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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[ccp4bb] Job Posting: Beamline Scientist at the Swiss Light Source

[Wojdyla Justyna Aleksandra (PSI)]

Dear All,


I would like draw your attention to the new position available in the 
Macromolecular Crystalligraphy group at the Swiss Light Source.


We are looking for a
Beamline Scientist
Macromolecular Crystallography
Your tasks
You will be a part of the Macromolecular Crystallography (MX) team and 
participate in development and user operation of the three MX beamlines at the 
Swiss Light Source with the following main tasks:

  *   Streamline and automate user experience from sample logistics and sample 
delivery to fully automated data acquisition and data analysis
  *   Assist further development of sample changer and sample delivery for 
conventional and serial crystallography
  *   Support academic and industrial users, as well as attract new user groups
  *   Serve as a liaison between the MX group and industry users
  *Write research proposals and acquire 3rd party funding
  *   Publish in peer-reviewed scientific journals and present at international 
conferences and workshops
  *   Supervision of assigned personnel, mentoring of PhD students and Postdocs

In addition, you will participate in the SLS 2.0 upgrade of MX beamlines and 
contribute to the operation of the MX instruments at the SwissFEL.
Your profile
You hold a PhD degree in biology, chemistry or physics and have substantial 
experience in macromolecular crystallography and beamline instrumentation at 
storage rings. Familiarity and proficiency in developing and commissioning 
beamline instrumentation is a plus. You have experience in supervisory or 
managerial role, great organizational skills and an eye for details. Very good 
command of written and spoken English is necessary, while knowledge of German 
is an advantage. If you are a strong team player with excellent communication 
skills and sense of responsibility, this position will offer you a great 
opportunity to develop your career in an exciting and highly multidisciplinary 
environment.
We offer

Our institution is based on an interdisciplinary, innovative and dynamic 
collaboration. You will profit from a systematic training on the job, in 
addition to personal development possibilities and our pronounced vocational 
training culture. If you wish to optimally combine work and family life or 
other personal interests, we are able to support you with our modern employment 
conditions and the on-site infrastructure.

This is a Tenure Track position. The employment contract will initially be 
limited to three years.

For further information please contact Dr. Meitian Wang, phone +41 56 310 41 75.

Please submit your application online by 28 October 2019 (including list of 
publications and addresses of referees) for the position as a Beamline 
Scientist (index no. 6121-01).

Paul Scherrer Institut Human Resources Management, Elke Baumann, 5232 Villigen 
PSI, Switzerland

(link is external)

For applications, please follow the link: 
https://www.psi.ch/en/pa/job-opportunities/30560-beamline-scientist

Best regards,
Justyna
--
Dr Justyna Aleksandra Wojdyla
Beamline Scientist &
Industry Liaison Scientist
WSLA-222
Swiss Light Source
Forschungsstrasse 111
5232 Villigen-PSI
tel: +41 56 310 5428
e-mail: justyna.wojd...@psi.ch




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[ccp4bb] General interest

[John R Helliwell]

Dear Colleagues,
I draw your attention to my posting at the IUCr Committee on Data Public Forum 
( https://forums.iucr.org/viewtopic.php?f=39=423 ) about the recent USA 
National Academies Report on Reproducibility and Replicability in Science.
Best wishes,
John 
Emeritus Professor John R Helliwell DSc
Chairman of the IUCr Committee on Data






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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.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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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
> >
> >
> >
> >
> >   > signature?utm_medium=email_source=link_campaign=sig-
> > email_content=webmail> Virus-free. www.avg.com
> >  > signature?utm_medium=email_source=link_campaign=sig-
> > 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
> >
> >   > signature?utm_medium=email_source=link_campaign=sig-
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> > email_content=webmail>
> >
> >
> > 
> >
> >
> >   To unsubscribe from the CCP4BB list, click the following
> link:
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> > bin/webadmin?SUBED1=CCP4BB=1
> >
> >
> >
> >   --
> >
> >   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

[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
> 
> 
> 
> 
>   signature?utm_medium=email_source=link_campaign=sig-
> email_content=webmail> Virus-free. www.avg.com
>  signature?utm_medium=email_source=link_campaign=sig-
> 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
> 
>   signature?utm_medium=email_source=link_campaign=sig-
> email_content=webmail> Virus-free. www.avg.com
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> email_content=webmail>
> 
> 
> 
> 
> 
>   To unsubscribe from the CCP4BB list, click the following link:
>   https://www.jiscmail.ac.uk/cgi-
> bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
>   --
> 
>   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.
> 
> 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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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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<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
>
> --
>
>
>
>
>
>
>
>
>
>
>
> *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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> email_content=webmail> Virus-free. www.avg.com
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> email_content=webmail>
> 
> 
> 
> 
> 
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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

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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Re: [ccp4bb] Reg: water pentagon at dimer interface

[Vijaykumar Pillalamarri]

Thank you all for the overwhelming responses.

To answer your questions

The protein is monomer in solution.
Complex formation significance score shown by PISA is "Zero" and suggested
that the interface does not play any role in complex formation and seems to
be a result of crystal packing only.
The buried surface area is ~4% to that of solvent accessible surface area.

 As suggested by Bohdan and Loris, though the arrangement looks beautiful,
the waters are just present at the dimer interface, stabilizing the dimer

Thank you

On Mon, 30 Sep 2019 at 15:54, Rudolph, Markus 
wrote:

> Hello  Vijaykumar,
>
> working in pharma structural biology, I see these pentamers all the time.
> I suspect the reason for the stable structure of the five-membered ring is
> that
> the outer angle of a regular flat pentagon is 108 degrees, which is very
> close to
> the 104.5 degrees in water, so orientation of atoms for H-bonding is
> near-perfect.
> I have no statistics to back that up, though.
>
> Best regards,
>
> Markus
>
> _
>
> *Markus G. Rudolph*
> Structural Biology
> F. Hoffmann-La Roche Ltd.
> pRED, Lead Discovery
> Roche Innovation Center Basel
>
> Bldg./Room 65/312C
> Grenzacherstrasse 124
> 4070 Basel
> Switzerland
>
> Phone: +41 61 6886420
>
> [image: Biophysical_Chemistry.jpg]
> Link to CRC
>
> 
>
> On Fri, Sep 27, 2019 at 1:34 PM Vijaykumar Pillalamarri <
> vijaypkuma...@gmail.com> wrote:
>
>> Dear Community,
>>
>> I solved the structure of a protein from vibrio. There are two
>> molecules in the asymmetric unit of this protein. At the dimer interface,
>> the C-termini of both the chains interact with each other with the help of
>> five water molecules that form a pentagon. I have attached an image showing
>> both the chains and stereo image of dimer interface in the inset. I was
>> wondering if there is any significance to this or if there is any relevant
>> literature that explains this behavior.
>>
>> Thank you
>> Vijaykumar Pillalamarri
>> C/O: Dr. Anthony Addlagatta
>> Principal Scientist
>> CSIR-IICT, Tarnaka
>> Hyderabad, India-57
>> Mobile: +918886922975
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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>>
>

-- 
Vijaykumar Pillalamarri
UGC-SRF
C/O: Dr. Anthony Addlagatta
Principal Scientist
CSIR-IICT, Tarnaka
Hyderabad, India-57
Mobile: +918886922975



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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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[ccp4bb] Final reminder: MicroED Workshop 2019

[Johan Hattne]

Final reminder: the application deadline for the 2019 MicroED workshop is 
October 1, 2019.  From the initial announcement:

The Gonen Laboratory will hold the 5th MicroED Workshop in 2019.  The workshop 
will be held at the MicroED Imaging Center at the UCLA David Geffen School of 
Medicine during December 9-12, 2019 and is open to both academia and industry.  
Space is limited and historically, the workshop is typically oversubscribed. 

Topics covered:
* MicroED conception, practice, and future opportunities
* Electron optics for MicroED
* Microscope alignment and calibration for MicroED
* Sample preparation: protein and organic/inorganic materials, small molecules
* Data collection for both protein and small molecules
* Data analysis software, structure solution, and refinement
* Choice of electron microscope hardware and cameras
* MicroED publication standards: what statistics to include and when is your 
structure publication-ready?

Further application information is available from

https://cryoem.ucla.edu/pages/Workshop

// Best wishes; Johan, on behalf of the organizers


 Research Specialist @ Gonen Lab

 UCLA * 615 Charles E. Young Drive South
BSRB #347 * Los Angeles, CA 90095



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