Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

[Bernhard Rupp]

I the software used for that is PhotoBlot®

 

BR

 

From: Phoebe A. Rice [mailto:pr...@uchicago.edu] 
Sent: Tuesday, March 21, 2017 17:19
To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] Positive densities map on selective residues on Coot
or Pymol

 

Thank you Bernard. 

 

I'd like to add that carving the density shown in a figure (especially
without explicitly describing the carve radius used) is the moral equivalent
of showing only 1mm of background above and below the band of interest in a
western blot. 

 

 Phoebe

 

  _  

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernhard Rupp
[hofkristall...@gmail.com]
Sent: Tuesday, March 21, 2017 3:29 AM
To: CCP4BB@JISCMAIL.AC.UK  
Subject: Re: [ccp4bb] Positive densities map on selective residues on Coot
or Pymol

> and carve=2.0 means the mesh is created within 2.0 Å of the selected
atoms.  Adjust these values to suit.

 

I would advise extreme care when employing such presentation features. They
are useful for display 

purposes and only when their use is stated as such, but they also open a
venue for cognitive biases. 

One might want to have a look at how creative use of these ‘blob’ features
until things ‘suit’ can 

betray the true believer…

 

http://www.ruppweb.org/cvs/br/rupp_2001_NSB_questions_BotA.pdf

https://www.dropbox.com/s/iul2cjbuu4x2o9f/Hanson_2009_retraction_bot_nsmb070
9-795.pdf?dl=0

 

Best, BR 

 

The first principle is that you must not fool yourself and you are the
easiest person to fool.”

Richard P. Feynman

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

[Phoebe A. Rice]

Thank you Bernard.

I'd like to add that carving the density shown in a figure (especially without 
explicitly describing the carve radius used) is the moral equivalent of showing 
only 1mm of background above and below the band of interest in a western blot.

 Phoebe


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernhard Rupp 
[hofkristall...@gmail.com]
Sent: Tuesday, March 21, 2017 3:29 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Positive densities map on selective residues on Coot or 
Pymol

> and carve=2.0 means the mesh is created within 2.0 Å of the selected atoms.  
> Adjust these values to suit.

I would advise extreme care when employing such presentation features. They are 
useful for display
purposes and only when their use is stated as such, but they also open a venue 
for cognitive biases.
One might want to have a look at how creative use of these ‘blob’ features 
until things ‘suit’ can
betray the true believer…

http://www.ruppweb.org/cvs/br/rupp_2001_NSB_questions_BotA.pdf
https://www.dropbox.com/s/iul2cjbuu4x2o9f/Hanson_2009_retraction_bot_nsmb0709-795.pdf?dl=0

Best, BR

The first principle is that you must not fool yourself and you are the easiest 
person to fool.”
Richard P. Feynman

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

[Bernhard Rupp]

> and carve=2.0 means the mesh is created within 2.0 Å of the selected atoms.  
> Adjust these values to suit.

 

I would advise extreme care when employing such presentation features. They are 
useful for display 

purposes and only when their use is stated as such, but they also open a venue 
for cognitive biases. 

One might want to have a look at how creative use of these ‘blob’ features 
until things ‘suit’ can 

betray the true believer…

 

http://www.ruppweb.org/cvs/br/rupp_2001_NSB_questions_BotA.pdf

https://www.dropbox.com/s/iul2cjbuu4x2o9f/Hanson_2009_retraction_bot_nsmb0709-795.pdf?dl=0

 

Best, BR 

 

The first principle is that you must not fool yourself and you are the easiest 
person to fool.”

Richard P. Feynman

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

[Xiao Lei]

Hi Martin,

I followed your instructions and everything works. Thank you for your
illustration!

On Mon, Mar 20, 2017 at 3:52 AM, Martin Montgomery 
wrote:

> Hello,
>
> You need to tell pymol what to do with the map.
>
> Load your pdb file
> Load the map
>
> create an object with residues you wish to display the map around.  You
> can use the create command to do this or you can click on all the residues
> that you want to use in the main window then go to the object called (sele)
> in the right hand sidebar, click A and then copy to object.  This will
> create an object called obj01 with the selected residues.  You can rename
> this if you wish.
>
> Then you need to use the isomesh command to display the map.
>
>
> isomesh mapname, mapfilename.ccp4, 2.5, obj01, carve=2.0
>
> mapname is the name you want to appear in the right hand sidebar for the
> mesh (can be the same as the mapfilename if you wish)
>
> mapfilename would be D83Vchimmap1 (from your screen shot).
>
> 2.5 is the sigma setting and carve=2.0 means the mesh is created within
> 2.0 Å of the selected atoms.  Adjust these values to suit.
>
> You might want to go back to go back and check your FFT log and look at
> the grid settings.  It is a good idea to re run the FFT job but double the
> grid values from the original job.
>
> It is all covered here:
>
> https://pymolwiki.org/index.php/Display_CCP4_Maps
>
> Regards
>
> MGM
>
> Martin G Montgomery
> ATP Synthase Group
> Medical Research Council Mitochondrial Biology Unit
> University of Cambridge
> Wellcome Trust/MRC Building
> Cambridge Biomedical Campus
> Hills Road
> Cambridge
> Great Britain
> CB2 0XY
>
> www.mrc-mbu.cam.ac.uk
>
>
>
>
>
>
> On 18 Mar 2017, at 10:43, Eleanor Dodson 
> wrote:
>
> I think CCP4MG does this very selectively?
>
> Eleanor Dodson
>
> On 17 March 2017 at 17:03, Xiao Lei  wrote:
>
>> Dear All,
>>
>> Thanks for the information.
>> I tried the way suggested by pymol wiki, but pymol fail to display the
>> map.
>> This is what I did: Run Fft to generate simple mapin ccp4i, input mtz map
>> from refmac, set F1=FWT and PHIC=PHWT, Sigma=SigF, Weight=FOM.  Add the
>> file extension .map.ccp4 to the generated output map. After open by pymol,
>> only a unit cell sign is shown (I attach here), no map is displayed.. I
>> use Pymol 1.8.X in Win7.
>>
>> Any further input is appreciated.
>>
>>
>>
>> .
>>
>>
>>
>>
>> On Fri, Mar 17, 2017 at 7:41 AM, Xiao Lei  wrote:
>>
>>> Dear All,
>>>
>>> In Coot, I could adjust the densities of map (2Fo-Fc in my case) radius,
>>> but I'd like to show the density on selective residues, not on the
>>> unselected part of structure, is there a way to do it? I am using WinCoot
>>> 0.81.
>>>
>>> In addition, could Pymol do it?
>>>
>>> Thanks ahead!
>>>
>>
>>
>
>

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

[Martin Montgomery]

Hello,

You need to tell pymol what to do with the map.

Load your pdb file
Load the map

create an object with residues you wish to display the map around.  You can use 
the create command to do this or you can click on all the residues that you 
want to use in the main window then go to the object called (sele) in the right 
hand sidebar, click A and then copy to object.  This will create an object 
called obj01 with the selected residues.  You can rename this if you wish.

Then you need to use the isomesh command to display the map.


isomesh mapname, mapfilename.ccp4, 2.5, obj01, carve=2.0

mapname is the name you want to appear in the right hand sidebar for the mesh 
(can be the same as the mapfilename if you wish)

mapfilename would be D83Vchimmap1 (from your screen shot).

2.5 is the sigma setting and carve=2.0 means the mesh is created within 2.0 Å 
of the selected atoms.  Adjust these values to suit.

You might want to go back to go back and check your FFT log and look at the 
grid settings.  It is a good idea to re run the FFT job but double the grid 
values from the original job.

It is all covered here:

https://pymolwiki.org/index.php/Display_CCP4_Maps 


Regards

MGM

Martin G Montgomery
ATP Synthase Group
Medical Research Council Mitochondrial Biology Unit
University of Cambridge
Wellcome Trust/MRC Building
Cambridge Biomedical Campus
Hills Road 
Cambridge
Great Britain
CB2 0XY

www.mrc-mbu.cam.ac.uk






> On 18 Mar 2017, at 10:43, Eleanor Dodson  wrote:
> 
> I think CCP4MG does this very selectively?
> 
> Eleanor Dodson
> 
> On 17 March 2017 at 17:03, Xiao Lei  > wrote:
> Dear All,
> 
> Thanks for the information.
> I tried the way suggested by pymol wiki, but pymol fail to display the map. 
> This is what I did: Run Fft to generate simple mapin ccp4i, input mtz map 
> from refmac, set F1=FWT and PHIC=PHWT, Sigma=SigF, Weight=FOM.  Add the file 
> extension .map.ccp4 to the generated output map. After open by pymol, only a 
> unit cell sign is shown (I attach here), no map is displayed.. I use Pymol 
> 1.8.X in Win7.
> 
> Any further input is appreciated.
> 
> 
> 
> .
> 
> 
> 
> 
> On Fri, Mar 17, 2017 at 7:41 AM, Xiao Lei  > wrote:
> Dear All,
> 
> In Coot, I could adjust the densities of map (2Fo-Fc in my case) radius, but 
> I'd like to show the density on selective residues, not on the unselected 
> part of structure, is there a way to do it? I am using WinCoot 0.81.
> 
> In addition, could Pymol do it? 
> 
> Thanks ahead!
> 
> 

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

[Eleanor Dodson]

I think CCP4MG does this very selectively?

Eleanor Dodson

On 17 March 2017 at 17:03, Xiao Lei  wrote:

> Dear All,
>
> Thanks for the information.
> I tried the way suggested by pymol wiki, but pymol fail to display the
> map.
> This is what I did: Run Fft to generate simple mapin ccp4i, input mtz map
> from refmac, set F1=FWT and PHIC=PHWT, Sigma=SigF, Weight=FOM.  Add the
> file extension .map.ccp4 to the generated output map. After open by pymol,
> only a unit cell sign is shown (I attach here), no map is displayed.. I
> use Pymol 1.8.X in Win7.
>
> Any further input is appreciated.
>
>
>
> .
>
>
>
>
> On Fri, Mar 17, 2017 at 7:41 AM, Xiao Lei  wrote:
>
>> Dear All,
>>
>> In Coot, I could adjust the densities of map (2Fo-Fc in my case) radius,
>> but I'd like to show the density on selective residues, not on the
>> unselected part of structure, is there a way to do it? I am using WinCoot
>> 0.81.
>>
>> In addition, could Pymol do it?
>>
>> Thanks ahead!
>>
>
>

[ccp4bb] Positive densities map on selective residues on Coot or Pymol

[Xiao Lei]

Dear All,

In Coot, I could adjust the densities of map (2Fo-Fc in my case) radius,
but I'd like to show the density on selective residues, not on the
unselected part of structure, is there a way to do it? I am using WinCoot
0.81.

In addition, could Pymol do it?

Thanks ahead!