Re: [ccp4bb] RMSF calculation in pymol

[Krieger, James M]

I don’t have one for pymol, but there is a function in prody for it.

Best wishes
James

On 14 Dec 2023, at 21:41, Srivastava, Dhiraj  
wrote:


Hi All
sorry for off topic question. does anyone have script for rmsf 
calculation of multistate pdb file in pymol? There used to be a script 
rmsf_states  written by Robert Campbell but with newer version of pymol, it's 
not working.

Thank you
Dhiraj



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[ccp4bb] RMSF calculation in pymol

[Srivastava, Dhiraj]

Hi All
sorry for off topic question. does anyone have script for rmsf 
calculation of multistate pdb file in pymol? There used to be a script 
rmsf_states  written by Robert Campbell but with newer version of pymol, it's 
not working.

Thank you
Dhiraj



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Re: [ccp4bb] solvent mask for partial ligands, addendum

[James Holton]

You guessed right.  Bulk solvent does not get a localized "occupancy". 
It is set to "0" anywhere near modeled atoms, even if those atoms have 
an occupancy of 0.01.  Yes, it might seem sensible to do "occupancy" for 
the bulk, but in practice it is tricky.  I tried my hand at a "fuzzy" 
bulk solvent mask, which can be read in by refmac. It tends to perform 
better than the default masks, but is rather computationally intensive 
to make. Script here:

https://github.com/bl831/fuzzymask

This is perhaps a closer approximation to what you are thinking a bulk 
solvent mask should be?


You might also want to try the Babinet inverse type of bulk solvent 
model. refmac supports this if you use "scale type bulk".


-James Holton
MAD Scientist

On 12/14/2023 2:40 AM, Palm, Gottfried wrote:
I can only guess that the solvent at the place of the EPE is set to 0 
(instead of 0.5)




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[ccp4bb] BCA 2024 Spring Meeting Abstracts Open Now!

[Crawshaw, Adam (DLSLtd,RAL,LSCI)]

Dear CCP4BB,



Register now for the British Crystallographic Association's (BCA) Spring 
Meeting
 (University of Leeds 25th-28th March 2024)!



Abstract submission deadline: 19th January (09:00 GMT)

We strongly encourage abstracts across all areas of structural biology (i.e. 
Cryo-EM, crystallography, Cryo-ET and NMR). If you feel your work does not fit 
into the individual sessions, there is an Open Session which will consider all 
structural biology abstracts.



The Biological Structures Group (BSG) have a programme covering areas at the 
forefront of structural biology aimed at all career stages. The theme of this 
meeting is breaking barriers and the sessions have been centred around this 
(see below), with additional sessions exploring the career paths of those 
skilled in crystallography and how to get the most from synchrotrons.



BSG Sessions and Plenary:



  *   BSG Plenary. Prof. Syma Khalid (University of Oxford) “When structural 
data gets messy: insights from molecular simulations.



  *   Artificial intelligence in structural biology. Keynote: Dr Isabel Moraes 
(Google Deepmind) “Integrative Structural Biology with AI”



  *   Getting the most from your protein crystals at the synchrotron. Keynote: 
Dr David Aragao (Diamond Light Source) “Title TBC”



  *   Early career stage joint session: Breaking the field boundary: careers 
between chemical and biological crystallography. Panel Discussion with 5 
scientists including Dr Helen Ginn and Dr Briony Yorke.



  *   Industrial group joint session: Exploring synergies at the small 
molecule-biomolecule boundary. Keynote: Dr Duncan Johnstone (GSK) “Title TBC”



  *   Breaking barriers with emerging technology in structural biology. 
Keynote: Dr Pedro Nunes (Diamond Light Source) “The High-energy Electron 
Xtallography Instrument: a new tool for macromolecular structure determination”



  *   BSG: Open Session. Keynote: Prof. Tanmay Bharat (MRC Laboratory of 
Molecular Biology) “Solving Structures of Crystals in Cells using Electron 
Tomography”



There is also the Bragg prize lecture which will be of interest to many 
structural biologists.



  *   Bragg Prize Lecture. Prof. Arwen Pearson (University of Hamburg ) “The 
future of macromolecular crystallography in the age of machine learning”



We look forward to seeing you in Leeds in March 2024!



Dr Adam Crawshaw and Dr Rachael Wilkinson

BCA Spring Meeting 2024 Organisation Committee



Please send any enquiries to 
adam.craws...@diamond.ac.uk or 
rachael.wilkin...@path.ox.ac.uk


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Re: [ccp4bb] solvent mask for partial ligands

[Roberto Steiner]

Dear Gottfried

Assuming your modelling is correct you can always try occupancy refinement of 
your ligand (or simply test alternative values). Maybe that will help.
You can also play with bulk solvent mask parameters. Keywords (both occupancy 
and mask parameters) can be found in
https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html#id.b236767394ac

Best wishes
Roberto


Roberto A Steiner
www.steinerlab.org
https://twitter.com/steiner_lab

roberto.stei...@kcl.ac.uk
Randall Centre for Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London
Room 3.10A
New Hunt's House, Guy's Campus
SE1 1UL, London, UK
Phone 0044 20 78488216
Fax0044 20 78486435

roberto.stei...@unipd.it
Dipartimento di Scienze Biomediche
Università degli Studi di Padova
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Telefono 0039 049 8276409

Responses to emails are not expected outside of your normal working hours.








On 14 Dec 2023, at 11:20, Palm, Gottfried 
>
 wrote:

You don't often get email from 
b793af054fc6-dmarc-requ...@jiscmail.ac.uk.
 Learn why this is important
Dear all,
  I have a modelling problem, which probably has something to do with the 
solvent mask.
There is a positive density blob at the surface of my protein, which I can more 
or less satisfy with a Hepe (EPE). Hepes is in the buffer, the sulfonic acid 
H-bonds to a lysine side chain and a main chain N, one of the ring nitrogens to 
a glutamate side chain. At occupancy 1.0 I get B-factors twice as high as the 
protein and negative difference density. Thus, I set the occupancy to 0.5 and 
get the whole EPE covered in positive difference density at 3 sig, peaking at 6 
sig. This positive density is much larger than without EPE. On first glance, 
this looked contradictory to me: more positive density after putting more atoms 
there. I can only guess that the solvent at the place of the EPE is set to 0 
(instead of 0.5), so I get positive density because of only 0.5 occupied EPE. 
Can I refine with half a ligand and half solvent?
Greetings
  Gottfried


On Tuesday, 12-12-2023 at 09:50 Krieger, James M wrote:
There is also discussion about this for chaperonins such as CCT and GroEL. It 
may be that beryllium fluoride works better.

Best wishes
James

> On 12 Dec 2023, at 05:30, Matthew BOWLER 
> mailto:mbow...@embl.fr>> wrote:
>
> Dear Jinyu,
> we observed exactly this in PGK - see https://doi.org/10.1021/ja100974t where 
> we confirmed it by both crystallography and 19F NMR
>
> In fact ALF3 does not exist as a trigonal bipyramid - all cases where this 
> geometry is observed are likely MgF3 that does adopt this geometry and will 
> replace the aluminium at pH values above 8 as Al will precipitate as AlOH.
>
> We only saw the water replacing the F when a catalytic residue charge was 
> removed and proposed the hypothesis that phos transfer enzymes need to 
> balance the charge in the active site exactly therefore selecting the neutral 
> AlF3 over negative AlF4- that both exist in solution.
>
> Best wishes, Matt
>
>> On 2023-12-12 03:40, Friday wrote:
>> Dear CCP4 community,
>> I recently tried to use AlF3 to mimic the transition of an enzyme. In
>> all the publications I can find, when mimicking the 3rd phosphate of
>> the transition state, the AlF3 forms a trigonal bipyramid
>> coordination, and the G(A)DP oxygen to the AL  is about equal distance
>> to that from the AL to the catalytic water oxygen (2.2A).
>> However, I got a completely different geometry of ALF3, I think I have
>> the ALF3OH bound and it's a  tetrahedron geometry instead of trigonal
>> pyramidal. The G(A)DP oxygen to the AL  is about 3.1A and  the AL to
>> the catalytic water oxygen is about 1.8A.
>> I am pretty sure it is not the ALF4 but the ALF3OH since the AL-OH
>> distance is longer than the Al-F distance (1.8A verse 1.6A) and I have
>> a very high resolution structure.
>> Can anyone explain this to me, have you ever encountered this before?
>> Your answer is much appreciated!
>> Jinyu
>> -
>> 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/
> ===
>
> 

[ccp4bb] solvent mask for partial ligands, addendum

[Palm, Gottfried]

Dear all, 




  I have a modelling problem, which probably has something to do with
the solvent mask. 

There is a positive density blob at the surface of my protein, which I
can more or less satisfy with a Hepe (EPE). Hepes is in the buffer,
the sulfonic acid H-bonds to a lysine side chain and a main chain N,
one of the ring nitrogens to a glutamate side chain. At occupancy 1.0
I get B-factors twice as high as the protein and negative difference
density. Thus, I set the occupancy to 0.5 and get the whole EPE
covered in positive difference density at 3 sig, peaking at 6 sig.
This positive density is much larger than without EPE. On first
glance, this looked contradictory to me: more positive density after
putting more atoms there. I can only guess that the solvent at the
place of the EPE is set to 0 (instead of 0.5), so I get positive
density because of only 0.5 occupied EPE. Can I refine with half a
ligand and half solvent?
Greetings
  Gottfried


I should add that I am refining with refmac version 5.8.0419.
parameters: 

SCALE TYPE SIMPLE
SOLVENT YES



Sorry for the confusion because of hijacking another thread of the
bulletin board.



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[ccp4bb] solvent mask for partial ligands

[Palm, Gottfried]

Dear all, 

  I have a modelling problem, which probably has something to do with
the solvent mask. 

There is a positive density blob at the surface of my protein, which I
can more or less satisfy with a Hepe (EPE). Hepes is in the buffer,
the sulfonic acid H-bonds to a lysine side chain and a main chain N,
one of the ring nitrogens to a glutamate side chain. At occupancy 1.0
I get B-factors twice as high as the protein and negative difference
density. Thus, I set the occupancy to 0.5 and get the whole EPE
covered in positive difference density at 3 sig, peaking at 6 sig.
This positive density is much larger than without EPE. On first
glance, this looked contradictory to me: more positive density after
putting more atoms there. I can only guess that the solvent at the
place of the EPE is set to 0 (instead of 0.5), so I get positive
density because of only 0.5 occupied EPE. Can I refine with half a
ligand and half solvent?
Greetings
  Gottfried



On Tuesday, 12-12-2023 at 09:50 Krieger, James M wrote:



There is also discussion about this for chaperonins such as CCT and
GroEL. It may be that beryllium fluoride works better.

Best wishes
James

> On 12 Dec 2023, at 05:30, Matthew BOWLER  wrote:
>
> Dear Jinyu,
> we observed exactly this in PGK - see
https://doi.org/10.1021/ja100974t where we confirmed it by both
crystallography and 19F NMR
>
> In fact ALF3 does not exist as a trigonal bipyramid - all cases
where this geometry is observed are likely MgF3 that does adopt this
geometry and will replace the aluminium at pH values above 8 as Al
will precipitate as AlOH.
>
> We only saw the water replacing the F when a catalytic residue
charge was removed and proposed the hypothesis that phos transfer
enzymes need to balance the charge in the active site exactly
therefore selecting the neutral AlF3 over negative AlF4- that both
exist in solution.
>
> Best wishes, Matt
>
>> On 2023-12-12 03:40, Friday wrote:
>> Dear CCP4 community,
>> I recently tried to use AlF3 to mimic the transition of an enzyme.
In
>> all the publications I can find, when mimicking the 3rd phosphate
of
>> the transition state, the AlF3 forms a trigonal bipyramid
>> coordination, and the G(A)DP oxygen to the AL  is about equal
distance
>> to that from the AL to the catalytic water oxygen (2.2A).
>> However, I got a completely different geometry of ALF3, I think I
have
>> the ALF3OH bound and it's a  tetrahedron geometry instead of
trigonal
>> pyramidal. The G(A)DP oxygen to the AL  is about 3.1A and  the
AL to
>> the catalytic water oxygen is about 1.8A.
>> I am pretty sure it is not the ALF4 but the ALF3OH since the AL-OH
>> distance is longer than the Al-F distance (1.8A verse 1.6A) and I
have
>> a very high resolution structure.
>> Can anyone explain this to me, have you ever encountered this
before?
>> Your answer is much appreciated!
>> Jinyu
>> -
>> 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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