[ccp4bb] Zn+2 proteases

[chemocev marker]

Dear All

I have a questions about the Zn+2 proteases (Thermolysin based Zn+2 site)

As Zinc is trouble metal when it comes to test the activity.

Which is better substitute for it.

Is MgCl2 or MncCl2

Why one is preferred over the other.

best

Jiri



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[ccp4bb] Electrostatic Potential: Poisson-Boltzmann criteria

[chemocev marker]

Hi
I am just calculating the Electrostatic Potential, and I wanted to know
your opinion which force field is better.What is criteria to choose and not
to choose the pKA...

best

Jiri

Re: [ccp4bb] Van der waals force

[chemocev marker]

Hi
Thanks for your good help and I am wondering is there clear way to show
these forces like H-bond. I tried KING and can see the VDW radii but not
the visual representation. Does coot has any option for this.
best
Jiri

On Fri, Dec 8, 2017 at 8:57 AM, HERMAN VAN TILBEURGH <
herman.van-tilbeu...@u-psud.fr> wrote:

> jiri, VDW forces are always acting and between any pair of atoms
> the optimal distance (most favourable interaction energy) depends on the
> pair of atoms involved in the interaction, but is a big bitter than the sum
> of atomic radii
> all the best
> herman
> Herman van Tilbeurgh
> Professor structural biology
> Directeur Adjoint Ecole Doctorale Innovation Thérapeutique: du fondamental
> à l'appliqué
>
> Institut de Biologie Intégrative de la Cellule - I2BC
> UMR 9198 CNRS- Université Paris Sud
> Team: Fonction et Architecture des Assemblages MacroMoléculaires
> http://www.i2bc.paris-saclay.fr/spip.php?article256
>
> Batiment 430
> 91405 Orsay
> France
>
> Tel: 33 1 69 15 31 55
> fax: 33 1 69 85 37 15
> herman.van-tilbeu...@u-psud.fr
>
>
>
>
>
>
> Le 8 déc. 2017 à 08:52, KLAHOLZ bruno <klah...@igbmc.fr> a écrit :
>
>
> Hello,
>
> van der Waals interactions are very weak, this is why we usually speak
> about van der Waals *contacts* rather than *interactions*.
> These are usually in the range of 3.5-3.8/4 Å (smaller than that may
> indicate a close contact or steric clash of an atomic model under
> refinement), corresponding to the packing of the van der Waals spheres of
> the individual atoms.
> In hydrogen bond interactions, the term “interaction” normally implies
> sharing a hydrogen atom between two polar residues, for example between the
> hydroxyl group of a threonine side chain with a carbonyl group of the main
> chain peptide backbone; in there one should take into account the geometry
> as well (e.g. ~120°-180° is favorable, 90° is not). Note that some
> positions such as Calpha-H can be slightly polarized (these contribute to
> bifurcated H-bonds in beta sheets for example, see e.g.
> https://www.ncbi.nlm.nih.gov/pubmed/12220491 ).
> In the context of series of van der Waals contacts between hydrophobic
> residues there can be additive effects of the weak interactions with then
> sum up, but in this context one should also consider entropic effects such
> as de-solvatation which becomes favorable energetically.
>
> Hope this helps.
>
> Best regards,
>
> Bruno
>
>
> 
> ###
> Bruno P. Klaholz
> Centre for Integrative Biology
> Institute of Genetics and of Molecular and Cellular Biology
> 67404 ILLKIRCH
> FRANCE
> http://igbmc.fr/Klaholz
>
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
> <CCP4BB@JISCMAIL.AC.UK>] *On Behalf Of *chemocev marker
> *Sent:* 08 December 2017 07:55
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Van der waals force
>
> Hi
>
> I just have a basic question if the Van der waals interaction will exist
> between the hydrophobic residues or it can also be contributed by the polar
> residues as well. What distance is required for the Van der waals
> interaction.
>
> best
> Jiri
>
>
>

[ccp4bb] Van der waals force

[chemocev marker]

Hi
I just have a basic question if the Van der waals interaction will exist
between the hydrophobic residues or it can also be contributed by the polar
residues as well. What distance is required for the Van der waals
interaction.

best

Jiri

[ccp4bb] Electrostatic Potential: Poisson-Boltzmann

[chemocev marker]

Hi

I am calculating the Electrostatic Potential of my protein. But there were
few flexible region with high B-factor and I deleted that part of the
protein and then recalculated it. But there I can see a big change.As I
have a structure in the presence and the absence of the peptide and the
these flexible regions have a better map in the structure without peptide
and with peptide I have to delete them.
I have a question, should I model these missing regions

or

I should ignor them

best

Jiri

[ccp4bb] drawing of peptide interaction

[chemocev marker]

Hi
I wanted to draw a peptide interaction in the catalytic site together with
side chain of the enzyme. What is a good program to do that, or web based
service. I see the LIGPLOT and I am wondering if there are some other
alternatives of that.

best

Jiri

[ccp4bb] prodrg in coot

[chemocev marker]

Dear members
I am wondering how to activate the prodrg tool in coot. Does it has to be
purchased to get licence??. If I made the ligand in ligand builder and
click apply, it gives window info no cprogrg not found. I am using the coot
0.8.4 from the ccp4 site. Does the enhanced ligand tools has to be
purchased??

best

Jiri

[ccp4bb] ligand with out space group information

[chemocev marker]

Hi
I have model of ligand molecule and it does not open in coot. Its not a
crystal structure. I can view it in the pymol or chimera but not in the
coot. It gives error that it does not have any space group information. Is
there is a way to open it in coot.

best

Jiri

[ccp4bb] surface area

[chemocev marker]

Hi
I am comparing some protein complex with PISA analysis. Can someone make a
note what is difference between interface area and buried surface area. I
think buried surface area also include the interface area + the area
encloses with in the protein. Does it make sense to mentioned the interface
area separately if we count the buried area??

best

Jiri

[ccp4bb] case study of peptides

[chemocev marker]

Hi
I am looking for some literature or the structure of the metallopeptidases
where the substrate bound with the ezyme but with shifted P2-P1-P1'-P2'
cleavage site. May be some theoretical case study is there.

Best

Jiri

[ccp4bb] secondary structure assignment to PDB file

[chemocev marker]

Hi
Is there any tool that can assign secondary structure to the PDB file. The
problem is if I used different modelling tools, there are regions in the
protein which does not remain consistent and looks different in different
application.

best

J. Vitali

Re: [ccp4bb] Visualize symmetry operations

[chemocev marker]

Hi Aaron
may be this tool can be helpful
https://symd.nci.nih.gov/
or
in the pymol there is script


https://pymolwiki.org/index.php/Symmetry_Axis

Visualizing the transformation between two selections/objects

https://pymolwiki.org/index.php/RotationAxis

PDB has a symmetry browser

http://www.rcsb.org/pdb/staticHelp.do?p=help/advancedsearch/proteinSymmetryBrowser.html

may be it will be helpful

best

Jiri



On Wed, Jan 4, 2017 at 5:20 PM, Aaron Finke  wrote:

> Dear CCP4-keteers,
>
> Is there a program that can visualize symmetry operation positions (e.g.
> twofold screws, fourfolds) in protein structures, like CCDC Mercury does
> for small molecules?
>
> Thanks in advance,
> Aaron
>
> --
> Aaron Finke
> Staff Scientist, MacCHESS
> Cornell University
> e-mail: af...@cornell.edu
>
>

[ccp4bb] intrasubunit rotation axis

[chemocev marker]

Hi All

I am interested to measure the symmetry axis of individual sub-unit (chain
A & chain B) along with the symmetry axis of the heterdimer (AB). Each
chain is also 2 fold axis, and I can measure by removing 1 chain and
measure for the other and then combine all the symmetry axis in the 1 PDB
file. Is there is a way to do it with out removing the either chain.

I searched and there was a FIT program on the DOMOV server, which is not
active any more.
If there is some other programs that can do it.

best

Jiri

[ccp4bb] Symmetry axes

[chemocev marker]

Dear All
can some one advise that how to calculate/draw the symmetry axes on the
structure. On the deposited structure one can do in the Jmol by selecting
the symmetry option but how to do it off line.

best

Jiri

[ccp4bb] good images

[chemocev marker]

Dear All
I am making the images of the structure in the CCP4MG, I want to ask which
format is best for good quality images JPEG or TIFF and what dpi is best. I
add the legends in corel draw.
If somebody have useful tips or suggestions.

best

Jiri

[ccp4bb] cutaway view of the electrostatic potential

[chemocev marker]

Hi All
I am trying to make images of the electrostatic surface of structure. I
don't know how to make a cutaway view in this representation. I don't see
any option in the CCP4MG. Is thiere any tutorial for this in chimera or
other programs??

best


J. Vitali