[ccp4bb] QTMG can not recognise phosphate carbon bond

[Khushboo Patel]

Hi
I have a ligand with phosphate that works well in coot and pymol but when I
open it in QTMG it shows phosphate as a separate moiety than the rest of
the ligand. There are two methyl groups attached to the phosphate but those
bonds are not visible too. so the whole compound looks like there are two
separate methyl groups, one phosphate attached to oxygen and rest of the
compound. It looks like the application is not able to attach the phosphate
atom to surrounding carbon atoms. The compound is called Hoe704.  I am
running the version 2.10.11 on macOS Catalina.
I have attached the screenshots
Has anyone else faced a similar problem?

Thank you

Khushboo



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

[Tim Gruene]

Hi Eike,

one of the points is that, only because you got used to a certain
operation (over many years after someone showed it to you), does not
mean it is intuitive. This could be judged by e.g. showing an ignorant
user both methods and let the person judge which one is easier to use...

Cheers,
Tim

On Wed, 9 Sep 2020 20:27:55
+ "Schulz, Eike-Christian"  wrote:

> Hi Tim, 
> 
> I don't think that metaphor is quite correct. To me it seems that no
> matter what button you pushed you got coffee. In my opinion intuitive
> software is a blessing and should not easily be disregarded. 
> 
> But as I said before, I am happy to read into new stuff. 
> 
> Also there seem to be mixed experiences here. Might this be
> map-resolution related ? 
> 
> Best, 
> 
> Eike
> 
> 
> 
> -Original Message-
> From: CCP4 bulletin board  on behalf of Georg
> Zocher  Reply to: Georg Zocher 
> Date: Wednesday, 9. September 2020 at 22:17
> To: "CCP4BB@JISCMAIL.AC.UK" 
> Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot
> 0.8
> 
> Dear Herman,
> 
> Am 09.09.2020 um 17:46 schrieb Schreuder, Herman /DE:
> > The old real-space refinement was intuitive and easy to use and
> > did exactly what the user expected, without having to consult
> > the manual! The result might not have been perfect, but was
> > good enough for subsequent Refmac, Buster, Phenix refinement.  
> 
> That fits perfectly to my user experience with RSR in coot 0.8.x.
> and also explains why at least a number of people having some issues
> with the new RSR.
> 
> All the best,
> 
> Georg
> 
> 
> 
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-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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pgp75IU5ikbNx.pgp
Description: OpenPGP digital signature

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

[Georg Zocher]

Dear Herman,

Am 09.09.2020 um 17:46 schrieb Schreuder, Herman /DE:

The old real-space refinement was intuitive and easy to use and did exactly 
what the user expected, without having to consult the manual! The result might 
not have been perfect, but was good enough for subsequent Refmac, Buster, 
Phenix refinement.


That fits perfectly to my user experience with RSR in coot 0.8.x. and 
also explains why at least a number of people having some issues with 
the new RSR.


All the best,

Georg



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Re: [ccp4bb] AW: Going back to Coot 0.8

[Georg Zocher]

Dear Tim,

I really like your example.


Has anyone of the disappointed users asked how to do it properly? Maybe
it is just as easy.


I think it's also up to me to do it properly and put more effort in it. 
Often we are restrained in time and improving your toolboox in an 
unexpected manner is harder to except than. But that's ok as this keeps 
one flexible. I hope, I will find the time soon and get used to it as 
much as whatever "the thing labelled as coffee" was;-)


Thank you all for your contributions,

Georg


Cheers,
Tim

On Wed, 9 Sep 2020 17:22:27 +0200
Georg Zocher  wrote:


Dear Paul,

people are complaining that they have issues fitting their model in
real space using coot 0.9.x. Personally, I very briefly used coot
other the last months but also have problems using RSR properly
because I'm used to do it the way it was over the last 10 years. This
might be due to my ignorance that I did not have a more closer look
into the new features of RSR in 0.9 release and how to use them. But
from the user site it's different to handle now.

I do not understand your Ferrari comparison (sorry) as I would not
buy one even if I would have more money than one can spend. But I
would take a cup of coffee as an example. If you always go to the
same dealer to get your coffee in the morning as you know you get a
very descent and excellent tasting cup of coffee that you fully enjoy
every morning than you really get used to it. It might be than a hard
time for you if your coffee dealer tells you: Sorry guys, I do have
now an optimized coffee that is much better, taste a lot better, is
fair produced,... It's just not the coffee you drunk over the last 10
years and I will not offer that one anymore. You might give the new
one a chance, you might find it as excellent as the dealer but you
might not. From my point of view it's the lack of choice that
personally I do not like so much, especially if there is no other
coffee dealer around...

Nevertheless, I'm aware and fully respect all the effort you put in
the development of coot and I'm really grateful that coot is
available.

All the best,
Georg



Am 08.09.20 um 17:44 schrieb Paul Emsley:

On 08/09/2020 16:25, Georg Zocher wrote:


we have the same experience in our lab.


What experience is that? I am still in the dark about you think is
now worse.

  

Personally, I did would not like to judge here, as so far, I did
not have had enough time to get into the new RSR of coot 0.9.x by
myself. But many colleagues did not like the new refinement module
maybe just as they are used to the method in all coot versions
before.


You have a Ferrari parked beside your house but you want to to take
the bus to work because that's what you've always done. Or maybe
the Ferrari is parked around the back and you don't know it's there?

  

I just thought if it wouldn't be an option to let the user decide
what kind of RSR implementation she/he would like to use and give
them the choice via an option in coot preferences?


That would be possible but not easy. Unlike much of the CCP4 suite,
Coot is Free Software. But, again... why would you want to take the
bus? Explain.


regards,


Paul.



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[ccp4bb] COOT v. 0.9

[F . Xavier Gomis-Rüth]

Dear all,
after the plethora of complaints about v. 0.9 when compared to v. 0.8, I 
would like to argue in favour of the new version.
I find RSR is now much more robust, with a larger radius of convergence, 
with very useful tools like tandem refinement, etc. which are
particularly useful with cryoEM maps but also work well with 
conventional crystallography. I will certainly NOT go back

to 0.8.
There are only two issues that are annoying and maybe Paul could have an 
eye on them:
-When performing RSR, crystallographic symmetry mates are not 
considered. But this was already happening with 0.8.
-In some instances but not always, when there is a break of missing 
residues in the model, RSR would force the residues flanking the

gap to join.
Having said that, thanks a lot, Paul, for your dedication to this superb 
program over the years.

All the best,
Xavier
--



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Re: [ccp4bb] AW: Going back to Coot 0.8

[Tim Gruene]

Dear Georg and others, 

if I followed the thread correctly, the coffee story should really go
like this:

for years you have been pushing the button of a machine
showing a cup with a black liquid inside. After ten years, the
manufacturer of the machine tells you:
"Sorry guy, it is not coffee what you have been drinking. If
you want to drink coffee, you should push the button down here, which
is labelled 'coffee'."
Because you drank the other liquid for years, you are very
disappointed by the taste of real coffee and keep on pushing the old
button that you got used to.

That's how I interpret Paul's statement 
"[...] many people learnt (I discovered, rather late in the day) [...]"

Has anyone of the disappointed users asked how to do it properly? Maybe
it is just as easy.

Cheers,
Tim

On Wed, 9 Sep 2020 17:22:27 +0200
Georg Zocher  wrote:

> Dear Paul,
> 
> people are complaining that they have issues fitting their model in
> real space using coot 0.9.x. Personally, I very briefly used coot
> other the last months but also have problems using RSR properly
> because I'm used to do it the way it was over the last 10 years. This
> might be due to my ignorance that I did not have a more closer look
> into the new features of RSR in 0.9 release and how to use them. But
> from the user site it's different to handle now.
> 
> I do not understand your Ferrari comparison (sorry) as I would not
> buy one even if I would have more money than one can spend. But I
> would take a cup of coffee as an example. If you always go to the
> same dealer to get your coffee in the morning as you know you get a
> very descent and excellent tasting cup of coffee that you fully enjoy
> every morning than you really get used to it. It might be than a hard
> time for you if your coffee dealer tells you: Sorry guys, I do have
> now an optimized coffee that is much better, taste a lot better, is
> fair produced,... It's just not the coffee you drunk over the last 10
> years and I will not offer that one anymore. You might give the new
> one a chance, you might find it as excellent as the dealer but you
> might not. From my point of view it's the lack of choice that
> personally I do not like so much, especially if there is no other
> coffee dealer around...
> 
> Nevertheless, I'm aware and fully respect all the effort you put in
> the development of coot and I'm really grateful that coot is
> available.
> 
> All the best,
> Georg
> 
> 
> 
> Am 08.09.20 um 17:44 schrieb Paul Emsley:
> > On 08/09/2020 16:25, Georg Zocher wrote:  
> >>
> >>
> >> we have the same experience in our lab.  
> >
> >
> > What experience is that? I am still in the dark about you think is
> > now worse.
> >
> >  
> >> Personally, I did would not like to judge here, as so far, I did
> >> not have had enough time to get into the new RSR of coot 0.9.x by
> >> myself. But many colleagues did not like the new refinement module
> >> maybe just as they are used to the method in all coot versions
> >> before.  
> >
> >
> > You have a Ferrari parked beside your house but you want to to take 
> > the bus to work because that's what you've always done. Or maybe
> > the Ferrari is parked around the back and you don't know it's there?
> >
> >  
> >>
> >> I just thought if it wouldn't be an option to let the user decide 
> >> what kind of RSR implementation she/he would like to use and give 
> >> them the choice via an option in coot preferences?  
> >
> >
> > That would be possible but not easy. Unlike much of the CCP4 suite, 
> > Coot is Free Software. But, again... why would you want to take the 
> > bus? Explain.
> >
> >
> > regards,
> >
> >
> > Paul.
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a 
> > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are 
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> 
> 
> 
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-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

[Schreuder, Herman /DE]

Dear Paul,

I fully agree with Georg and the others. As I said in my first reaction, with 
the new coot, the inhibitor or side chain often does not end up a little wrong, 
but goes off completely in the wrong direction, which makes me wonder whether I 
had somehow selected the wrong map. It might also be that the default settings 
that had been distributed with coot are wrong. I will try to find an example 
that is non-confidential, but often the moment you want something to go wrong, 
everything works perfectly. 

The old real-space refinement was intuitive and easy to use and did exactly 
what the user expected, without having to consult the manual! The result might 
not have been perfect, but was good enough for subsequent Refmac, Buster, 
Phenix refinement.  

Best regards,
Herman


-Ursprüngliche Nachricht-
Von: CCP4 bulletin board  Im Auftrag von Georg Zocher
Gesendet: Mittwoch, 9. September 2020 17:22
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8

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



Dear Paul,

people are complaining that they have issues fitting their model in real space 
using coot 0.9.x. Personally, I very briefly used coot other the last months 
but also have problems using RSR properly because I'm used to do it the way it 
was over the last 10 years. This might be due to my ignorance that I did not 
have a more closer look into the new features of RSR in 0.9 release and how to 
use them. But from the user site it's different to handle now.

I do not understand your Ferrari comparison (sorry) as I would not buy one even 
if I would have more money than one can spend. But I would take a cup of coffee 
as an example. If you always go to the same dealer to get your coffee in the 
morning as you know you get a very descent and excellent tasting cup of coffee 
that you fully enjoy every morning than you really get used to it. It might be 
than a hard time for you if your coffee dealer tells you: Sorry guys, I do have 
now an optimized coffee that is much better, taste a lot better, is fair 
produced,... It's just not the coffee you drunk over the last 10 years and I 
will not offer that one anymore. You might give the new one a chance, you might 
find it as excellent as the dealer but you might not. From my point of view 
it's the lack of choice that personally I do not like so much, especially if 
there is no other coffee dealer around...

Nevertheless, I'm aware and fully respect all the effort you put in the 
development of coot and I'm really grateful that coot is available.

All the best,
Georg



Am 08.09.20 um 17:44 schrieb Paul Emsley:
> On 08/09/2020 16:25, Georg Zocher wrote:
>>
>>
>> we have the same experience in our lab.
>
>
> What experience is that? I am still in the dark about you think is now 
> worse.
>
>
>> Personally, I did would not like to judge here, as so far, I did not 
>> have had enough time to get into the new RSR of coot 0.9.x by myself.
>> But many colleagues did not like the new refinement module maybe just 
>> as they are used to the method in all coot versions before.
>
>
> You have a Ferrari parked beside your house but you want to to take 
> the bus to work because that's what you've always done. Or maybe the 
> Ferrari is parked around the back and you don't know it's there?
>
>
>>
>> I just thought if it wouldn't be an option to let the user decide 
>> what kind of RSR implementation she/he would like to use and give 
>> them the choice via an option in coot preferences?
>
>
> That would be possible but not easy. Unlike much of the CCP4 suite, 
> Coot is Free Software. But, again... why would you want to take the 
> bus? Explain.
>
>
> regards,
>
>
> Paul.
>
> ##
> ##
>
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Re: [ccp4bb] AW: Going back to Coot 0.8

[Georg Zocher]

Dear Paul,

people are complaining that they have issues fitting their model in real 
space using coot 0.9.x. Personally, I very briefly used coot other the 
last months but also have problems using RSR properly because I'm used 
to do it the way it was over the last 10 years. This might be due to my 
ignorance that I did not have a more closer look into the new features 
of RSR in 0.9 release and how to use them. But from the user site it's 
different to handle now.


I do not understand your Ferrari comparison (sorry) as I would not buy 
one even if I would have more money than one can spend. But I would take 
a cup of coffee as an example. If you always go to the same dealer to 
get your coffee in the morning as you know you get a very descent and 
excellent tasting cup of coffee that you fully enjoy every morning than 
you really get used to it. It might be than a hard time for you if your 
coffee dealer tells you: Sorry guys, I do have now an optimized coffee 
that is much better, taste a lot better, is fair produced,... It's just 
not the coffee you drunk over the last 10 years and I will not offer 
that one anymore. You might give the new one a chance, you might find it 
as excellent as the dealer but you might not. From my point of view it's 
the lack of choice that personally I do not like so much, especially if 
there is no other coffee dealer around...


Nevertheless, I'm aware and fully respect all the effort you put in the 
development of coot and I'm really grateful that coot is available.


All the best,
Georg



Am 08.09.20 um 17:44 schrieb Paul Emsley:

On 08/09/2020 16:25, Georg Zocher wrote:



we have the same experience in our lab.



What experience is that? I am still in the dark about you think is now 
worse.



Personally, I did would not like to judge here, as so far, I did not 
have had enough time to get into the new RSR of coot 0.9.x by myself. 
But many colleagues did not like the new refinement module maybe just 
as they are used to the method in all coot versions before.



You have a Ferrari parked beside your house but you want to to take 
the bus to work because that's what you've always done. Or maybe the 
Ferrari is parked around the back and you don't know it's there?





I just thought if it wouldn't be an option to let the user decide 
what kind of RSR implementation she/he would like to use and give 
them the choice via an option in coot preferences?



That would be possible but not easy. Unlike much of the CCP4 suite, 
Coot is Free Software. But, again... why would you want to take the 
bus? Explain.



regards,


Paul.



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Re: [ccp4bb] metal coordination at low resolution - restraints

[Frank von Delft]

Surely an opportunity for machine learning to make a real difference?  
There's enough data in the PDB by now, that you can conceive of a 
classifier generating the most likely set of restraints appropriate 
given an OMIT map.




On 09/09/2020 11:37, Eleanor Dodson wrote:
I know how difficult it is to get the chemistry right, and that really 
has to be up to the researcher..
 a database of high resolution structures with metals would be useful 
as a sanity check. Robbie mentioned

 MetalPDB (http://metalweb.cerm.unifi.it/).

E

On Wed, 9 Sep 2020 at 11:18, Garib Murshudov > wrote:


Hi Eleanor,

Obviously I agree that people should use restraints for metals. It
will make metal refinement easy and coordination consistent with
chemistry

For distance and angle restraints there is an external distance
restraint mechanism. PDB-REDO can generate for some of the metals.
Unfortunately it is not easy in general. But can be done manually.

If you know metal and coordinating atoms and coordination then
putting restraints manually in ccp4i2 refmac keyword part should
be straightforward. For example (I think it is correct)

External distance first chain A residue 239 atom ZN second chain A
residue 500 atom O value 1.95 sigma 0.032 type 0
External distance first chain A residue 239 atom ZN second chain A
residue 145 atom ND1 value 2.03 sigma 0.05 type 0
External angle first chain A residue 500 atom O next chain A
residue 239 atom ZN next chain residue 145 atom ND1 value 109
sigma 5 type 0


Unfortunately these restraints do not account for the fact that
when Zn is bound to O or N atoms then it may change the nature of
bonds (i.e. ZN bonds are often covalent like, as Robbie says:
these are d-block atoms for you)
The values above assume that ZN coordination is 4 and it is
tetrahedral. For others similar restraints could be added.

In future we would like to semi-automate metal refinement. At the
moment it is pretty much users’ responsibility to design correct
restraints (it is not ideal, not because we do not trust users but
because the knowledge is not easily transferable from one
refinement to another).


Regards
Garib





On 8 Sep 2020, at 20:51, Eleanor Dodson
mailto:eleanor.dod...@york.ac.uk>> wrote:

Yes Garib - all true but I dont think people should try to impose
restraints initially in refinement of metals.

I never (knowingly)  keep the metals in my MR model. Searching
for them with phases from a putative MR solution is one of the
best verifications that it is right...

You can use anomalous fouriers to fix the metals as accurately as
possible. That could help with issue 3. And peak heights give you
a bit of information re occupancy.

Surely issue 2) shouldnt happen!  Do you mean BUCCANEER builds
the sequence wrongly?

Na etc.. Impossible - hate them..

4) & 5) are more or less the same .. occupancy is tricky - again
anom peaks ? Occupancy refinement? all difficult at low resolution..

On Tue, 8 Sep 2020 at 20:29, Garib Murshudov
mailto:ga...@mrc-lmb.cam.ac.uk>> wrote:

Hi Jan,


It is my experience also that if atoms are in more or less
correct positions then non-bonding interaction together keep
metals in correct positions, perhaps with a little bit
different metal-coordinating atom distances.
Problems arise when 1) one or several of the corrdinating
atoms are missing which is the case at low resolution. Light
atoms are almost invisible around heavy atoms (series
termination and B value effects); 2) there are conflicting
restraints which often happens with SS-bond (wrong SS-bond)
and Zn-Cys bonds; 3) Starting atomic coordinates are far from
right positions (which happens after molecular replacement
when conformations are not exactly same around metals; 4)
Metals are not fully occupied (which happens when metals
involve reaction and they arrive during or as a part of
reaction); 5) non-specific metal binding sites (which happens
when metals are not part of the molecule but are used as a
part of sample preparation - crystallisation or otherwise).
6) light metals (Na and similar) when metals are difficult to
distinguish from water molecules; 7) highly mobile metals.


Regards
Garib



On 8 Sep 2020, at 13:01, Jan Dohnalek mailto:dohnalek...@gmail.com>> wrote:

Hi Garib,




On 8 Sep 2020, at 11:39, Jan Dohnalek
mailto:dohnalek...@gmail.com>>
wrote:

These are structural.


Are they tetrahedral or octahedral? From the list of
neighbours they do not look like tetrahedral. Some of
them do look like octahedral.

They 

[ccp4bb] Webinar: Cryo-EM in Drug Discovery

[H. Raaijmakers]

You are invited to join a Thermo Fisher Scientific webinar on Sep 29. 

_Cryo-EM and MicroED in drug discovery_ (incl. routine structure
determination) 

Lectures: 

* Dr. Christopher Phillips,  Astra Zeneca
* Prof. Paul Midgley, University of Cambridge
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A round table:  How to setup a successful cryo-EM Workflow? 

* Dr. Rebecca Ebenhoch, Boehringer Ingelheim
* Dr. Alexey Rak, Sanofi
* Dr. Denis Zeyer, NovAliX
* Dr. Jeremy Rees, Thermo Fisher Scientific
* Dr. Chun-wa Chung, GSK
* Dr. Jason van Rooyen, eBIC

More information and registration at: https://ter.li/57d6wg 

Cheers, 

Hans Raaijmakers



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Re: [ccp4bb] metal coordination at low resolution - restraints

[Eleanor Dodson]

I know how difficult it is to get the chemistry right, and that really has
to be up to the researcher..
 a database of high resolution structures with metals would be useful as a
sanity check. Robbie mentioned
 MetalPDB (http://metalweb.cerm.unifi.it/).

E

On Wed, 9 Sep 2020 at 11:18, Garib Murshudov 
wrote:

> Hi Eleanor,
>
> Obviously I agree that people should use restraints for metals. It will
> make metal refinement easy and coordination consistent with chemistry
>
> For distance and angle restraints there is an external distance restraint
> mechanism. PDB-REDO can generate for some of the metals. Unfortunately it
> is not easy in general. But can be done manually.
>
> If you know metal and coordinating atoms and coordination then putting
> restraints manually in ccp4i2 refmac keyword part should be
> straightforward. For example (I think it is correct)
>
> External distance first chain A residue 239 atom ZN second chain A residue
> 500 atom O value 1.95 sigma 0.032 type 0
> External distance first chain A residue 239 atom ZN second chain A residue
> 145 atom ND1 value 2.03 sigma 0.05 type 0
> External angle first chain A residue 500 atom O next chain A residue 239
> atom ZN next chain residue 145 atom ND1 value 109 sigma 5 type 0
>
>
> Unfortunately these restraints do not account for the fact that when Zn is
> bound to O or N atoms then it may change the nature of bonds (i.e. ZN bonds
> are often covalent like, as Robbie says: these are d-block atoms for you)
> The values above assume that ZN coordination is 4 and it is tetrahedral.
> For others similar restraints could be added.
>
> In future we would like to semi-automate metal refinement. At the moment
> it is pretty much users’ responsibility to design correct restraints (it is
> not ideal, not because we do not trust users but because the knowledge is
> not easily transferable from one refinement to another).
>
>
> Regards
> Garib
>
>
>
>
> On 8 Sep 2020, at 20:51, Eleanor Dodson  wrote:
>
> Yes Garib - all true but I dont think people should try to impose
> restraints initially in refinement of metals.
>
> I never (knowingly)  keep the metals in my MR model. Searching for them
> with phases from a putative MR solution is one of the best verifications
> that it is right...
>
> You can use anomalous fouriers to fix the metals as accurately as
> possible. That could help with issue 3. And peak heights give you a bit of
> information re occupancy.
>
> Surely issue 2) shouldnt happen!  Do you mean BUCCANEER builds the
> sequence wrongly?
>
> Na etc.. Impossible - hate them..
>
> 4) & 5) are more or less the same .. occupancy is tricky - again anom
> peaks ? Occupancy refinement? all difficult at low resolution..
>
> On Tue, 8 Sep 2020 at 20:29, Garib Murshudov 
> wrote:
>
>> Hi Jan,
>>
>>
>> It is my experience also that if atoms are in more or less correct
>> positions then non-bonding interaction together keep metals in correct
>> positions, perhaps with a little bit different metal-coordinating atom
>> distances.
>> Problems arise when 1) one or several of the corrdinating atoms are
>> missing which is the case at low resolution. Light atoms are almost
>> invisible around heavy atoms (series termination and B value effects); 2)
>> there are conflicting restraints which often happens with SS-bond (wrong
>> SS-bond) and Zn-Cys bonds; 3) Starting atomic coordinates are far from
>> right positions (which happens after molecular replacement when
>> conformations are not exactly same around metals; 4) Metals are not fully
>> occupied (which happens when metals involve reaction and they arrive during
>> or as a part of reaction); 5) non-specific metal binding sites (which
>> happens when metals are not part of the molecule but are used as a part of
>> sample preparation - crystallisation or otherwise). 6) light metals (Na and
>> similar) when metals are difficult to distinguish from water molecules; 7)
>> highly mobile metals.
>>
>>
>> Regards
>> Garib
>>
>>
>> On 8 Sep 2020, at 13:01, Jan Dohnalek  wrote:
>>
>> Hi Garib,
>>
>>
>>>
>>> On 8 Sep 2020, at 11:39, Jan Dohnalek  wrote:
>>>
>>> These are structural.
>>>
>>>
>>> Are they tetrahedral or octahedral? From the list of neighbours they do
>>> not look like tetrahedral. Some of them do look like octahedral.
>>>
>>> They are involved in reaction.
>> Two are ~ octahedral (skewed though, two positions filled by catalysis
>> participant), one is ~tetrahedral, but actually can also accept a fifth
>> coordinating atom.
>>
>> But as I said - in all our structures restraining the coordination
>> geometry is not necessary, they hold nice.
>>
>> Jan
>>
>>
>> Jan
>>
>>
>> On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov 
>> wrote:
>>
>>> What are these numbers?
>>>
>>> If I understand these numbers correctly: none of your Zn atoms is
>>> structural (4 coordinated tetrahedral). If that is the case then you need
>>> specific links or restraints. If my reading of your numbers is correct then
>>> there could be 

Re: [ccp4bb] metal coordination at low resolution - restraints

[Garib Murshudov]

Hi Eleanor, 

Obviously I agree that people should use restraints for metals. It will make 
metal refinement easy and coordination consistent with chemistry

For distance and angle restraints there is an external distance restraint 
mechanism. PDB-REDO can generate for some of the metals. Unfortunately it is 
not easy in general. But can be done manually.

If you know metal and coordinating atoms and coordination then putting 
restraints manually in ccp4i2 refmac keyword part should be straightforward. 
For example (I think it is correct)

External distance first chain A residue 239 atom ZN second chain A residue 500 
atom O value 1.95 sigma 0.032 type 0
External distance first chain A residue 239 atom ZN second chain A residue 145 
atom ND1 value 2.03 sigma 0.05 type 0
External angle first chain A residue 500 atom O next chain A residue 239 atom 
ZN next chain residue 145 atom ND1 value 109 sigma 5 type 0


Unfortunately these restraints do not account for the fact that when Zn is 
bound to O or N atoms then it may change the nature of bonds (i.e. ZN bonds are 
often covalent like, as Robbie says: these are d-block atoms for you)
The values above assume that ZN coordination is 4 and it is tetrahedral. For 
others similar restraints could be added. 

In future we would like to semi-automate metal refinement. At the moment it is 
pretty much users’ responsibility to design correct restraints (it is not 
ideal, not because we do not trust users but because the knowledge is not 
easily transferable from one refinement to another).


Regards
Garib




> On 8 Sep 2020, at 20:51, Eleanor Dodson  wrote:
> 
> Yes Garib - all true but I dont think people should try to impose restraints 
> initially in refinement of metals.
> 
> I never (knowingly)  keep the metals in my MR model. Searching for them with 
> phases from a putative MR solution is one of the best verifications that it 
> is right...
> 
> You can use anomalous fouriers to fix the metals as accurately as possible. 
> That could help with issue 3. And peak heights give you a bit of information 
> re occupancy.
> 
> Surely issue 2) shouldnt happen!  Do you mean BUCCANEER builds the sequence 
> wrongly?
> 
> Na etc.. Impossible - hate them..
> 
> 4) & 5) are more or less the same .. occupancy is tricky - again anom peaks ? 
> Occupancy refinement? all difficult at low resolution..
> 
> On Tue, 8 Sep 2020 at 20:29, Garib Murshudov  > wrote:
> Hi Jan,
> 
> 
> It is my experience also that if atoms are in more or less correct positions 
> then non-bonding interaction together keep metals in correct positions, 
> perhaps with a little bit different metal-coordinating atom distances.
> Problems arise when 1) one or several of the corrdinating atoms are missing 
> which is the case at low resolution. Light atoms are almost invisible around 
> heavy atoms (series termination and B value effects); 2) there are 
> conflicting restraints which often happens with SS-bond (wrong SS-bond) and 
> Zn-Cys bonds; 3) Starting atomic coordinates are far from right positions 
> (which happens after molecular replacement when conformations are not exactly 
> same around metals; 4) Metals are not fully occupied (which happens when 
> metals involve reaction and they arrive during or as a part of reaction); 5) 
> non-specific metal binding sites (which happens when metals are not part of 
> the molecule but are used as a part of sample preparation - crystallisation 
> or otherwise). 6) light metals (Na and similar) when metals are difficult to 
> distinguish from water molecules; 7) highly mobile metals.
> 
> 
> Regards
> Garib
> 
> 
>> On 8 Sep 2020, at 13:01, Jan Dohnalek > > wrote:
>> 
>> Hi Garib,
>> 
>> 
>> 
>>> On 8 Sep 2020, at 11:39, Jan Dohnalek >> > wrote:
>>> 
>>> These are structural.
>> 
>> Are they tetrahedral or octahedral? From the list of neighbours they do not 
>> look like tetrahedral. Some of them do look like octahedral.
>> 
>> They are involved in reaction.
>> Two are ~ octahedral (skewed though, two positions filled by catalysis 
>> participant), one is ~tetrahedral, but actually can also accept a fifth 
>> coordinating atom.
>>  
>> But as I said - in all our structures restraining the coordination geometry 
>> is not necessary, they hold nice.
>> 
>> Jan
>> 
>>> 
>>> Jan
>>> 
>>> 
>>> On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov >> > wrote:
>>> What are these numbers?
>>> 
>>> If I understand these numbers correctly: none of your Zn atoms is 
>>> structural (4 coordinated tetrahedral). If that is the case then you need 
>>> specific links or restraints. If my reading of your numbers is correct then 
>>> there could be some chemistry change of the surrounding residues.
>>> 
>>> If it is not structural Zn then it is likely that coordination is 6. But 
>>> without seeing coordinates and maps it is difficult to say what is there.
>>> 

Re: [ccp4bb] AW: Going back to Coot 0.8

[Schulz, Eike-Christian]

Dear Paul, 

sorry for the delay. 

I did not answer your previous questions in detail, because going back to coot 
0.8 did solve the problem for me, which kept me busy. But of course, to do sth. 
about the situation you need to understand a lot better what is going on. 

What I have is a “phenotype” (coot 0.9) that presents differently than the 
previous generation (coot 0.8) and since it’s not possible for me to revert any 
of the mutations its hard to pinpoint the cause of the problem. The most 
general description I can come up with: in coot 0.9 the model moves “funny” – 
different from coot 0.8. Some (new?) restraints seem to act on the atoms 
preventing them to stay where I put them. This "hidden-thinking" coot 0.9 
appears to apply confuses me. 

*I don’t think this description is a major improvement from before, maybe 
someone else (Georg?, Eleanor? Herman?) can give it a try?

However, I have a hunch that the root of our communication trouble is that the 
way you and I are using coot is very different. Therefore, I think it maybe 
best if (a) I told you how I use it most of the time and (b) provide you with a 
specific example (off-list). Maybe you can reproduce the trouble if you follow 
my procedure. 

Staying in the picture of your Ferrari/bus metaphor, I think I am probably 
walking to work:

I am predominantly using the real-space refine options, going through the 
structure bit by bit, putting the model where (I think) it belongs. I also make 
use of the stepped-refine procedure, but I know more than one colleague who 
considers that “cheating” already or do not know about that option at all. Of 
course, I am making use of the validation, measurement, map and model tools, 
but hardly of any automation (§). No special key-binding, no scripts - just out 
of the box, default settings, iterative cycles with refinement. That may not be 
what you have intended, but the people in my echo chamber just do the same. 

Eigen-flip, jiggle-fit, pepflip, JED-flip, backrub, interactive contact dots, 
acedrg – sorry I’ve never heard of them. 

You mentioned a blog and/or other coot info before. With coot 0.9 I tried 
finding more information but your coot-website and the included tutorials 
appear to be a bit older https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/. 

Is there a new source of info somewhere? - I am happy to look into it. 

Best, 

Eike


§ automatic building of alternate conformations for HR-structures would be 
really helpful though. 


-Original Message-
From: CCP4 bulletin board  on behalf of Paul Emsley 

Reply to: Paul Emsley 
Date: Tuesday, 8. September 2020 at 17:44
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] AW: Going back to Coot 0.8

On 08/09/2020 16:25, Georg Zocher wrote:
>
>
> we have the same experience in our lab.


What experience is that? I am still in the dark about you think is now 
worse.


> Personally, I did would not like to judge here, as so far, I did not 
> have had enough time to get into the new RSR of coot 0.9.x by myself. 
> But many colleagues did not like the new refinement module maybe just 
> as they are used to the method in all coot versions before.


You have a Ferrari parked beside your house but you want to to take the 
bus to work because that's what you've always done. Or maybe the Ferrari 
is parked around the back and you don't know it's there?


>
> I just thought if it wouldn't be an option to let the user decide what 
> kind of RSR implementation she/he would like to use and give them the 
> choice via an option in coot preferences?


That would be possible but not easy. Unlike much of the CCP4 suite, Coot 
is Free Software. But, again... why would you want to take the bus? Explain.


regards,


Paul.



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Re: [ccp4bb] taking information from a deposited structure

[Firdous Tarique]

Hi

Thanks a lot for your feedback.

Best

Kahkashan

On Wed, Sep 9, 2020 at 11:58 AM Randy Read  wrote:

> It’s perfectly normal and accepted to use a released entry from the PDB,
> even if there’s no underlying publication.  That is true of many of the
> structures from the structural genomics initiatives, for instance.  As you
> say, you should cite the PDB entry ID and it would be nice also to name the
> authors of the entry.
>
> Best wishes,
>
> Randy Read
>
> -
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: +44 1223 336500
> The Keith Peters Building   Fax: +44 1223
> 336827
> Hills Road   E-mail:
> rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
> > On 9 Sep 2020, at 06:41, Firdous Tarique 
> wrote:
> >
> > Dear CCP4 community members.
> >
> > I have solved  a crystal structure of a protein and am now trying to get
> a structure with a ligand bound to it, but so far unsuccessful. A
> homologous structure with the same ligand is present in the RCSB PDB (un
> published). Is it permissible to fetch structural information from that
> unpublished data and use it for docking and simulation studies with my
> protein? Will it be copyright infringement or it is just a normal thing.  I
> will be mentioning in my manuscript that I have used this unpublished
> structure (deposited by this author) for these studies.
> >
> > Best
> >
> > Kahkashan
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >
>
>



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Re: [ccp4bb] taking information from a deposited structure

[Robbie Joosten]

Dear Kahkashan,That is totally fine as long as you make it clear that you used this PDB entry. That's what the PDB is for.Just make sure you check the model with the electron density from EDS or pdb-redo. Cheers,RobbieOn 9 Sep 2020 07:41, Firdous Tarique  wrote:Dear CCP4 community members.I have solved  a crystal structure of a protein and am now trying to get a structure with a ligand bound to it, but so far unsuccessful. A homologous structure with the same ligand is present in the RCSB PDB (un published). Is it permissible to fetch structural information from that unpublished data and use it for docking and simulation studies with my protein? Will it be copyright infringement or it is just a normal thing.  I will be mentioning in my manuscript that I have used this unpublished structure (deposited by this author) for these studies. BestKahkashan


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Re: [ccp4bb] taking information from a deposited structure

[Randy Read]

It’s perfectly normal and accepted to use a released entry from the PDB, even 
if there’s no underlying publication.  That is true of many of the structures 
from the structural genomics initiatives, for instance.  As you say, you should 
cite the PDB entry ID and it would be nice also to name the authors of the 
entry.

Best wishes,

Randy Read

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
The Keith Peters Building   Fax: +44 1223 336827
Hills Road   E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.  
www-structmed.cimr.cam.ac.uk

> On 9 Sep 2020, at 06:41, Firdous Tarique  wrote:
> 
> Dear CCP4 community members.
> 
> I have solved  a crystal structure of a protein and am now trying to get a 
> structure with a ligand bound to it, but so far unsuccessful. A homologous 
> structure with the same ligand is present in the RCSB PDB (un published). Is 
> it permissible to fetch structural information from that unpublished data and 
> use it for docking and simulation studies with my protein? Will it be 
> copyright infringement or it is just a normal thing.  I will be mentioning in 
> my manuscript that I have used this unpublished structure (deposited by this 
> author) for these studies. 
> 
> Best
> 
> Kahkashan
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 



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