[ccp4bb] programs to representation of common surface feature from a series of PDB files

[Green, Todd Jason]

Hello All-


I am overlaying a series of structures that have a similar sequences and the 
same topology, and I would like to represent an illustration to shown 
commonality or lack thereof across the  surface of the protein. I am most 
interested in surface, ie. differences in peaks and valleys. Does anyone know 
of a program that I could use to show a composite surface difference versus a 
reference or a way to numerically represent the differences?


Thanks in advance.

-Todd



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Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies

[Eleanor Dodson]

But you know that each rotation matrix still only fits one semi-tetramer to
its symmetry partner?

Eleanor

On Sun, 3 Feb 2019 at 16:54, Klontz, Erik 
wrote:

> Thank you all for your feedback. I received many helpful responses. To
> summarize them, users might find the following resources helpful:
>
> http://img.chem.ucl.ac.uk/sgp/LARGE/sgp.htm
> http://achesym.ibch.poznan.pl
> http://eppic-web.org
> http://www.ruppweb.org/new_comp/spacegroup_decoder.htm
> http://www.ebi.ac.uk/msd-srv/prot_int/cgi-bin/piserver
>
> In my own example, my crystal was C 2 2 21 with unit cell 89.30, 137.12,
> 264.71, 90, 90, 90
>
>
> The easiest solution I found to generate the 3x4 translation/rotation
> matrix was to open the structure in Coot, turn on symmetry mates
> (Draw-->Cell & Symmetry) and then middle mouse click on the correct chain
> that completes the biological assembly (or alternatively, File-->Save
> Symmetry Coordinates-->left click chain). The symmetry operator shows in
> the bottom left of the window in Coot. In my case, this gave an output of
> "(X, -Y, -Z) + (0 0 0)" for one, and "(-X, Y, -Z + 1/2) + (-1 0 -1)" for
> the other. In the 3x4 translation/rotation matrix format required for PDB
> deposition, these correspond to:
>
>
> Format:
> R1-1 R1-2 R1-3 T1
> R2-1 R2-2 R2-3 T2
> R3-1 R3-2 R3-3 T3
>
>
> Solutions:
>
> 1 0 0 0
>
> 0 -1 0 0
>
> 0 0 -1 0
>
>
> -1 0 0 -89.3
>
> 0 1 0 0
>
> 0 0 -1 -132.35
>
>
> To check your work, you can save the symmetry coordinates and then load
> them into the ccp4 program "superpose". Superimpose your original PDB onto
> the symmetry mate. The output contains a rotation matrix and a translation
> vector that should correspond to the same solution.
>
>
> Thanks everyone!
>
> Erik
>
> --
> *From:* CCP4 bulletin board  on behalf of Eleanor
> Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
> *Sent:* Sunday, February 3, 2019 6:21:41 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Generating rotation/translation matrices for
> biological assemblies
>
> Well - you have one of many examples where your 4 chains do not form the
> biological tetramer, but as you say there are two half tetramers in the
> asymmetric unit, I would expect that Pisa has already told you there is an
> interface between AC and it’s summetry equivalent and told you the symmetry
> operator that generates this? Look st interfaced output
> And the same for the BD interface .  Lots of haemoobin examples of this.
>
> On Sun, 3 Feb 2019 at 22:42, Bernhard Rupp 
> wrote:
>
> The most trivial procedure is probably to generate the symmetry mates in
> Coot
>
> (color by symop makes selection easier), pick the ones completing your
> known biological
>
> assembly, and saving those using File/Save Symmetry Coordinates.
>
>
>
> Once you have the correct model you can superimpose the dimers in Coot and
> read the DCM and
>
> the translation vector – if that is what you want. If you click any of the
> atoms in a symop-ed
>
> molecule, you get the crystallographic operator and translation.
>
>
>
> If you want the crystallographic symops in symbolic and matrix format, you
> can use
>
> http://www.ruppweb.org/new_comp/spacegroup_decoder.htm
>
> Standard settings only.
>
>
>
> Best, BR
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Klontz,
> Erik
> *Sent:* Saturday, February 2, 2019 22:05
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Generating rotation/translation matrices for
> biological assemblies
>
>
>
> Hi all,
>
>
>
> I'm working on a protein that I believe is tetrameric based on AUC, gel
> filtration, and crystallography. However, although my asymmetric unit has 4
> chains, I cannot form the tetramer within the asymmetric unit. Instead, the
> asymmetric unit has two half-tetramers ('dimers'), and each full tetramer
> is completed by pairing up with another half-tetramer from a symmetry mate.
> If I load this structure into PISA, it recognizes that each of the 'dimers'
> forms a stable assembly, but cannot seem to assemble the tetramer. However,
> if I the generate symmetry mates in pymol to create a new PDB for the
> biological tetramer and give this to PISA, it recognizes a stable tetramer.
>
>
>
> Specifically, chains A and C in the original PDB pair with chains A and C
> of the second symmetry mate generated in pymol, while chains B and D in the
> original pair with chains B and D of the third symmetry mate. How do I use
> this knowledge to generate a 3x4 rotation with translation matrix for PDB
> deposition?
>
>
>
> Thanks,
> Erik Klontz
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
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>
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>
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Re: [ccp4bb] Generating Additional Phasing Statistics

[Georg Mlynek]

Dear All, asking a few years back the question why phasing power is not 
reported, I got following answer:


No, we don't generate phasing power statistics in Phaser, just the 
figuresof merit, which usually give a good indication of how well 
things haveworked. Phasing power is defined in terms of things that 
make more sense with old-fashioned least-squares programs.


Br, Georg.

On 01.02.19 16:55, Clemens Vonrhein wrote:

On Fri, Feb 01, 2019 at 03:00:09PM +, Eleanor Dodson wrote:

Mlphare still exists! It gives you all that information...

Indeed ... or SHARP ;-)

I must say I stopped looking at R-Cullis/R-Kraut values a long time
ago (maybe I still should), but found phasing power immensely useful -
much more than FOM.

Of course, if you used program A to get those SIRAS phases at the time
you should only report statistics as given by that program. Maybe
Phenix has those stats "somewhere": asking the phenixBB? I would be
surprised if it doesn't compute phasing power, but maybe it doesn't.

If the stats aren't there then this is just what it is. Re-running a
different program B to get statistics is rather confusing: the
resulting phases could be worse (and stats misleadingly poor) ... or
of course could be much better. But then: some better phasing might
give you nice stats for reporting - but it wasn't what actually
happened at the time. It might be ok to convince a referee, but should
probably not be put into a deposition/paper.


or just Argue that the map is good?

Yes :-)

Clemens


On Fri, 1 Feb 2019 at 13:54, McCoy, Jason (mccoyj5) 
wrote:


Dear CCP4bb members,

I am compiling a rebuttal for a manuscript that utilized experimental
SIRAS phasing in order to generate coordinates that I could then use for
molecular replacement.  For phasing, I used phenix auto-sol and I was able
to successfully generate a suitable model for MR on a native data set.
However, a reviewer requested additional phasing statistics, such as the
phasing power and Cullis-R. It appears phenix auto-sol does not produce
these statistics. I have reported the FOM pre and post density
modification. I am looking to generate additional phasing statistics for my
reviewer. Do you have any recommendations?

Thank you in advance,
Jason McCoy

--

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Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies

[Klontz, Erik]

Thank you all for your feedback. I received many helpful responses. To 
summarize them, users might find the following resources helpful:

http://img.chem.ucl.ac.uk/sgp/LARGE/sgp.htm
http://achesym.ibch.poznan.pl
http://eppic-web.org
http://www.ruppweb.org/new_comp/spacegroup_decoder.htm
http://www.ebi.ac.uk/msd-srv/prot_int/cgi-bin/piserver

In my own example, my crystal was C 2 2 21 with unit cell 89.30, 137.12, 
264.71, 90, 90, 90


The easiest solution I found to generate the 3x4 translation/rotation matrix 
was to open the structure in Coot, turn on symmetry mates (Draw-->Cell & 
Symmetry) and then middle mouse click on the correct chain that completes the 
biological assembly (or alternatively, File-->Save Symmetry Coordinates-->left 
click chain). The symmetry operator shows in the bottom left of the window in 
Coot. In my case, this gave an output of "(X, -Y, -Z) + (0 0 0)" for one, and 
"(-X, Y, -Z + 1/2) + (-1 0 -1)" for the other. In the 3x4 translation/rotation 
matrix format required for PDB deposition, these correspond to:


Format:

R1-1 R1-2 R1-3 T1
R2-1 R2-2 R2-3 T2
R3-1 R3-2 R3-3 T3


Solutions:

1 0 0 0

0 -1 0 0

0 0 -1 0


-1 0 0 -89.3

0 1 0 0

0 0 -1 -132.35


To check your work, you can save the symmetry coordinates and then load them 
into the ccp4 program "superpose". Superimpose your original PDB onto the 
symmetry mate. The output contains a rotation matrix and a translation vector 
that should correspond to the same solution.


Thanks everyone!

Erik



From: CCP4 bulletin board  on behalf of Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: Sunday, February 3, 2019 6:21:41 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Generating rotation/translation matrices for biological 
assemblies

Well - you have one of many examples where your 4 chains do not form the 
biological tetramer, but as you say there are two half tetramers in the 
asymmetric unit, I would expect that Pisa has already told you there is an 
interface between AC and it’s summetry equivalent and told you the symmetry 
operator that generates this? Look st interfaced output
And the same for the BD interface .  Lots of haemoobin examples of this.

On Sun, 3 Feb 2019 at 22:42, Bernhard Rupp 
mailto:hofkristall...@gmail.com>> wrote:

The most trivial procedure is probably to generate the symmetry mates in Coot

(color by symop makes selection easier), pick the ones completing your known 
biological

assembly, and saving those using File/Save Symmetry Coordinates.



Once you have the correct model you can superimpose the dimers in Coot and read 
the DCM and

the translation vector – if that is what you want. If you click any of the 
atoms in a symop-ed

molecule, you get the crystallographic operator and translation.



If you want the crystallographic symops in symbolic and matrix format, you can 
use

http://www.ruppweb.org/new_comp/spacegroup_decoder.htm

Standard settings only.



Best, BR



From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of Klontz, Erik
Sent: Saturday, February 2, 2019 22:05
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Generating rotation/translation matrices for biological 
assemblies



Hi all,



I'm working on a protein that I believe is tetrameric based on AUC, gel 
filtration, and crystallography. However, although my asymmetric unit has 4 
chains, I cannot form the tetramer within the asymmetric unit. Instead, the 
asymmetric unit has two half-tetramers ('dimers'), and each full tetramer is 
completed by pairing up with another half-tetramer from a symmetry mate. If I 
load this structure into PISA, it recognizes that each of the 'dimers' forms a 
stable assembly, but cannot seem to assemble the tetramer. However, if I the 
generate symmetry mates in pymol to create a new PDB for the biological 
tetramer and give this to PISA, it recognizes a stable tetramer.



Specifically, chains A and C in the original PDB pair with chains A and C of 
the second symmetry mate generated in pymol, while chains B and D in the 
original pair with chains B and D of the third symmetry mate. How do I use this 
knowledge to generate a 3x4 rotation with translation matrix for PDB deposition?



Thanks,
Erik Klontz







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Re: [ccp4bb] Generating Additional Phasing Statistics

[Natesh Ramanathan]

Dear Jason McCoy,
 You can refine the heavy atom coordinates in mlphare and you
should be able to get both the values Phasing Power and Cullis-R for your
SIRAS.
Best wishes,
Natesh

On Fri, 1 Feb 2019 at 19:24, McCoy, Jason (mccoyj5) 
wrote:

> Dear CCP4bb members,
>
> I am compiling a rebuttal for a manuscript that utilized experimental
> SIRAS phasing in order to generate coordinates that I could then use for
> molecular replacement.  For phasing, I used phenix auto-sol and I was able
> to successfully generate a suitable model for MR on a native data set.
> However, a reviewer requested additional phasing statistics, such as the
> phasing power and Cullis-R. It appears phenix auto-sol does not produce
> these statistics. I have reported the FOM pre and post density
> modification. I am looking to generate additional phasing statistics for my
> reviewer. Do you have any recommendations?
>
> Thank you in advance,
> Jason McCoy
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
--
"Live Simply and do Serious Things .. "
- Dorothy Mary Crowfoot Hodgkin OM, FRS

"In Science truth always wins"
- Max Ferdinand Perutz OM FRS
--
Dr. Ramanathan Natesh
Assistant Professor,
School of Biology,
Indian Institute of Science Education and Research Thiruvananthapuram
(IISER-TVM),
Maruthamala P.O., Vithura,
Thiruvananthapuram,  695551, Kerala, India

nat...@iisertvm.ac.in
http://www.researcherid.com/rid/C-4488-2008
ORCID: http://orcid.org/-0002-1145-5962
https://publons.com/author/1520837/ramanathan-natesh#profile
http://faculty.iisertvm.ac.in/natesh

Office Ph. 0091- 471-2778087



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Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies

[Eleanor Dodson]

Well - you have one of many examples where your 4 chains do not form the
biological tetramer, but as you say there are two half tetramers in the
asymmetric unit, I would expect that Pisa has already told you there is an
interface between AC and it’s summetry equivalent and told you the symmetry
operator that generates this? Look st interfaced output
And the same for the BD interface .  Lots of haemoobin examples of this.

On Sun, 3 Feb 2019 at 22:42, Bernhard Rupp  wrote:

> The most trivial procedure is probably to generate the symmetry mates in
> Coot
>
> (color by symop makes selection easier), pick the ones completing your
> known biological
>
> assembly, and saving those using File/Save Symmetry Coordinates.
>
>
>
> Once you have the correct model you can superimpose the dimers in Coot and
> read the DCM and
>
> the translation vector – if that is what you want. If you click any of the
> atoms in a symop-ed
>
> molecule, you get the crystallographic operator and translation.
>
>
>
> If you want the crystallographic symops in symbolic and matrix format, you
> can use
>
> http://www.ruppweb.org/new_comp/spacegroup_decoder.htm
>
> Standard settings only.
>
>
>
> Best, BR
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Klontz,
> Erik
> *Sent:* Saturday, February 2, 2019 22:05
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Generating rotation/translation matrices for
> biological assemblies
>
>
>
> Hi all,
>
>
>
> I'm working on a protein that I believe is tetrameric based on AUC, gel
> filtration, and crystallography. However, although my asymmetric unit has 4
> chains, I cannot form the tetramer within the asymmetric unit. Instead, the
> asymmetric unit has two half-tetramers ('dimers'), and each full tetramer
> is completed by pairing up with another half-tetramer from a symmetry mate.
> If I load this structure into PISA, it recognizes that each of the 'dimers'
> forms a stable assembly, but cannot seem to assemble the tetramer. However,
> if I the generate symmetry mates in pymol to create a new PDB for the
> biological tetramer and give this to PISA, it recognizes a stable tetramer.
>
>
>
> Specifically, chains A and C in the original PDB pair with chains A and C
> of the second symmetry mate generated in pymol, while chains B and D in the
> original pair with chains B and D of the third symmetry mate. How do I use
> this knowledge to generate a 3x4 rotation with translation matrix for PDB
> deposition?
>
>
>
> Thanks,
> Erik Klontz
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies

[Bernhard Rupp]

The most trivial procedure is probably to generate the symmetry mates in
Coot

(color by symop makes selection easier), pick the ones completing your known
biological 

assembly, and saving those using File/Save Symmetry Coordinates.

 

Once you have the correct model you can superimpose the dimers in Coot and
read the DCM and

the translation vector - if that is what you want. If you click any of the
atoms in a symop-ed

molecule, you get the crystallographic operator and translation. 

 

If you want the crystallographic symops in symbolic and matrix format, you
can use

http://www.ruppweb.org/new_comp/spacegroup_decoder.htm

Standard settings only.

 

Best, BR

 

From: CCP4 bulletin board  On Behalf Of Klontz, Erik
Sent: Saturday, February 2, 2019 22:05
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Generating rotation/translation matrices for biological
assemblies

 

Hi all, 

 

I'm working on a protein that I believe is tetrameric based on AUC, gel
filtration, and crystallography. However, although my asymmetric unit has 4
chains, I cannot form the tetramer within the asymmetric unit. Instead, the
asymmetric unit has two half-tetramers ('dimers'), and each full tetramer is
completed by pairing up with another half-tetramer from a symmetry mate. If
I load this structure into PISA, it recognizes that each of the 'dimers'
forms a stable assembly, but cannot seem to assemble the tetramer. However,
if I the generate symmetry mates in pymol to create a new PDB for the
biological tetramer and give this to PISA, it recognizes a stable tetramer.

 

Specifically, chains A and C in the original PDB pair with chains A and C of
the second symmetry mate generated in pymol, while chains B and D in the
original pair with chains B and D of the third symmetry mate. How do I use
this knowledge to generate a 3x4 rotation with translation matrix for PDB
deposition?

 

Thanks, 
Erik Klontz

 

 

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