" plots with 
PyMOL can be generated,at least for the backbone variation,following the 
same procedure.


Cheers, Arne



Am 05.01.24 um 11:49 schrieb Tomas Malinauskas:

Dear All,

I apologize for asking a somewhat off-topic question.

I have multiple aligned PDB files loaded in PyMOL, each representing
different conformations of the same protein. I'm interested in
creating a graph displaying RMSD per residue, similar to those shown
at 
https://www.ks.uiuc.edu/Training/Tutorials/science/aars/aars_html.bak/node22.html
or 
https://www.compchems.com/how-to-compute-the-rmsf-using-gromacs/#the-gmx-rmsf-command.

I'm wondering if anyone has a script available that can calculate RMSD
per residue and write the data to a text file for graph generation. If
so, would they be able to share it with everyone?

Thank you for your help.

Best wishes,
Tomas



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--
Prof. Dr. Arne Skerra
Lehrstuhl f. Biologische Chemie  |  Technische Universitaet Muenchen
Emil-Erlenmeyer-Forum 5  |  85354 Freising (Weihenstephan)  |  Germany
Phone: +49 8161 71 4351  |  Fax: 4352
eMail: ske...@tum.de  |  http://biologische-chemie.userweb.mwn.de



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[ccp4bb] RMSD per residue graph for multiple aligned PDB files

[Tomas Malinauskas]

Dear All,

I apologize for asking a somewhat off-topic question.

I have multiple aligned PDB files loaded in PyMOL, each representing
different conformations of the same protein. I'm interested in
creating a graph displaying RMSD per residue, similar to those shown
at 
https://www.ks.uiuc.edu/Training/Tutorials/science/aars/aars_html.bak/node22.html
or 
https://www.compchems.com/how-to-compute-the-rmsf-using-gromacs/#the-gmx-rmsf-command.

I'm wondering if anyone has a script available that can calculate RMSD
per residue and write the data to a text file for graph generation. If
so, would they be able to share it with everyone?

Thank you for your help.

Best wishes,
Tomas



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