Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

[Chris Fage]

Dear Murpholino,

Yes, I think you're right. For now, directly exporting my maps from Coot is
the most efficient solution. The normalization commands will certainly be
helpful to me and other users in the future, though. Thanks!

Best,
Chris


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On Mon, Sep 30, 2019 at 9:02 PM Murpholino Peligro 
wrote:

> I think this is part of the problem.
> https://pymolwiki.org/index.php/Normalize_ccp4_maps
>
> El lun., 30 de sep. de 2019 a la(s) 10:09, Chris Fage (fage...@gmail.com)
> escribió:
>
>> Hi Paul,
>>
>> After exporting the maps from Coot, they are directly comparable in
>> Pymol. That's quite a convenient feature I was never aware of. Thanks!
>>
>> Yes, I was comparing the map from FFT in Coot and PyMOL.
>>
>> Best,
>> Chris
>>
>>
>> 
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>>
>> On Mon, Sep 30, 2019 at 3:04 PM Paul Emsley 
>> wrote:
>>
>>> On 30/09/2019 13:00, Chris Fage wrote:
>>> > Dear Paul, Herman, Robbie, and Santosh,
>>> >
>>> >
>>> > My version of Pymol doesn't support loading of mtz files. I think it's
>>> > only in the incentive version.
>>> >
>>> > Paul wrote: "No need to do this - just export the map (or the map
>>> > fragment)." I'm not sure how to do this without going through FFT!
>>>
>>>
>>> File -> Export Map...
>>>
>>>
>>> >
>>> > But when I generate a new set of maps with F1=FWT and PHI=PHWT and
>>> > load them into Pymol, they are still not comparable to those in Coot.
>>> > Again, the maps for ligands 1 and 2 in Pymol look about the same.
>>>
>>>
>>> Are you comparing the map from FFT in Coot and PyMOL?
>>>
>>>
>>> Paul.
>>>
>>> 
>>>
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>>
>> --
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>



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Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

[Murpholino Peligro]

I think this is part of the problem.
https://pymolwiki.org/index.php/Normalize_ccp4_maps

El lun., 30 de sep. de 2019 a la(s) 10:09, Chris Fage (fage...@gmail.com)
escribió:

> Hi Paul,
>
> After exporting the maps from Coot, they are directly comparable in Pymol.
> That's quite a convenient feature I was never aware of. Thanks!
>
> Yes, I was comparing the map from FFT in Coot and PyMOL.
>
> Best,
> Chris
>
>
> 
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>
> On Mon, Sep 30, 2019 at 3:04 PM Paul Emsley 
> wrote:
>
>> On 30/09/2019 13:00, Chris Fage wrote:
>> > Dear Paul, Herman, Robbie, and Santosh,
>> >
>> >
>> > My version of Pymol doesn't support loading of mtz files. I think it's
>> > only in the incentive version.
>> >
>> > Paul wrote: "No need to do this - just export the map (or the map
>> > fragment)." I'm not sure how to do this without going through FFT!
>>
>>
>> File -> Export Map...
>>
>>
>> >
>> > But when I generate a new set of maps with F1=FWT and PHI=PHWT and
>> > load them into Pymol, they are still not comparable to those in Coot.
>> > Again, the maps for ligands 1 and 2 in Pymol look about the same.
>>
>>
>> Are you comparing the map from FFT in Coot and PyMOL?
>>
>>
>> Paul.
>>
>> 
>>
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>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
> --
>
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Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

[Chris Fage]

Hi Paul,

After exporting the maps from Coot, they are directly comparable in Pymol.
That's quite a convenient feature I was never aware of. Thanks!

Yes, I was comparing the map from FFT in Coot and PyMOL.

Best,
Chris


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On Mon, Sep 30, 2019 at 3:04 PM Paul Emsley 
wrote:

> On 30/09/2019 13:00, Chris Fage wrote:
> > Dear Paul, Herman, Robbie, and Santosh,
> >
> >
> > My version of Pymol doesn't support loading of mtz files. I think it's
> > only in the incentive version.
> >
> > Paul wrote: "No need to do this - just export the map (or the map
> > fragment)." I'm not sure how to do this without going through FFT!
>
>
> File -> Export Map...
>
>
> >
> > But when I generate a new set of maps with F1=FWT and PHI=PHWT and
> > load them into Pymol, they are still not comparable to those in Coot.
> > Again, the maps for ligands 1 and 2 in Pymol look about the same.
>
>
> Are you comparing the map from FFT in Coot and PyMOL?
>
>
> Paul.
>
> 
>
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Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

[Paul Emsley]

On 30/09/2019 13:00, Chris Fage wrote:
> Dear Paul, Herman, Robbie, and Santosh,
>
>
> My version of Pymol doesn't support loading of mtz files. I think it's
> only in the incentive version.
>
> Paul wrote: "No need to do this - just export the map (or the map
> fragment)." I'm not sure how to do this without going through FFT!


File -> Export Map...


>
> But when I generate a new set of maps with F1=FWT and PHI=PHWT and
> load them into Pymol, they are still not comparable to those in Coot.
> Again, the maps for ligands 1 and 2 in Pymol look about the same.


Are you comparing the map from FFT in Coot and PyMOL?


Paul.



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Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

[Chris Fage]

Hi Robbie,

I guess that solves part of the problem. But when I generate a new set of
maps with F1=FWT and PHI=PHWT and load them into Pymol, they are still not
comparable to those in Coot. Again, the maps for ligands 1 and 2 in Pymol
look about the same.

Best,
Chris

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On Mon, Sep 30, 2019 at 1:26 PM Robbie Joosten 
wrote:

> Hi Chris,
>
> You made an Fobs map not a 2Fo-Fc map. You can leave sigma empty if you
> want to make a map in this case.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> > Chris Fage
> > Sent: Monday, September 30, 2019 14:00
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol
> >
> > Dear Paul, Herman, Robbie, and Santosh,
> >
> > Thanks for your quick replies.
> >
> > The FFT-generated maps and mtz maps look roughly equivalent in Coot, but
> > there are minor differences even at the same e/A^3 level (the mtz maps
> > actually look a bit weaker). I generated them using the default settings
> in
> > FFT: simple map, format to cover asymmetric unit, F1=F_XDSdataset,
> > Sigma=SIGF_XDSdataset, PHI=PHIC. Perhaps, as Robbie mentioned, the
> > problem lies in column selection, since Coot uses FWT and PHWT. I can
> assign
> > F1 and PHI to these values, respectively, but what should I choose for
> Sigma?
> >
> > My version of Pymol doesn't support loading of mtz files. I think it's
> only in
> > the incentive version.
> >
> > Paul wrote: "No need to do this - just export the map (or the map
> > fragment)." I'm not sure how to do this without going through FFT!
> >
> > I can also try generating maps in Phenix, as Santosh suggested. However,
> if
> > the maps can be directly exported, as Paul suggested, I would prefer to
> > follow that route.
> >
> > Best wishes,
> > Chris
> >
> >
> >
> >
> >  <http://www.avg.com/email-
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> > email_content=webmail>
> >
> >
> > On Mon, Sep 30, 2019 at 12:49 PM Santhosh Gatreddi
> >  wrote:
> >
> >
> >   Hi Chris,
> >
> >   I also observed similar thing when I have generated 2Fo-Fc maps in
> > CCP4 FFT. But when I have generated 2Fo-Fc maps in Phenix then my maps
> > were similar  in Pymol and Coot. I request you to generate maps with
> Phenix
> > and verify it in Pymol. It worked for me.
> >
> >   One possible reason for this is map averaging in Pymol. Make sure
> > that you uncheck it before loading your map in Pymol.
> >
> >   I hope that above suggestion works for you.
> >
> >   Regards,
> >   Santhosh
> >
> >   On Mon, Sep 30, 2019 at 4:06 PM Chris Fage 
> > wrote:
> >
> >
> >   Dear All,
> >
> >   I recently obtained structures of a protein bound to two
> > different small molecules. When viewing the structures in Coot with a
> similar
> > contour setting, the 2Fo-Fc map around ligand 1 is clearly much weaker
> than
> > that around ligand 2.However, after generating 2Fo-Fc maps in FFT and
> > loading them in Pymol (again, choosing equal contour levels), the maps
> > surrounding ligands 1 and 2 have nearly the same quality. Is there a
> > difference in scaling between the two programs that can account for this?
> > Thanks for any advice!
> >
> >   Best wishes,
> >   Chris
> >
> >  <http://www.avg.com/email-
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> > 
> >
> >
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> >   --
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> >   With regards
> >
> >  

Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

[Robbie Joosten]

Hi Chris,

You made an Fobs map not a 2Fo-Fc map. You can leave sigma empty if you want to 
make a map in this case.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Chris Fage
> Sent: Monday, September 30, 2019 14:00
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol
> 
> Dear Paul, Herman, Robbie, and Santosh,
> 
> Thanks for your quick replies.
> 
> The FFT-generated maps and mtz maps look roughly equivalent in Coot, but
> there are minor differences even at the same e/A^3 level (the mtz maps
> actually look a bit weaker). I generated them using the default settings in
> FFT: simple map, format to cover asymmetric unit, F1=F_XDSdataset,
> Sigma=SIGF_XDSdataset, PHI=PHIC. Perhaps, as Robbie mentioned, the
> problem lies in column selection, since Coot uses FWT and PHWT. I can assign
> F1 and PHI to these values, respectively, but what should I choose for Sigma?
> 
> My version of Pymol doesn't support loading of mtz files. I think it's only in
> the incentive version.
> 
> Paul wrote: "No need to do this - just export the map (or the map
> fragment)." I'm not sure how to do this without going through FFT!
> 
> I can also try generating maps in Phenix, as Santosh suggested. However, if
> the maps can be directly exported, as Paul suggested, I would prefer to
> follow that route.
> 
> Best wishes,
> Chris
> 
> 
> 
> 
>  <http://www.avg.com/email-
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> email_content=webmail>
> 
> 
> On Mon, Sep 30, 2019 at 12:49 PM Santhosh Gatreddi
>  wrote:
> 
> 
>   Hi Chris,
> 
>   I also observed similar thing when I have generated 2Fo-Fc maps in
> CCP4 FFT. But when I have generated 2Fo-Fc maps in Phenix then my maps
> were similar  in Pymol and Coot. I request you to generate maps with Phenix
> and verify it in Pymol. It worked for me.
> 
>   One possible reason for this is map averaging in Pymol. Make sure
> that you uncheck it before loading your map in Pymol.
> 
>   I hope that above suggestion works for you.
> 
>   Regards,
>   Santhosh
> 
>   On Mon, Sep 30, 2019 at 4:06 PM Chris Fage 
> wrote:
> 
> 
>   Dear All,
> 
>   I recently obtained structures of a protein bound to two
> different small molecules. When viewing the structures in Coot with a similar
> contour setting, the 2Fo-Fc map around ligand 1 is clearly much weaker than
> that around ligand 2.However, after generating 2Fo-Fc maps in FFT and
> loading them in Pymol (again, choosing equal contour levels), the maps
> surrounding ligands 1 and 2 have nearly the same quality. Is there a
> difference in scaling between the two programs that can account for this?
> Thanks for any advice!
> 
>   Best wishes,
>   Chris
> 
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> 
> 
>   --
> 
>   With regards
> 
>   Santhosh Gatreddi (Research Scholar)
>   c/o Dr.Insaf Ahmed Qureshi,
>   Dept. of Biotechnology & Bioinformatics,
>   School of lifesciences,
>   University of Hyderabad,
>   Hyderabad-500046(A.P),
>   India.
>   Ph.no-9160628684.
> 
> 
> 
> 
> 
> 
> 
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Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

[Chris Fage]

Dear Paul, Herman, Robbie, and Santosh,

Thanks for your quick replies.

The FFT-generated maps and mtz maps look roughly equivalent in Coot, but
there are minor differences even at the same e/A^3 level (the mtz maps
actually look a bit weaker). I generated them using the default settings in
FFT: simple map, format to cover asymmetric unit, F1=F_XDSdataset,
Sigma=SIGF_XDSdataset, PHI=PHIC. Perhaps, as Robbie mentioned, the problem
lies in column selection, since Coot uses FWT and PHWT. I can assign F1 and
PHI to these values, respectively, but what should I choose for Sigma?

My version of Pymol doesn't support loading of mtz files. I think it's only
in the incentive version.

Paul wrote: "No need to do this - just export the map (or the map
fragment)." I'm not sure how to do this without going through FFT!

I can also try generating maps in Phenix, as Santosh suggested. However, if
the maps can be directly exported, as Paul suggested, I would prefer to
follow that route.

Best wishes,
Chris





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On Mon, Sep 30, 2019 at 12:49 PM Santhosh Gatreddi 
wrote:

> Hi Chris,
>
> I also observed similar thing when I have generated 2Fo-Fc maps in CCP4
> FFT. But when I have generated 2Fo-Fc maps in Phenix then my maps were
> similar  in Pymol and Coot. I request you to generate maps with Phenix and
> verify it in Pymol. It worked for me.
>
> One possible reason for this is map averaging in Pymol. Make sure that you
> uncheck it before loading your map in Pymol.
>
> I hope that above suggestion works for you.
>
> Regards,
> Santhosh
>
> On Mon, Sep 30, 2019 at 4:06 PM Chris Fage  wrote:
>
>> Dear All,
>>
>> I recently obtained structures of a protein bound to two different small
>> molecules. When viewing the structures in Coot with a similar contour
>> setting, the 2Fo-Fc map around ligand 1 is clearly much weaker than that
>> around ligand 2.However, after generating 2Fo-Fc maps in FFT and loading
>> them in Pymol (again, choosing equal contour levels), the maps surrounding
>> ligands 1 and 2 have nearly the same quality. Is there a difference in
>> scaling between the two programs that can account for this? Thanks for any
>> advice!
>>
>> Best wishes,
>> Chris
>>
>>
>> 
>>  Virus-free.
>> www.avg.com
>> 
>> <#m_-501199200969567658_m_-8793236030949751887_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>>
>> --
>>
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>>
>
>
> --
>
>
>
>
>
>
>
>
>
>
>
> *With regardsSanthosh Gatreddi (Research Scholar)c/o Dr.Insaf Ahmed
> Qureshi, Dept. of Biotechnology & Bioinformatics,School of
> lifesciences,University of
> Hyderabad,Hyderabad-500046(A.P),India.Ph.no-9160628684.*
>



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Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

[Robbie Joosten]

Are you sure you used the right columns in FFT? AFAIK Coot uses FWT and PHWT.

I thought the more recent PyMOL versions finally had MTZ support, or is this 
just for the incentive version? Also if it is for looking at the structure and 
making figures, perhaps try  CCP4mg. It has proper MTZ support and it is of 
course much better integrated with CCP4. It also is boss-proof for figures, 
i.e. it puts a recovery file next to the figure so you can go back quickly to 
change the carbon colours to a more mauve-y shade of pinky russet. 

Cheers,
Robbie



> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Chris Fage
> Sent: Monday, September 30, 2019 12:37
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol
> 
> Dear All,
> 
> I recently obtained structures of a protein bound to two different small
> molecules. When viewing the structures in Coot with a similar contour
> setting, the 2Fo-Fc map around ligand 1 is clearly much weaker than that
> around ligand 2.However, after generating 2Fo-Fc maps in FFT and loading
> them in Pymol (again, choosing equal contour levels), the maps surrounding
> ligands 1 and 2 have nearly the same quality. Is there a difference in scaling
> between the two programs that can account for this? Thanks for any advice!
> 
> Best wishes,
> Chris
> 
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[ccp4bb] AW: [EXTERNAL] [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

[Herman . Schreuder]

Dear Chris,

The first thing I would do is to load the FFT map (not the mtz) in coot and see 
how densities of both ligands compare in that case. Also in FFT, did you 
calculate exactly one unit cell, or did you select a region just around the 
protein? If you contour the maps in terms of RMSD, the amount of solvent 
included in the maps influences the RMSD level. For comparison it would be 
better to look at contour levels in electrons/Å**3. Finally, you could also 
look at the contour levels of the surrounding protein atoms, to get an idea how 
the ligand density compares to the protein density.

Best,
Herman

Von: CCP4 bulletin board  Im Auftrag von Chris Fage
Gesendet: Montag, 30. September 2019 12:37
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@jiscmail.ac.uk>

Dear All,

I recently obtained structures of a protein bound to two different small 
molecules. When viewing the structures in Coot with a similar contour setting, 
the 2Fo-Fc map around ligand 1 is clearly much weaker than that around ligand 
2.However, after generating 2Fo-Fc maps in FFT and loading them in Pymol 
(again, choosing equal contour levels), the maps surrounding ligands 1 and 2 
have nearly the same quality. Is there a difference in scaling between the two 
programs that can account for this? Thanks for any advice!

Best wishes,
Chris

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Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

[Paul Emsley]

On 30/09/2019 11:36, Chris Fage wrote:



I recently obtained structures of a protein bound to two different small molecules. When viewing the 
structures in Coot with a similar contour setting, the 2Fo-Fc map around ligand 1 is clearly much weaker 
than that around ligand 2.However, after generating 2Fo-Fc maps in FFT


No need to do this - just export the map (or the map fragment).

and loading them in Pymol (again, 
choosing equal contour levels), the maps surrounding ligands 1 and 2 have nearly the same quality. Is there 
a difference in scaling between the two programs that can account for this? Thanks for any advice!


How does the map from FFT look in Coot? I imagine that it would look just the same as the mtz map - but we 
should rule out the generation of the map as a factor before proceeding.


As a side-note, when comparing contour levels between coot and PyMOL, be sure 
to use absolute levels, not rmsds.

Paul.



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[ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

[Chris Fage]

Dear All,

I recently obtained structures of a protein bound to two different small
molecules. When viewing the structures in Coot with a similar contour
setting, the 2Fo-Fc map around ligand 1 is clearly much weaker than that
around ligand 2.However, after generating 2Fo-Fc maps in FFT and loading
them in Pymol (again, choosing equal contour levels), the maps surrounding
ligands 1 and 2 have nearly the same quality. Is there a difference in
scaling between the two programs that can account for this? Thanks for any
advice!

Best wishes,
Chris


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