Re: [ccp4bb] Interface Configuration and Mapslicer Question

[Jon Cooper]

Thank you for clarifying that. It may not be much consolation but I thought it 
might be useful to know that there are no problems with running mapslicer from 
the command line on linux but my font could be better ;-0

https://u.cubeupload.com/jbcooper/mapslicer.png

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent with [Proton Mail](https://proton.me/) secure email.

On Sunday, 18 February 2024 at 19:03, Bernhard Rupp  
wrote:

> Thanks, Jon. Finding the peaks is not the problem; the *.ha file contains 
> those, as do the pdf. map sections.
>
> It is that I don’t know how to properly fix that Interface Configuration file 
> to have the PS distiller and mapslicer display the output.
>
> This problem occurs on 2 independent CCP4i installations on different Windows 
> 10/11 computers
>
> Thx, BR
>
> From: CCP4 bulletin board  On Behalf Of Jon Cooper
> Sent: Sunday, February 18, 2024 09:39
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Interface Configuration and Mapslicer Question
>
> You could search for peaks of decreasing height by stepping back through 
> through alphabet with your text searches. Of course, peakmax will do a good 
> job of finding them anyway.
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>  Original Message 
> On 18 Feb 2024, 17:35, Jon Cooper < 
> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> I think we used to use mapsig for printing map sections with single 
>> characters to show peak height. You could set it so that low or no density 
>> was just a dot and higher values were 0...9 ... A... Z ... * #, etc. up to 
>> the maximum or maybe it was another one of Ian's programs. It made peak 
>> searching with a text editor pretty easy just by searching for the 
>> characters corressponding to the high values. I don't know if that's any use.
>>
>> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>>
>> Sent from Proton Mail mobile
>>
>>  Original Message 
>> On 18 Feb 2024, 03:29, Bernhard Rupp < hofkristall...@gmail.com> wrote:
>>
>>> Der CCP4 Experts & Developers,
>>>
>>> I am exercising in CCP4i (Windows, 8.0.017) some old-fashioned native 
>>> Patterson maps for NCS analysis, using ‘patterson’ of FFT which produces 
>>> the *.map (dump) file and 3 Harker *.plt files.
>>>
>>> Unfortunately, epic fail on the display of the results.
>>>
>>> The ghostview (cf. image) I cannot install (some dll error) and it also 
>>> seems deprecated.
>>>
>>> As a workaround I use pltdev to generate a *.ps file and distil it into a 
>>> pdf and then display. Works, but ghostly 20th century
>>>
>>> ...or I display the map directly in Coot and eyeball the 
>>> peakssurprisingly neat and educational.
>>>
>>> Q1: Do we have a direct way in the GUI to convert/display these CCP4 plt 
>>> files?
>>>
>>> I failed adding as PSviewer "C:\Program Files (x86)\Adobe\Acrobat 
>>> DC\Acrobat\acrodist.exe" in the interface configuration (problem maybe the 
>>> blanks).
>>>
>>> But the entry in the Interface Configuration (config.def) seems sensibly 
>>> quoted:
>>>
>>> PS_PREVIEW_NAME,4 _text acrodist.exe
>>>
>>> PS_PREVIEW_COM,4 _text "C:\Program Files (x86)\Adobe\Acrobat 
>>> DC\Acrobat\acrodist.exe"
>>>
>>> Q2: how do I properly enter the path to the distiller in the interface 
>>> configuration?
>>>
>>> Mapslicer is also uncooperative (cf. img).
>>>
>>> The Interface Configuration entry informs me that “ccp4mapwish [file join 
>>> [GetEnvPath CCP4I_TOP] bin mapslicer.tcl]”.
>>>
>>> Q3: How should I fix this (I swear I did not wish with the installation)?
>>>
>>> In search of a more modern approach to this map analysis I also tried 
>>> CCP4i2 and Phenix, but there was no task like
>>>
>>> “Make a native Patterson and show me the *&%# map” to be found.
>>>
>>> Q4: would this be a useful task to provide?
>>>
>>> (a selfrotation task exists in ccp4i2 via molrep, and there, PS viewing 
>>> works just fine).
>>>
>>> Cheers, BR
>>>
>>> --
>>>
>>> Bernhard Rupp, Psilosopher
>>>
>>> https://psilosophy.org/
>>>
>>> https://www.hofkristallamt.org/
>>>
>>> b...@hofkristallamt.

Re: [ccp4bb] Interface Configuration and Mapslicer Question

[Bernhard Rupp]

Thanks, Jon. Finding the peaks is not the problem; the *.ha file contains 
those, as do the pdf. map sections.

It is that I don’t know how to properly fix that Interface Configuration file 
to have the PS distiller and mapslicer display the output.

 

This problem occurs on 2 independent CCP4i installations on different Windows 
10/11 computers

 

Thx, BR

From: CCP4 bulletin board  On Behalf Of Jon Cooper
Sent: Sunday, February 18, 2024 09:39
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Interface Configuration and Mapslicer Question

 

You could search for peaks of decreasing height by stepping back through 
through alphabet with your text searches. Of course, peakmax will do a good job 
of finding them anyway. 


Best wishes, Jon Cooper. jon.b.coo...@protonmail.com 
<mailto:jon.b.coo...@protonmail.com> 

Sent from Proton Mail mobile



 Original Message 
On 18 Feb 2024, 17:35, Jon Cooper < 
488a26d62010-dmarc-requ...@jiscmail.ac.uk 
<mailto:488a26d62010-dmarc-requ...@jiscmail.ac.uk> > wrote:


I think we used to use mapsig for printing map sections with single characters 
to show peak height. You could set it so that low or no density was just a dot 
and higher values were 0...9 ... A... Z ... * #, etc. up to the maximum or 
maybe it was another one of Ian's programs. It made peak searching with a text 
editor pretty easy just by searching for the characters corressponding to the 
high values. I don't know if that's any use. 


Best wishes, Jon Cooper. jon.b.coo...@protonmail.com 
<mailto:jon.b.coo...@protonmail.com> 

Sent from Proton Mail mobile



 Original Message 
On 18 Feb 2024, 03:29, Bernhard Rupp < hofkristall...@gmail.com 
<mailto:hofkristall...@gmail.com> > wrote:

 

Der CCP4 Experts & Developers,

 

I am exercising in CCP4i (Windows, 8.0.017) some old-fashioned native Patterson 
maps for NCS analysis, using ‘patterson’ of FFT which produces the *.map (dump) 
file and 3 Harker *.plt files.

 

Unfortunately, epic fail on the display of the results. 

The ghostview (cf. image) I cannot install (some dll error) and it also seems 
deprecated.

As a workaround I use pltdev to generate a *.ps file and distil it into a pdf 
and then display. Works, but ghostly 20th century

...or I display the map directly in Coot and eyeball the peakssurprisingly 
neat and educational.

 

Q1: Do we have a direct way in the GUI to convert/display these CCP4 plt files?

 

I failed adding as PSviewer "C:\Program Files (x86)\Adobe\Acrobat 
DC\Acrobat\acrodist.exe" in the interface configuration (problem maybe the 
blanks).

But the entry in the Interface Configuration (config.def) seems sensibly quoted:

PS_PREVIEW_NAME,4 _text acrodist.exe

PS_PREVIEW_COM,4  _text "C:\Program Files 
(x86)\Adobe\Acrobat DC\Acrobat\acrodist.exe"

 

Q2: how do I properly enter the path to the distiller in the interface 
configuration? 

 

Mapslicer is also uncooperative (cf. img). 

The Interface Configuration entry informs me that “ccp4mapwish [file join 
[GetEnvPath CCP4I_TOP] bin mapslicer.tcl]”.

 

Q3: How should I fix this (I swear I did not wish with the installation)?  

 

In search of a more modern approach to this map analysis I also tried CCP4i2 
and Phenix, but there was no task like 

“Make a native Patterson and show me the *&%# map” to be found.

 

Q4: would this be a useful task to provide?

 

(a selfrotation task exists in ccp4i2 via molrep, and there, PS viewing works 
just fine).

 

Cheers, BR 

 

--

Bernhard Rupp, Psilosopher

 <https://psilosophy.org/> https://psilosophy.org/

 <https://www.hofkristallamt.org/> https://www.hofkristallamt.org/

 <mailto:b...@hofkristallamt.org> b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

All models are wrong but some are useful.

--

 

 


  _  


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

 


  _  


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

 

  _  

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




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

Re: [ccp4bb] Interface Configuration and Mapslicer Question

[Jon Cooper]

You could search for peaks of decreasing height by stepping back through 
through alphabet with your text searches. Of course, peakmax will do a good job 
of finding them anyway.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 18 Feb 2024, 17:35, Jon Cooper wrote:

> I think we used to use mapsig for printing map sections with single 
> characters to show peak height. You could set it so that low or no density 
> was just a dot and higher values were 0...9 ... A... Z ... * #, etc. up to 
> the maximum or maybe it was another one of Ian's programs. It made peak 
> searching with a text editor pretty easy just by searching for the characters 
> corressponding to the high values. I don't know if that's any use.
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
> Sent from Proton Mail mobile
>
>  Original Message 
> On 18 Feb 2024, 03:29, Bernhard Rupp wrote:
>
>> Der CCP4 Experts & Developers,
>>
>> I am exercising in CCP4i (Windows, 8.0.017) some old-fashioned native 
>> Patterson maps for NCS analysis, using ‘patterson’ of FFT which produces the 
>> *.map (dump) file and 3 Harker *.plt files.
>>
>> Unfortunately, epic fail on the display of the results.
>>
>> The ghostview (cf. image) I cannot install (some dll error) and it also 
>> seems deprecated.
>>
>> As a workaround I use pltdev to generate a *.ps file and distil it into a 
>> pdf and then display. Works, but ghostly 20th century
>>
>> ...or I display the map directly in Coot and eyeball the 
>> peakssurprisingly neat and educational.
>>
>> Q1: Do we have a direct way in the GUI to convert/display these CCP4 plt 
>> files?
>>
>> I failed adding as PSviewer "C:\Program Files (x86)\Adobe\Acrobat 
>> DC\Acrobat\acrodist.exe" in the interface configuration (problem maybe the 
>> blanks).
>>
>> But the entry in the Interface Configuration (config.def) seems sensibly 
>> quoted:
>>
>> PS_PREVIEW_NAME,4 _text acrodist.exe
>>
>> PS_PREVIEW_COM,4 _text "C:\Program Files (x86)\Adobe\Acrobat 
>> DC\Acrobat\acrodist.exe"
>>
>> Q2: how do I properly enter the path to the distiller in the interface 
>> configuration?
>>
>> Mapslicer is also uncooperative (cf. img).
>>
>> The Interface Configuration entry informs me that “ccp4mapwish [file join 
>> [GetEnvPath CCP4I_TOP] bin mapslicer.tcl]”.
>>
>> Q3: How should I fix this (I swear I did not wish with the installation)?
>>
>> In search of a more modern approach to this map analysis I also tried CCP4i2 
>> and Phenix, but there was no task like
>>
>> “Make a native Patterson and show me the *&%# map” to be found.
>>
>> Q4: would this be a useful task to provide?
>>
>> (a selfrotation task exists in ccp4i2 via molrep, and there, PS viewing 
>> works just fine).
>>
>> Cheers, BR
>>
>> --
>>
>> Bernhard Rupp, Psilosopher
>>
>> https://psilosophy.org/
>>
>> https://www.hofkristallamt.org/
>>
>> b...@hofkristallamt.org
>>
>> +1 925 209 7429
>>
>> +43 676 571 0536
>>
>> --
>>
>> All models are wrong but some are useful.
>>
>> --
>>
>> ---
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>> ---
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] Interface Configuration and Mapslicer Question

[Jon Cooper]

I think we used to use mapsig for printing map sections with single characters 
to show peak height. You could set it so that low or no density was just a dot 
and higher values were 0...9 ... A... Z ... * #, etc. up to the maximum or 
maybe it was another one of Ian's programs. It made peak searching with a text 
editor pretty easy just by searching for the characters corressponding to the 
high values. I don't know if that's any use.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile

 Original Message 
On 18 Feb 2024, 03:29, Bernhard Rupp wrote:

> Der CCP4 Experts & Developers,
>
> I am exercising in CCP4i (Windows, 8.0.017) some old-fashioned native 
> Patterson maps for NCS analysis, using ‘patterson’ of FFT which produces the 
> *.map (dump) file and 3 Harker *.plt files.
>
> Unfortunately, epic fail on the display of the results.
>
> The ghostview (cf. image) I cannot install (some dll error) and it also seems 
> deprecated.
>
> As a workaround I use pltdev to generate a *.ps file and distil it into a pdf 
> and then display. Works, but ghostly 20th century
>
> ...or I display the map directly in Coot and eyeball the 
> peakssurprisingly neat and educational.
>
> Q1: Do we have a direct way in the GUI to convert/display these CCP4 plt 
> files?
>
> I failed adding as PSviewer "C:\Program Files (x86)\Adobe\Acrobat 
> DC\Acrobat\acrodist.exe" in the interface configuration (problem maybe the 
> blanks).
>
> But the entry in the Interface Configuration (config.def) seems sensibly 
> quoted:
>
> PS_PREVIEW_NAME,4 _text acrodist.exe
>
> PS_PREVIEW_COM,4 _text "C:\Program Files (x86)\Adobe\Acrobat 
> DC\Acrobat\acrodist.exe"
>
> Q2: how do I properly enter the path to the distiller in the interface 
> configuration?
>
> Mapslicer is also uncooperative (cf. img).
>
> The Interface Configuration entry informs me that “ccp4mapwish [file join 
> [GetEnvPath CCP4I_TOP] bin mapslicer.tcl]”.
>
> Q3: How should I fix this (I swear I did not wish with the installation)?
>
> In search of a more modern approach to this map analysis I also tried CCP4i2 
> and Phenix, but there was no task like
>
> “Make a native Patterson and show me the *&%# map” to be found.
>
> Q4: would this be a useful task to provide?
>
> (a selfrotation task exists in ccp4i2 via molrep, and there, PS viewing works 
> just fine).
>
> Cheers, BR
>
> --
>
> Bernhard Rupp, Psilosopher
>
> https://psilosophy.org/
>
> https://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> All models are wrong but some are useful.
>
> --
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] interface energetics

[Steven Darnell]

Andreas,

Thanks for clarifying the situation. I have one other suggestion you can 
think about based on your description of a "monomeric hybrid." Since you 
are mutating your original yeast protein sequence to human/yeast 
chimeras, you could directly model the mutations in Rosetta and skip the 
homology modeling. Of course, this assumes you are not introducing 
deletions or insertions. This approach will also calculate a DDG for you 
automatically.


Your mutation combinations can be defined by creating a "resfile," and a 
standard Rosetta command call can automate the entire process.


http://www.rosettacommons.org/tiki/tiki-index.php?page=resfile+example


Based on my own experience, I would recommend the following flags:

-Wpack_only, -soft_rep_design: softens the repulsive term and 
accommodates mild clashes between atoms


-ex1, -ex2, -extrachi_cutoff 1: allows rotamers to deviate from their 
most probabilistic side chain conformations


-multi_cool_annealer: compared to Rosetta’s standard annealing scheme, 
multi-cool simulated annealing lowers the system to a cooler temperature 
and considers nearly ten times as many rotamer substitutions before 
selecting a low energy structure


-repack_neighbors: mutated residues and adjacent residues are allowed to 
relax



Here are some other relevant flag combinations with regard to interface 
repacking that you can read up on:


-repack_neighbors and -relax_unbound
-min_interface

Good luck,
Steve


Andreas Förster said the following on 9/12/08 4:42 AM:
Thanks to all who responded to my question regarding the energetics of 
a known interface applied to orthogolous dimers.


Steven Darnell asked me for some clarifications. I have the structure 
of a homodimer, defined the dimerization interface and substituted the 
residues at said interface with those of each of four human orthologs 
of the original yeast protein. What I call monomeric hybrids are thus 
yeast proteins with different humanized dimerization interface. I 
recombine these monomeric hybrids to give four humanized homodimers 
and six humanized heterodimers. It is the likelihood that these dimers 
form that I'm interested in.


Following Diana Tomchick's suggestion, I had PISA analyze the 
interface of the original dimer and learned that it might be worth to 
consider one other region besides the main helix.


For modeling of the monomeric hybrid, MODELLER is suggested because it 
does simulated annealing by default. To get the energetics, Rosetta 
with the "-interface" or "-ddg_only" flags might be a good tool. I 
have to read up on the details. An alternative is molecular dynamics 
in Gromacs.


Thanks for your help.


Andreas

Re: [ccp4bb] interface energetics

[Andreas Förster]

Thanks to all who responded to my question regarding the energetics of a 
known interface applied to orthogolous dimers.


Steven Darnell asked me for some clarifications.  I have the structure 
of a homodimer, defined the dimerization interface and substituted the 
residues at said interface with those of each of four human orthologs of 
the original yeast protein.  What I call monomeric hybrids are thus 
yeast proteins with different humanized dimerization interface.  I 
recombine these monomeric hybrids to give four humanized homodimers and 
six humanized heterodimers.  It is the likelihood that these dimers form 
that I'm interested in.


Following Diana Tomchick's suggestion, I had PISA analyze the interface 
of the original dimer and learned  that it might be worth to consider 
one other region besides the main helix.


For modeling of the monomeric hybrid, MODELLER is suggested because it 
does simulated annealing by default.  To get the energetics, Rosetta 
with the "-interface" or "-ddg_only" flags might be a good tool.  I have 
to read up on the details.  An alternative is molecular dynamics in Gromacs.


Thanks for your help.


Andreas



Steven Darnell wrote:

Andreas,

Here's my $0.02.  Would you mind clarifying a few things for me?

I am working on (the theoretical side of) a protein complex whose 
structure has been solved.  The protein homo-dimerizes, mediated 
primarily by two long helices.


So you have a structure of a homodimer...

Using sequencing alignment and the WHAT IF server, I built monomeric 
hybrid models containing the bulk of the known structure and the 
dimerization helices of homologous proteins.  Naturally, I want to 
know how likely they are to form dimers.


Could you explain what you mean by "monomeric hybrid"?  I'm guessing you
want to thread two copies of monomer B onto the backbones of homodimer A.

To look at the energetics, I've run the phenix geometry regularization 
algorithm to minimize clashes and side chain energies. 


I've never used phenix and I don't know what sort of search function it
uses.  If it's a deterministic algorithm, like dead end elimination,
you'll get the global minimum energy conformation with one run (if it
converges, that is).  If it's a stochastic algorithm, like Monte Carlo,
you'll never know if you're at the global minimum.  Your best bet is to
run multiple independent minimizations, say 50-100 for starters, and
pick the conformation with the lowest energy score.  I'm betting its the
latter.

The backbone conformation only changes minimally.  Next I calculated 
in Rosetta the energetic scores of the models before and after 
regularization and compared with that of the native structure.  This 
gave me some numbers that are not inconsistent with experiments.


The following assumes I correctly stated your design problem.  Rosetta
does not account for conformational entropy, so the closer the backbones
are between the homodimer A and modeled homodimer B to one another, the
better.  You might want to consider fixing the backbones during
minimization.

Also, I don't understand the purpose of calculating the energy of the
non-optimized structure.  I would be more interested in the change in
binding energy between the bound and unbound state of the minimized
structure.  Rosetta can calculate that in "-interface" mode.  There's a
flag to keep Rosetta from performing any design calculations; I think
its "-ddg_only" or something like that.  Note that this calculation
assumes the monomers behave like rigid bodies.

Finally, I would minimize homodimer A the same way you minimize modeled
homodimer B as a control, then use Rosetta to calculate its change in
binding energy.  Side chain flips of His, Asn, and Gln will make a big
difference.  This will give you a number to compare to your modeled dimer.

Before I sit down and write this up, I wanted to ask the community if 
what I've done makes sense and if there are alternative methods for 
minimizing and calculating interface energies.  I don't necessarily 
need docking algorithms as the interface is known.  I just want to get 
an energetic description.


If it were me, I would create the homology model using MODELLER (it uses
simulated annealing by default), minimize/relax the structure using
Rosetta, then calculate the change in binding energy with Rosetta.
Remember to repeat stochastic processes.  The 50-100 time guideline was
given to me by Deanne Sammond, as in:

Sammond DW, Eletr ZM, Purbeck C, Kimple RJ, Siderovski DP, Kuhlman B.
Structure-based protocol for identifying mutations that enhance 
protein-protein

binding affinities.
J Mol Biol. 2007 Aug 31;371(5):1392-404. Epub 2007 Jun 8.
PMID: 17603074 [PubMed - indexed for MEDLINE]


Thank you.


No worries.  Does any one else have any suggestions or corrections?
I've only had 7 hours of sleep since Saturday.

~Steve

--
Steven Darnell
Univeristy of Wisconsin-Madison
Madison, WI USA

[EMAIL PROTECTED]



--
Andreas Förster, Research Ass

Re: [ccp4bb] interface energetics

[Steven Darnell]

Andreas,

Here's my $0.02.  Would you mind clarifying a few things for me?

I am working on (the theoretical side of) a protein complex whose 
structure has been solved.  The protein homo-dimerizes, mediated 
primarily by two long helices.


So you have a structure of a homodimer...

Using sequencing alignment and the WHAT IF server, I built monomeric 
hybrid models containing the bulk of the known structure and the 
dimerization helices of homologous proteins.  Naturally, I want to 
know how likely they are to form dimers.


Could you explain what you mean by "monomeric hybrid"?  I'm guessing you
want to thread two copies of monomer B onto the backbones of homodimer A.

To look at the energetics, I've run the phenix geometry regularization 
algorithm to minimize clashes and side chain energies. 


I've never used phenix and I don't know what sort of search function it
uses.  If it's a deterministic algorithm, like dead end elimination,
you'll get the global minimum energy conformation with one run (if it
converges, that is).  If it's a stochastic algorithm, like Monte Carlo,
you'll never know if you're at the global minimum.  Your best bet is to
run multiple independent minimizations, say 50-100 for starters, and
pick the conformation with the lowest energy score.  I'm betting its the
latter.

The backbone conformation only changes minimally.  Next I calculated 
in Rosetta the energetic scores of the models before and after 
regularization and compared with that of the native structure.  This 
gave me some numbers that are not inconsistent with experiments.


The following assumes I correctly stated your design problem.  Rosetta
does not account for conformational entropy, so the closer the backbones
are between the homodimer A and modeled homodimer B to one another, the
better.  You might want to consider fixing the backbones during
minimization.

Also, I don't understand the purpose of calculating the energy of the
non-optimized structure.  I would be more interested in the change in
binding energy between the bound and unbound state of the minimized
structure.  Rosetta can calculate that in "-interface" mode.  There's a
flag to keep Rosetta from performing any design calculations; I think
its "-ddg_only" or something like that.  Note that this calculation
assumes the monomers behave like rigid bodies.

Finally, I would minimize homodimer A the same way you minimize modeled
homodimer B as a control, then use Rosetta to calculate its change in
binding energy.  Side chain flips of His, Asn, and Gln will make a big
difference.  This will give you a number to compare to your modeled dimer.

Before I sit down and write this up, I wanted to ask the community if 
what I've done makes sense and if there are alternative methods for 
minimizing and calculating interface energies.  I don't necessarily 
need docking algorithms as the interface is known.  I just want to get 
an energetic description.


If it were me, I would create the homology model using MODELLER (it uses
simulated annealing by default), minimize/relax the structure using
Rosetta, then calculate the change in binding energy with Rosetta.
Remember to repeat stochastic processes.  The 50-100 time guideline was
given to me by Deanne Sammond, as in:

Sammond DW, Eletr ZM, Purbeck C, Kimple RJ, Siderovski DP, Kuhlman B.
Structure-based protocol for identifying mutations that enhance 
protein-protein

binding affinities.
J Mol Biol. 2007 Aug 31;371(5):1392-404. Epub 2007 Jun 8.
PMID: 17603074 [PubMed - indexed for MEDLINE]


Thank you.


No worries.  Does any one else have any suggestions or corrections?
I've only had 7 hours of sleep since Saturday.

~Steve

--
Steven Darnell
Univeristy of Wisconsin-Madison
Madison, WI USA

[EMAIL PROTECTED]

Re: [ccp4bb] interface

[Phil Evans]

This will in general be true in an asymmetric interface (between two  
different molecules) if you look at the "accessible" surface, defined  
by the locus of a water molecule rolling over the surface. The surface  
measured by that method is larger on a convex surface than on a  
concave one.


Phil


On 11 Aug 2008, at 11:06, P.J.Briggs wrote:

Not sure if this is relevant, however as an addendum: a couple of  
years

ago I looked at some data from a colleague using AREAIMOL and learned
that while it's not intuitively obvious, it is possible that the
calculated accessible surface area buried on one subunit may differ  
from

that buried on the other subunit in the same interaction i.e. more
surface area may be buried on one subunit than the other.

I think that this effect is simply an artefact of how the accessible
surface is defined, but it does mean that in some cases the simple
division by 2 of the total calculated buried area may not be accurate
for the individual subunits. In the example that I looked at the
differences could be quite significant - in the most extreme case the
split was 60/40 (although in others it was much smaller).

I suppose this is really just a curiosity, but it does add more weight
to the argument for reporting the total change in buried area due to
interface formation.

Best wishes

Peter

Steven Darnell wrote:

Phil,

I had a follow up conversation regarding this very topic.  Here is an
excerpt:


The following is from Chothia and Janin (1975) Nature, 256:705-708,
one of the early articles regarding buried surface area and protein
interfaces:

"The surface area buried in the complex is then defined as the
accessible surface area of one subunit plus that of the other  
subunit

minus that of the complex."

I believe that definition has not changed in 30 years.  While I will
agree that dividing by 2 approximates the physical area of the
interface, this does not represent the total amount of surface area
that is no longer accessible to solvent.  In terms of desolvating  
the

interface for binding, the latter is more appropriate.


As you point out, PISA appears to be reporting the area of the
interface, not the total surface area occluded from solvent.   
Confusing

indeed.

Regards,
Steve Darnell


Phil Jeffrey said the following on 8/8/08 10:03 AM:

Which brings up something about PISA.  If I run PISA on pdb entry
2IE3, which I'm familiar with, I get the following numbers from PISA
and CCP4's AREAIMOL  (surface areas in Angstrom^2) for the A:C  
interface.



PISA for 2IE3

   Automatic A:C interface selection 907.9
   (a crystal packing interface is larger than this, but this  
surface

is the A:C interface)


AreaIMol with some editing of 2IE3 to separate the chains

   Chain A25,604.4
   Chain C11,847.4
Total  37,451.8
   Chain AC   35,576.6
Difference  1,875.2
Difference/2  937.6


For buried S.A. I agree with Steve Darnell's definition.  However  
PISA

appears to be reporting half that value, or what it calls "interface
area".  Potentially confusing.

Phil Jeffrey
Princeton


--
___
Peter J Briggs, [EMAIL PROTECTED]   Tel: +44 1925 603826
CCP4,   [EMAIL PROTECTED]  Fax: +44 1925 603825
   http://www.ccp4.ac.uk/
Daresbury Laboratory, Daresbury, Warrington WA4 4AD

Re: [ccp4bb] interface

[P.J.Briggs]

Not sure if this is relevant, however as an addendum: a couple of years
ago I looked at some data from a colleague using AREAIMOL and learned
that while it's not intuitively obvious, it is possible that the
calculated accessible surface area buried on one subunit may differ from
that buried on the other subunit in the same interaction i.e. more
surface area may be buried on one subunit than the other.

I think that this effect is simply an artefact of how the accessible
surface is defined, but it does mean that in some cases the simple
division by 2 of the total calculated buried area may not be accurate
for the individual subunits. In the example that I looked at the
differences could be quite significant - in the most extreme case the
split was 60/40 (although in others it was much smaller).

I suppose this is really just a curiosity, but it does add more weight
to the argument for reporting the total change in buried area due to
interface formation.

Best wishes

Peter

Steven Darnell wrote:
> Phil,
> 
> I had a follow up conversation regarding this very topic.  Here is an
> excerpt:
> 
>> The following is from Chothia and Janin (1975) Nature, 256:705-708,
>> one of the early articles regarding buried surface area and protein
>> interfaces:
>>
>> "The surface area buried in the complex is then defined as the
>> accessible surface area of one subunit plus that of the other subunit
>> minus that of the complex."
>>
>> I believe that definition has not changed in 30 years.  While I will
>> agree that dividing by 2 approximates the physical area of the
>> interface, this does not represent the total amount of surface area
>> that is no longer accessible to solvent.  In terms of desolvating the
>> interface for binding, the latter is more appropriate.
> 
> As you point out, PISA appears to be reporting the area of the
> interface, not the total surface area occluded from solvent.  Confusing
> indeed.
> 
> Regards,
> Steve Darnell
> 
> 
> Phil Jeffrey said the following on 8/8/08 10:03 AM:
>> Which brings up something about PISA.  If I run PISA on pdb entry
>> 2IE3, which I'm familiar with, I get the following numbers from PISA
>> and CCP4's AREAIMOL  (surface areas in Angstrom^2) for the A:C interface.
>>
>> >> PISA for 2IE3
>> Automatic A:C interface selection 907.9
>> (a crystal packing interface is larger than this, but this surface
>> is the A:C interface)
>>
>> >> AreaIMol with some editing of 2IE3 to separate the chains
>> Chain A25,604.4
>> Chain C11,847.4
>> Total  37,451.8
>> Chain AC   35,576.6
>> Difference  1,875.2
>> Difference/2  937.6
>>
>>
>> For buried S.A. I agree with Steve Darnell's definition.  However PISA
>> appears to be reporting half that value, or what it calls "interface
>> area".  Potentially confusing.
>>
>> Phil Jeffrey
>> Princeton

-- 
___
Peter J Briggs, [EMAIL PROTECTED]   Tel: +44 1925 603826
CCP4,   [EMAIL PROTECTED]  Fax: +44 1925 603825
http://www.ccp4.ac.uk/
Daresbury Laboratory, Daresbury, Warrington WA4 4AD

Re: [ccp4bb] interface

[P Hubbard]

The way I look at it; BSA the the total surface area defined within two
bisecting 3D curves, interface area is the minimum surface area that
can be that can be produced by interpolation between regions at bisect
each other. Probably not the best definition.



On a side note: can one really use this approach to calculate BSA
between domains? I could see a situation where splitting domains into
two separate entities would calculate excess surface area for regions
that connect these domains. I recall using Insight2 ages ago to create
subsets, and then calculating Connolly surfaces within a given context.
>From what I remember, it was real pain. Any better software out there
for this?

Cheers,

AGS

> Date: Fri, 8 Aug 2008 11:03:59 -0400
> From: [EMAIL PROTECTED]
> Subject: Re: [ccp4bb] interface
> To: CCP4BB@JISCMAIL.AC.UK
> 
> Which brings up something about PISA.  If I run PISA on pdb entry 2IE3, 
> which I'm familiar with, I get the following numbers from PISA and 
> CCP4's AREAIMOL  (surface areas in Angstrom^2) for the A:C interface.
> 
>  >> PISA for 2IE3
>  Automatic A:C interface selection 907.9
>  (a crystal packing interface is larger than this, but this surface 
> is the A:C interface)
> 
>  >> AreaIMol with some editing of 2IE3 to separate the chains
>  Chain A25,604.4
>  Chain C11,847.4
> Total  37,451.8
>  Chain AC   35,576.6
> Difference  1,875.2
> Difference/2  937.6
> 
> 
> For buried S.A. I agree with Steve Darnell's definition.  However PISA 
> appears to be reporting half that value, or what it calls "interface 
> area".  Potentially confusing.
> 
> Phil Jeffrey
> Princeton
> 
> Steven Darnell wrote:
> > Sorry, that equation should read:
> > 
> > Buried_Surface_Area = ASA_unbound1 + ASA_unbound2 - ASA_bound
> > ASA = Accessible Surface Area
> > 
> > The way I wrote it before would give you a negative value.
> > 
> > Regards,
> > Steve Darnell
> > 

_
Reveal your inner athlete and share it with friends on Windows Live.
http://revealyourinnerathlete.windowslive.com?locale=en-us&ocid=TXT_TAGLM_WLYIA_whichathlete_us

Re: [ccp4bb] interface

[Steven Darnell]

Phil,

I had a follow up conversation regarding this very topic.  Here is an 
excerpt:


The following is from Chothia and Janin (1975) Nature, 256:705-708, 
one of the early articles regarding buried surface area and protein 
interfaces:


"The surface area buried in the complex is then defined as the 
accessible surface area of one subunit plus that of the other subunit 
minus that of the complex."


I believe that definition has not changed in 30 years.  While I will 
agree that dividing by 2 approximates the physical area of the 
interface, this does not represent the total amount of surface area 
that is no longer accessible to solvent.  In terms of desolvating the 
interface for binding, the latter is more appropriate.


As you point out, PISA appears to be reporting the area of the 
interface, not the total surface area occluded from solvent.  Confusing 
indeed.


Regards,
Steve Darnell


Phil Jeffrey said the following on 8/8/08 10:03 AM:
Which brings up something about PISA.  If I run PISA on pdb entry 
2IE3, which I'm familiar with, I get the following numbers from PISA 
and CCP4's AREAIMOL  (surface areas in Angstrom^2) for the A:C interface.


>> PISA for 2IE3
Automatic A:C interface selection 907.9
(a crystal packing interface is larger than this, but this surface 
is the A:C interface)


>> AreaIMol with some editing of 2IE3 to separate the chains
Chain A25,604.4
Chain C11,847.4
Total  37,451.8
Chain AC   35,576.6
Difference  1,875.2
Difference/2  937.6


For buried S.A. I agree with Steve Darnell's definition.  However PISA 
appears to be reporting half that value, or what it calls "interface 
area".  Potentially confusing.


Phil Jeffrey
Princeton

--
Steven Darnell
Department of Biochemistry
University of Wisconsin-Madison
Madison, WI USA

Re: [ccp4bb] interface

[Phil Jeffrey]

Which brings up something about PISA.  If I run PISA on pdb entry 2IE3, 
which I'm familiar with, I get the following numbers from PISA and 
CCP4's AREAIMOL  (surface areas in Angstrom^2) for the A:C interface.


>> PISA for 2IE3
Automatic A:C interface selection 907.9
(a crystal packing interface is larger than this, but this surface 
is the A:C interface)


>> AreaIMol with some editing of 2IE3 to separate the chains
Chain A25,604.4
Chain C11,847.4
Total  37,451.8
Chain AC   35,576.6
Difference  1,875.2
Difference/2  937.6


For buried S.A. I agree with Steve Darnell's definition.  However PISA 
appears to be reporting half that value, or what it calls "interface 
area".  Potentially confusing.


Phil Jeffrey
Princeton

Steven Darnell wrote:

Sorry, that equation should read:

Buried_Surface_Area = ASA_unbound1 + ASA_unbound2 - ASA_bound
ASA = Accessible Surface Area

The way I wrote it before would give you a negative value.

Regards,
Steve Darnell

Re: [ccp4bb] interface

[Alan Cheung]

The PISA tool at the EBI can calculate surface area contact, interacting 
residues and salt bridges/hydrogen bonds between proteins and lots of 
other things.  And it's easy to use.


http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html

Alan



Skrzypczak-Jankun, Ewa wrote:
What is the best and user-friendly program to calculate a surface of the 
interface between two proteins? Or two domains?


 

Is there any common criteria how to define boundary for that interface 
(other than van der Waals distance)?


 


Thanks in advance for good tips - Ewa

 




Dr Ewa Skrzypczak-Jankun  Associate 
Professor


University of ToledoOffice: 
Dowling Hall r.2257


Health Science Campus   Phone:  
419-383-5414


Urology Department Mail Stop #1091  Fax:  419-383-3785

3000 Arlington Ave. e-mail: 
[EMAIL PROTECTED] 


Toledo OH 43614-2598  web: 
http://golemxiv.dh.meduohio.edu/~ewa




 



--
Alan Cheung
Gene Center
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:  +49-89-2180-76999
E-mail: [EMAIL PROTECTED]

Re: [ccp4bb] interface

[Steven Darnell]

Sorry, that equation should read:

Buried_Surface_Area = ASA_unbound1 + ASA_unbound2 - ASA_bound
ASA = Accessible Surface Area

The way I wrote it before would give you a negative value.

Regards,
Steve Darnell

--
Steven Darnell
Department of Biochemistry
University of Wisconsin-Madison
Madison, WI USA

Re: [ccp4bb] interface

[Steven Darnell]

Ewa,


What is the best and user-friendly program to calculate a surface of 
the interface between two proteins?



If you want a list of interface residues...

The Protein-Protein Interface Database 
(http://ppidb.cs.iastate.edu/ppidb/InterfaceResidues) is easy to use, 
but it is only for structures in the PDB.  It will identify interface 
residues using a distance based measure or loss of surface area upon 
binding.


You could use the Protein Structure Analysis Package 
(http://iris.physics.iisc.ernet.in/psap/), but that server is down at 
this moment.


Another option is to use the WHAT IF Server 
(http://swift.cmbi.ru.nl/servers/html/index.html).  Its atomic contacts 
are based on the distance between VDW surfaces.  Since it reports all of 
the contacts, you'll need to look for contacts involving different chains.


The KFC Server (http://kfc.mitchell-lab.org) predicts binding hot spots 
within a protein-protein interface.  You could use this if you don't 
mind defining an interface residue as any residue within 4 A of the 
binding partner.  The output only lists interface residues.  
(Disclaimer: I was a principal developer)



If you want to calculate the buried surface area...

I would split the complex into separate files, then run MSMS on the 
unbound structures and the bound structure.  You can download the 
program at http://www.scripps.edu/~sanner/html/msms_home.html, or use it 
online at http://helixweb.nih.gov/structbio/basic.html.  You'll need to 
perform this calculation:


Buried_Surface_Area = ASA_bound - ASA_unbound1 - ASA_unbound2
ASA = Accessible Surface Area

Perhaps someone else knows of an easier way to do this.


Or two domains?
If you want to look between two domains, you'll probably want to break 
the molecule into two chains, and then run the analysis.  Since you're 
talking about domains, there should probably be a place to make a clean 
break.  If so, it's just a matter of inserting a TER record.


Is there any common criteria how to define boundary for that interface 
(other than van der Waals distance)? 

As stated above, you can use loss of surface area upon binding (assumes 
proteins are rigid bodies), distance between C-alpha atoms, distance 
between residue atoms, or distance between VDW surfaces.  They'll all 
produce similar results, but to my knowledge, there isn't a preferred 
method.  It's a matter of personal preference.


From a programming point-of-view, the distance between C-alpha or 
residue atoms is preferred because it's the easiest to implement and the 
fastest to compute.


Regards,
Steve Darnell

--
Steven Darnell
Department of Biochemistry
University of Wisconsin-Madison
Madison, WI USA