Re: [ccp4bb] Superpose program in CCP4

[Clement Angkawidjaja]

Dear Wenhe,

Have you looked at the Additional Log File from Superpose?

Cheers,
Clement

-Original Message- 
From: WENHE ZHONG

Sent: Sunday, October 30, 2016 12:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Superpose program in CCP4

Dear all,

I always use the SUPERPOSE tool in CCP4 to superpose molecules. This time I 
want to use the RMSD values of superposed C-alpha atoms to plot a RMSD graph 
(instead of using the graph automatically made by the program). However, 
there are many atoms missing in the RMSD list.


In the settings I chose “Superpose specific atoms/residues”, checked 
“Output all distances to a file”, fit “C-alpha atoms”. The superposed 
structures have exactly the same sequence.


My question is: is there any way to get the completed list of RMSD value for 
each C-alpha atom? Or is there any other program for this purpose?


Thank you!

Kind regards,
Wenhe 

Re: [ccp4bb] Superpose program in CCP4

[Reza Khayat]

I've done this sort of analysis in the past and it can be very useful depending 
on your story is. I'm not sure if any software offers this. My solution was to 
write a script to do the comparison after the superposition was done. 
Unfortunately I can't find the script.


Best wishes,
Reza


Reza Khayat, PhD

Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031

From: CCP4 bulletin board  on behalf of Edward Berry 

Sent: Sunday, October 30, 2016 9:13 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Superpose program in CCP4

WenHe,
I'm not sure if you want to superimpose a number of structures (as rmsd would 
imply) or just compare two structures.
If you want a complete list of the distances between corresponding atoms in two 
pdb files of identical sequence,
you can use the fortran program http://www.cytbc1.net/berry/for/pdbdist2b.for
(linux executable http://www.cytbc1.net/berry/for/pdbdist2b ).
You need to superpose the structures (if necessary) with something else, and 
save the two files.
Grep out C-alphas to two new files if you only care about them.

The program asks you for the names of the two files and the residue number at 
which
to start (this latter is to synch the files in case they have different start 
residues. If
sequences are identical, just give the first residue number)
It also asks for last residue to compare in first file - just give a large 
number to do all.
Then it asks for a threshold - only distances larger will be printed. Put -1 to 
print all.

You can put all parameters on the command line if you run it with the shell 
script pdbd2b:
echo 'Find distances greater than threshold between corresponding atoms in 2 
PDB files'
echo 'Usage: pdbd2b file1 file2 startres# [thresh]'
pdbdist2b <>> WENHE ZHONG  10/29/16 11:49 AM >>>
Dear all,

I always use the SUPERPOSE tool in CCP4 to superpose molecules. This time I 
want to use the RMSD values of superposed C-alpha atoms to plot a RMSD graph 
(instead of using the graph automatically made by the program). However, there 
are many atoms missing in the RMSD list.

In the settings I chose "Superpose specific atoms/residues", checked "Output 
all distances to a file", fit "C-alpha atoms". The superposed structures have 
exactly the same sequence.

My question is: is there any way to get the completed list of RMSD value for 
each C-alpha atom? Or is there any other program for this purpose?

Thank you!

Kind regards,
Wenhe

Re: [ccp4bb] Superpose program in CCP4

[Edward Berry]

WenHe,
I'm not sure if you want to superimpose a number of structures (as rmsd
would imply) or just compare two structures.
If you want a complete list of the distances between corresponding atoms
in two pdb files of identical sequence,
you can use the fortran program
http://www.cytbc1.net/berry/for/pdbdist2b.for 
(linux executable http://www.cytbc1.net/berry/for/pdbdist2b ).
You need to superpose the structures (if necessary) with something else,
and save the two files.
Grep out C-alphas to two new files if you only care about them.

The program asks you for the names of the two files and the residue
number at which
to start (this latter is to synch the files in case they have different
start residues. If 
sequences are identical, just give the first residue number)
It also asks for last residue to compare in first file - just give a
large number to do all.
Then it asks for a threshold - only distances larger will be printed.
Put -1 to print all.

You can put all parameters on the command line if you run it with the
shell script pdbd2b:
echo 'Find distances greater than threshold between corresponding atoms
in 2 PDB files'
echo 'Usage: pdbd2b file1 file2 startres# [thresh]'
pdbdist2b <>> WENHE ZHONG  10/29/16 11:49 AM >>>
Dear all,

I always use the SUPERPOSE tool in CCP4 to superpose molecules. This
time I want to use the RMSD values of superposed C-alpha atoms to plot a
RMSD graph (instead of using the graph automatically made by the
program). However, there are many atoms missing in the RMSD list. 

In the settings I chose “Superpose specific atoms/residues”, checked
“Output all distances to a file”, fit “C-alpha atoms”. The superposed
structures have exactly the same sequence.

My question is: is there any way to get the completed list of RMSD value
for each C-alpha atom? Or is there any other program for this purpose? 

Thank you!

Kind regards,
Wenhe

Re: [ccp4bb] Superpose program in CCP4

[Martyn Symmons]

I think superpose does not output CAs outwith a certain cut-off based
on the quality of the superimposition. It does try to match as many as
give reasonable RMSDs - but it is mainly focussed on the residues in
matching secondary elements as this is where it starts the
superimposition.

A simpler approach is to use LSQKAB which will report all CA RMSDs in
a file if you specify that you want DELTAS. But notice that as Gert
said this will probably give you a different kind of superimposition.
A workaround would be to restrict LSQKAB to the residue ranges
SUPERPOSE used - then it will produce the same superimposition but can
report DELTAS for _all_ residues (! phew).

A non-CCP4 approach is Chimera Multi-align Viewer which calculates
RMSD without doing any superimposition. So you could run it on your
SUPERPOSE output coordinate files. I recall RMSD is a 'header' in that
tool and can be output to a file.
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html
(You have to read your structures into Chimera before launching
Multi-align viewer).

hope that helps.
 Martyn

Martyn Symmons
Cambridge

On Sun, Oct 30, 2016 at 10:54 AM, Anastassis Perrakis  wrote:
> Dear Wenhe,
>
> Besides this advice, have a look at the
> http://webapps.embl-hamburg.de/rapido/ server.
>
> Sometimes its goodo to re-think of what you want to do, and wonder why its
> not easily doable in software (perhaps because its not the right thing to do
> …)
>
> A.
>
>
> On 30 Oct 2016, at 11:45, Gert Vriend  wrote:
>
> Dear Wenhe,
>
> No 3D superpose tool will always align/map all Calphas. If in the one
> protein the loop turns left, and in the other it turns right, then mapping
> those loops is meaningless and thus not done by good software. The other
> problem is that often two proteins that get compared do not even have
> equally many residues so that there will always be some unaligned/unmapped
> Calphas left at the end. Look for some articles by Arthur M Lesk on this
> topic, he has explained protein superposition (problems) very clearly.
>
> Gert
>
> Ps, if you want proteins superposed and get different output from what the
> standard software gives you, just mail me those PDB files and I can see what
> I can do.
>
>
> On 29-10-2016 17:47, WENHE ZHONG wrote:
>
> Dear all,
>
> I always use the SUPERPOSE tool in CCP4 to superpose molecules. This time I
> want to use the RMSD values of superposed C-alpha atoms to plot a RMSD graph
> (instead of using the graph automatically made by the program). However,
> there are many atoms missing in the RMSD list.
>
> In the settings I chose “Superpose specific atoms/residues”, checked “Output
> all distances to a file”, fit “C-alpha atoms”. The superposed structures
> have exactly the same sequence.
>
> My question is: is there any way to get the completed list of RMSD value for
> each C-alpha atom? Or is there any other program for this purpose?
>
> Thank you!
>
> Kind regards,
> Wenhe
>
>

Re: [ccp4bb] Superpose program in CCP4

[Anastassis Perrakis]

Dear Wenhe,

Besides this advice, have a look at the http://webapps.embl-hamburg.de/rapido/ 
 server.

Sometimes its goodo to re-think of what you want to do, and wonder why its not 
easily doable in software (perhaps because its not the right thing to do …)

A.


> On 30 Oct 2016, at 11:45, Gert Vriend  wrote:
> 
> Dear Wenhe,
> 
> No 3D superpose tool will always align/map all Calphas. If in the one protein 
> the loop turns left, and in the other it turns right, then mapping those 
> loops is meaningless and thus not done by good software. The other problem is 
> that often two proteins that get compared do not even have equally many 
> residues so that there will always be some unaligned/unmapped Calphas left at 
> the end. Look for some articles by Arthur M Lesk on this topic, he has 
> explained protein superposition (problems) very clearly.
> 
> Gert
> 
> Ps, if you want proteins superposed and get different output from what the 
> standard software gives you, just mail me those PDB files and I can see what 
> I can do.
> 
> 
> On 29-10-2016 17:47, WENHE ZHONG wrote:
>> Dear all,
>> 
>> I always use the SUPERPOSE tool in CCP4 to superpose molecules. This time I 
>> want to use the RMSD values of superposed C-alpha atoms to plot a RMSD graph 
>> (instead of using the graph automatically made by the program). However, 
>> there are many atoms missing in the RMSD list.
>> 
>> In the settings I chose “Superpose specific atoms/residues”, checked “Output 
>> all distances to a file”, fit “C-alpha atoms”. The superposed structures 
>> have exactly the same sequence.
>> 
>> My question is: is there any way to get the completed list of RMSD value for 
>> each C-alpha atom? Or is there any other program for this purpose?
>> 
>> Thank you!
>> 
>> Kind regards,
>> Wenhe

Re: [ccp4bb] Superpose program in CCP4

[Gert Vriend]

Dear Wenhe,

No 3D superpose tool will always align/map all Calphas. If in the one 
protein the loop turns left, and in the other it turns right, then 
mapping those loops is meaningless and thus not done by good software. 
The other problem is that often two proteins that get compared do not 
even have equally many residues so that there will always be some 
unaligned/unmapped Calphas left at the end. Look for some articles by 
Arthur M Lesk on this topic, he has explained protein superposition 
(problems) very clearly.


Gert

Ps, if you want proteins superposed and get different output from what 
the standard software gives you, just mail me those PDB files and I can 
see what I can do.



On 29-10-2016 17:47, WENHE ZHONG wrote:

Dear all,

I always use the SUPERPOSE tool in CCP4 to superpose molecules. This time I 
want to use the RMSD values of superposed C-alpha atoms to plot a RMSD graph 
(instead of using the graph automatically made by the program). However, there 
are many atoms missing in the RMSD list.

In the settings I chose “Superpose specific atoms/residues”, checked “Output 
all distances to a file”, fit “C-alpha atoms”. The superposed structures have 
exactly the same sequence.

My question is: is there any way to get the completed list of RMSD value for 
each C-alpha atom? Or is there any other program for this purpose?

Thank you!

Kind regards,
Wenhe