date:20200908

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.
>>
>> Regards
>> Garib
>>
>>
>> On 8 Sep 2020, at 11:11, Eleanor Dodson 
>> wrote:
>>
>> Hmm - here is my problem - a list of ZN contacts for the two molecules..
>> residue 602 is a phosphate, and there possibly should be a few more
>> waters ..
>> No idea how best to tackle it..
>> E
>>
>>
>>  Z  401 ZN   A   W   21 NA  2.057 X,Y,Z   1.00
>>   8.73
>>  Z  401 ZN   A   W   21 OA  2.220 X,Y,Z   1.00
>>   8.76
>>  Z  401 ZN   A   H   26 NE2  A  2.000 X,Y,Z   1.00
>>   8.39
>>  Z  401 ZN   A   D  139 OD1  A  2.085 X,Y,Z   1.00
>>   8.61
>>  Z  401 ZN   A   Z  601 O2   A  1.927 X,Y,Z   0.60
>> 10.74
>>  Z  401 ZN   A   O  821 OC  2.006 X,Y,Z   0.40
>>   7.51
>>
>>  Z  402 ZN   A   H   80 ND1  A  2.033 X,Y,Z   1.00
>>   8.94
>>  Z  402 ZN   A   H  135 NE2  A  2.032 X,Y,Z   1.00
>>   8.70
>>  Z  402 ZN   A   D  139 OD2  A  2.024 X,Y,Z   1.00
>>   8.70
>>  Z  402 ZN   A   Z  601 O2   A  2.131 X,Y,Z   0.60
>> 11.05
>>  Z  402 ZN   A   O  821 OC  1.829 X,Y,Z   0.40
>>   7.81
>>
>>  Z  403 ZN   A   H  145 NE2  A  2.027 X,Y,Z   1.00
>> 10.50
>>  Z  403 ZN   A   H  168 NE2  A  2.030 X,Y,Z   1.00
>> 10.19
>>  Z  403 ZN   A   D  172 OD2  A  2.062 X,Y,Z   1.00
>> 12.66
>>  Z  403 ZN   A   Z  601 O3   A  1.953 X,Y,Z   0.60
>> 11.54
>>  Z  403 ZN   A   O  820 OC  2.207 X,Y,Z   0.20
>>   9.09
>>  Z  403 ZN   A   O  822 OC  2.059 X,Y,Z   0.40
>> 13.79
>>
>>  Z  401 ZN   A   Z  402 ZN   A  3.349 X,Y,Z   1.00
>>   8.73
>>
>>
>>  Z  401 ZN   B   W   21 NB  2.099 X,Y,Z

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

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.
>> 
>> Regards
>> Garib
>> 
>> 
>>> On 8 Sep 2020, at 11:11, Eleanor Dodson >> > wrote:
>>> 
>>> Hmm - here is my problem - a list of ZN contacts for the two molecules..
>>> residue 602 is a phosphate, and there possibly should be a few more waters 
>>> .. 
>>> No idea how best to tackle it..
>>> E
>>> 
>>> 
>>>  Z  401 ZN   A   W   21 NA  2.057 X,Y,Z   1.00
>>> 8.73
>>>  Z  401 ZN   A   W   21 OA  2.220 X,Y,Z   1.00
>>> 8.76
>>>  Z  401 ZN   A   H   26 NE2  A  2.000 X,Y,Z   1.00
>>> 8.39
>>>  Z  401 ZN   A   D  139 OD1  A  2.085 X,Y,Z   1.00
>>> 8.61
>>>  Z  401 ZN   A   Z  601 O2   A  1.927 X,Y,Z   0.60   
>>> 10.74
>>>  Z  401 ZN   A   O  821 OC  2.006 X,Y,Z   0.40
>>> 7.51
>>> 
>>>  Z  402 ZN   A   H   80 ND1  A  2.033 X,Y,Z   1.00
>>> 8.94
>>>  Z  402 ZN   A   H  135 NE2  A  2.032 X,Y,Z   1.00
>>> 8.70
>>>  Z  402 ZN   A   D  139 OD2  A  2.024 X,Y,Z   1.00
>>> 8.70
>>>  Z  402 ZN   A   Z  601 O2   A  2.131 X,Y,Z   0.60   
>>> 11.05
>>>  Z  402 ZN   A   O  821 OC  1.829 X,Y,Z   0.40
>>> 7.81
>>> 
>>>  Z  403 ZN   A   H  145 NE2  A  2.027 X,Y,Z   1.00   
>>> 10.50
>>>  Z  403 ZN   A   H  168 NE2  A  2.030 X,Y,Z   1.00   
>>> 10.19
>>>  Z  403 ZN   A   D  172 OD2  A  2.062 X,Y,Z   1.00   
>>> 12.66
>>>  Z  403 ZN   A   Z  601 O3   A  1.953 X,Y,Z   0.60   
>>> 11.54
>>>  Z  403 ZN   A   O  820 OC  2.207 X,Y,Z   0.20
>>> 9.09
>>>  Z  403 ZN   A   O  822 OC  2.059 X,Y,Z   0.40   
>>> 13.79
>>> 
>>>  Z  401 ZN   A   Z  402 ZN   A  3.349 X,Y,Z   1.00
>>> 8.73
>>> 
>>> 
>>>  Z  401 ZN   B   W   21 NB  2.099 X,Y,Z   1.00
>>> 9.22
>>>  Z  401 ZN   B   W   21 OB  2.184 X,Y,Z   1.00
>>> 8.91
>>>  Z  401 ZN   B   H   26 NE2  B  2.009 X,Y,Z   1.00
>>> 8.79
>>>  Z  401 ZN   B   D  139 OD1  B  2.069 X,Y,Z   1.00
>>> 8.76
>>>  Z  401 ZN   B   Z  601 O3   B  1.981 X,Y,Z   0.70
>>> 9.31
>>> 
>>>  Z  402 ZN   B   H   80 ND1  B  2.032 X,Y,Z   1.00
>>> 9.49
>>>  Z  402 ZN   B   H  135 NE2  B  2.024 X,Y,Z   1.00
>>> 9.22
>>>  Z  402

Re: [ccp4bb] Best protocols to advance a low resolution twinned MR map

Hmmm -
not much help, but MR can work with twinned data ..
What's the sequence match between your models and your protein? And do you
expect them to form a dimer?

Presumably you found the d3:d3 dimer using MR? I would be a bit worried
that the twinning could mislead a dimer search - are the two d3-s related
by (x,y,z) (-x,-y,z)  and possibly a consequence of twinning imposing an
extra 2 fold axes in the data?

And what do you see in the self rotation function? Is there any indication
of how the two copies are related?
Lots of questions, no answers!
Eleanor

On Tue, 8 Sep 2020 at 19:53, Andrew Lovering  wrote:

> Dear all,
>
>
> I've a project with two historical datasets (i.e. not sure of when/if I
> can reproduce to solve problem by getting better data) that are twinned.
>
>
> The spacegroup is P32, with operator -h, -k, l
>
> cell = 83.5 83.5 64.2 90 90 120
>
>
> protein has three domains d1-d2-d3, likely 50% solvent, 2 copies in asu
>
>
> dataset 1, roughly 3.6 angstrom resolution, twin fraction 0.25
>
> dataset 2, roughly 3.1 angstrom resolution, twin fraction 0.4
>
>
> I've managed to solve this (unambiguously) by finding a d3:d3 dimer in
> detwinned data, then seeing via phenix autobuild that it finds a d2 also in
> map. At present the ability to interpret the map further stalls there, and
> it can't be "the limit" because lack of crystal contacts suggest there
> should be more protein to find.
>
>
> I realise I can go two ways, either using the detwinned data or using
> twinned data and supplying the operator.the former giving ridiculously
> optimistic R-values with a suspiciously "clean map", the latter giving
> noisier but maybe more informative maps.
>
>
> Two-fold averaging is not going to be great because the d2-d3 arrangement
> observed in monomer 1 clashes when placed over monomer 2 (so at present can
> only average the small % of ASU between d3 copies). Critically, looking for
> a second d2 using MR fails but the lack of crystal contacts suggests
> success should be possibleits really unlikely that a third entity is in
> there (d1 and d2 are actually 50% similar, so by searching for d2 and
> failing, I'm actually missing three spots it could potentially occupy if
> the protein is not proteolysed)
>
>
> Sorry for long email but the devil is in the details. My question would
> be, what is best practice in a low res poor twinned dataset where you can
> only fill roughly just over half of what should be in there?
>
>
> Feel free to tell me its doomed!
>
>
> Best wishes & thanks in advance
>
> Andy
>
> --
>
> 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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[ccp4bb] Best protocols to advance a low resolution twinned MR map

2020-09-08 Thread Andrew Lovering

Dear all,


I've a project with two historical datasets (i.e. not sure of when/if I can 
reproduce to solve problem by getting better data) that are twinned.


The spacegroup is P32, with operator -h, -k, l

cell = 83.5 83.5 64.2 90 90 120


protein has three domains d1-d2-d3, likely 50% solvent, 2 copies in asu


dataset 1, roughly 3.6 angstrom resolution, twin fraction 0.25

dataset 2, roughly 3.1 angstrom resolution, twin fraction 0.4


I've managed to solve this (unambiguously) by finding a d3:d3 dimer in 
detwinned data, then seeing via phenix autobuild that it finds a d2 also in 
map. At present the ability to interpret the map further stalls there, and it 
can't be "the limit" because lack of crystal contacts suggest there should be 
more protein to find.


I realise I can go two ways, either using the detwinned data or using twinned 
data and supplying the operator.the former giving ridiculously optimistic 
R-values with a suspiciously "clean map", the latter giving noisier but maybe 
more informative maps.


Two-fold averaging is not going to be great because the d2-d3 arrangement 
observed in monomer 1 clashes when placed over monomer 2 (so at present can 
only average the small % of ASU between d3 copies). Critically, looking for a 
second d2 using MR fails but the lack of crystal contacts suggests success 
should be possibleits really unlikely that a third entity is in there (d1 
and d2 are actually 50% similar, so by searching for d2 and failing, I'm 
actually missing three spots it could potentially occupy if the protein is not 
proteolysed)


Sorry for long email but the devil is in the details. My question would be, 
what is best practice in a low res poor twinned dataset where you can only fill 
roughly just over half of what should be in there?


Feel free to tell me its doomed!


Best wishes & thanks in advance

Andy



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

2020-09-08 Thread 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

2020-09-08 Thread Georg Zocher


Dear Paul,

we have the same experience in our lab. 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.


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?


All the best,
Georg




Am 08.09.20 um 03:10 schrieb Paul Emsley:

Dear Eike,


This is not about me trying to convince you to change. I was pleased
with Coot 0.8.9.2 when I released it and I am pleased that you like it
too.  I was trying to express that *I* think that the refinement in
0.9.x is across the board better and I am not seeing the problems that
you see.

Instead, this is about me trying to find out what you (and others)
think is going wrong.  This is about turning your email into a useful
bug report.  What I've got now is "it does not work any more and I
don't like it" - and that is not helpful.

You mentioned that you had problem with a ligand complex. I tried to
investigate further by asking you if you were using Acedrg-Coot. You
didn't answer.

You suggest that atom clashes may be a problem. I tried to investigate
further by asking you if you noticed a problem with Coot's description
of non-bonded contacts. You didn't answer.

To be clear, these were not rhetorical questions, they were an attempt
to address the problems - or at least begin to do so.

What I need is an example of *what* is going wrong.  Just one example
would be a start.  It seems to me that if the problem is as pervasive
as you seem to think it is, then it shouldn't be difficult for you to
conjure up a problematic case.  This is the sort of thing that I want:

   This model is based on 1xyz from the PDB, except that I've adjusted
   the model to create a problem.  See the region of A501 - you can
   see that that model and the map do not correspond. It is hard for
   me to fix it in 0.9 because when I do X, Coot does Y, but in 0.8.9
   all I had to do was A, B and C.

It might be the case that Coot can trivially solve the problem, but
you don't know about it - and that might be because I have
insufficiently explained how to do it. Or made the means by which you
can do so too opaque. Or maybe you have to type something. At the
moment I have no clue.

Normally, I would have taken to private correspondence by now.  I
recognise that your primarily interest is the latest and greatest of
the 0.8 series, and you may think that this may not be worth your
effort, so if you don't do this perhaps some of the other frustrated
Coot users may do so? Hence the public continuation of our discussion.


Regards,


Paul.

On 07/09/2020 10:28, Schulz, Eike-Christian wrote:

Dear Paul,

Thanks for the detailed response. The reason for me being a bit 
annoyed is really simple: basic model building did work well in coot 
0.8.x and (for me and others) it does not work anymore in coot 0.9. 
Because I like coot (and because most computer problems are usually 
30cm in front of the screen) I have tried to get used to it for a few 
month, but on the weekend I have switched back to coot 0.8 *  –>  
problem(s) solved, what a relief.


I realize that I have not been particularly helpful in bug-fixing, 
but the changes appear to be rather comprehensive and thus I can only 
comment on the user experience. This is (naturally) a subjective 
experience but what I hear from my colleagues tells me that I am not 
alone with my frustration.


Try to look at it from my point of view:
-    the previous version of coot does what I want,
-    I see few advantages of the new version,
-    the basic functionality (that I am used to) appears to be gone 
in the new version.


Since I am not convinced - why should I switch ?

Best regards,

Eike


* thanks to Bill Scott for the pre-compiled mac-binaries 
http://scottlab.ucsc.edu/xtal/wiki/index.php/Stand-Alone_Coot


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

Reply to: Paul Emsley 
Date: Saturday, 5. September 2020 at 02:05
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] AW: Going back to 
Coot 0.8


 Dear Eike,

 Yes, it helps a little.

 Changing weights on switching refinement maps is inconvenient, 
but not a

 point of failure.

 Alternative conformations may need some assistance - pin an atom 
using

 anchoring.

 When Coot starts a refinement it tells you in the terminal about 
the bad

 bonds and non-bonded contacts that it found in the model. Do you
 perceive that to be wrong or missing interactions?

 There are many ways to skin a covalent ligand complex. I use the
 Acedrg-Coot interface (as described in my blog). Do you?

 If you wish, you can calculate an average map, the tool for that 
can

Re: [ccp4bb] Going back to Coot 0.8

2020-09-08 Thread Paul Emsley

Dear Veronica,

Sorry to re-open old thread (staycatation...)

I don't think that it's old - just slow.

glad for you listening to the feedback - much appreciated.

Thank you, fellow in-liner. All that top posting was causing me mental anguish.

I think the situation has arisen because Coot users are bringing previous
experience of using RSR into their
use of 0.9. Because the movement of the non-dragged atoms in 0.8.x was
rather unsophisticated, many people
learnt (I discovered, rather late in the day) to "flick" the dragged atom
with a large and fast movement to
get over a local energy barrier. (Needless to say, I hadn't intended for

This +1 (everyone using coot, that I know does it)

Hmmm, :-(

For myself, by using eigen-flip and jiggle fit beforehand and then by
combining pepflip, JED Flip and
backrub rotamer during RSR I often don't even need to pull on the atoms. By

Do you mean in the new version: instead of simple "drag - large and
fast movement to get over a local energy barrier" - you recommend to
do this above multiple steps? Sadly, it would be a great decrease in
usability.

That's not what I meant, yes that would be a decrease in usability. Let me have another go. Interactive real
space refinement is a technique to which one turns only if faster, more automated methods fail. Initial
rotation/translation means that I don't have to pull on an atom go to the right place, it just sinks in.
That makes things quicker. Likewise JED flipping and pep-flipping.

Regards,

Paul.

p.s. Anna asked a question recently about metal restraints in Refmac. In Coot, the Acedrg tables have been
used to extract target distances for metals (e.g. share/coot/data/metal/metal-O-distance.table) and they are
automatically applied to the current model. So one can drag on a coordinating water and the metal and the
other ligands come along for the ride. This is another reason why 0.9 refinement is better.

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

2020-09-08 Thread anna anna

I am glad to see that my question generated a useful discussion! I'm
definitely not the only one with these troubles... Having a program able to
generate specific restraints would be great!!

I think that my case is quite tricky because my protein, that seems to be
involved in zinc trafficking acting as an exchanger or a kind of sensor,
has a relatively low affinity for zinc (kd 1 uM). Binding sites are
exposed, coordination is tetrahedral with always 2 His and a Asp/Glu while
the fourth position varies, I modelled it as H2O or His in different sites
and monomers.
In this context, it is very difficult for me to obtain a reasonable
conformation after refinement, especially for His in the fourth position.
I guess the best thing I can do is trying to model it properly and run
refmac with 0 cycles.

Thank you,
Anna





Il giorno mar 8 set 2020 alle ore 12:59 Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> ha scritto:

> I guess I have lived with Zn since I first learnt what a crystal was - ZN
> is part of insulin secretion and whether it is or is not present is
> fundamental to the biochemistry..
>
> I agree things have to be handled case by case - For insulin the three HIS
> are generated by symmetry and that causes horrible headaches for any
> restraint dictionary..
> And for Jan's case the resolution is excellent and the main links very
> clear. (In fact they were not restrained but all distances finish up near
> to 2A as expected.)
> However maybe something can be learnt from this structure which would help
> the query which started us off!
> Eleanor
>
> On Tue, 8 Sep 2020 at 11:49, Robbie Joosten 
> wrote:
>
>> Hi Jan,
>>
>> If you want targets for your metal site you could have a look at MetalPDB
>> (http://metalweb.cerm.unifi.it/). That has good tools to find similar
>> sites and get some statistics you can use to generate case-specific
>> restraints.
>>
>> Cheers,
>> Robbie
>>
>> > -Original Message-
>> > From: CCP4 bulletin board  On Behalf Of Garib
>> > Murshudov
>> > Sent: Tuesday, September 8, 2020 12:44
>> > To: CCP4BB@JISCMAIL.AC.UK
>> > Subject: Re: [ccp4bb] metal coordination at low resolution - restraints
>> >
>> > Hi Jan,
>> >
>> >
>> >
>> >
>> >   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 form the active site of our enzyme.
>> >
>> >
>> > So,are they  involved in reaction?
>> >
>> >
>> >   Normally there is no need to restrain these, they "behave".
>> >
>> >   But in general having such standard "restraint angles" available
>> > would be of use, I agree.
>> >
>> >
>> >
>> > For tetrahedral Zn we do have “bonds” and “angles” between Zn and
>> > coordinating residues. For general solution we need a bit different
>> approach
>> > (e.g. coordination analysis).
>> >
>> >
>> >
>> > Regards
>> > Garib
>> >
>> >
>> >
>> >
>> >   Jan
>> >
>> >
>> >   On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov > > lmb.cam.ac.uk  > 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.
>> >
>> >   Regards
>> >   Garib
>> >
>> >
>> >
>> >   On 8 Sep 2020, at 11:11, Eleanor Dodson
>> > mailto:eleanor.dod...@york.ac.uk> > wrote:
>> >
>> >   Hmm - here is my problem - a list of ZN contacts
>> for
>> > the two molecules..
>> >   residue 602 is a phosphate, and there possibly
>> should
>> > be a few more waters ..
>> >   No idea how best to tackle it..
>> >   E
>> >
>> >
>> >Z  401 ZN   A   W   21 NA  2.057 X,Y,Z
>> > 1.008.73
>> >Z  401 ZN   A   W   21 OA  2.220 X,Y,Z
>> > 1.008.76
>> >Z  401 ZN   A   H   26 NE2  A  2.000 X,Y,Z
>> > 1.008.39
>> >Z  401 ZN   A   D  139 OD1  A  2.085 X,Y,Z
>> > 1.008.61
>> >Z  401 ZN   A   Z  601 O2   A  1.927 X,Y,Z
>> > 0.60   10.74
>> >Z  401 ZN   A   O  821 OC  2.006 X,Y,Z
>> > 0.407.51
>> >
>> >
>> >Z  402 ZN   A   H   80 ND1  A  2.033 X,Y,Z
>> > 1.008.94
>> >Z  402 ZN

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

2020-09-08 Thread Jan Dohnalek

It is the active site which is very well defined, with high occupancy and
tight binding.
We also have high resolution structures of these ..
However, restraints (for protein-metal contacs) were not necessary to
refine these sites. Atoms site where they should be ...

Jan


On Tue, Sep 8, 2020 at 2:08 PM Oganesyan, Vaheh <
vaheh.oganes...@astrazeneca.com> wrote:

> Hi Jan,
>
>
>
> They hold nice because of high occupancy or because you have very high
> resolution and no restraints are necessary at all (even for protein part)?
>
>
>
> Thank you
>
>
>
> Vaheh
>
>
>
> *From:* CCP4 bulletin board  * On Behalf Of *Jan
> Dohnalek
> *Sent:* Tuesday, September 8, 2020 8:01 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] metal coordination at low resolution - restraints
>
>
>
> 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.
>
>
>
> Regards
>
> Garib
>
>
>
>
>
> On 8 Sep 2020, at 11:11, Eleanor Dodson  wrote:
>
>
>
> Hmm - here is my problem - a list of ZN contacts for the two molecules..
>
> residue 602 is a phosphate, and there possibly should be a few more waters
> ..
>
> No idea how best to tackle it..
>
> E
>
>
>
>
>
>  Z  401 ZN   A   W   21 NA  2.057 X,Y,Z   1.00
> 8.73
>
>  Z  401 ZN   A   W   21 OA  2.220 X,Y,Z   1.00
> 8.76
>
>  Z  401 ZN   A   H   26 NE2  A  2.000 X,Y,Z   1.00
> 8.39
>
>  Z  401 ZN   A   D  139 OD1  A  2.085 X,Y,Z   1.00
> 8.61
>
>  Z  401 ZN   A   Z  601 O2   A  1.927 X,Y,Z   0.60
> 10.74
>
>  Z  401 ZN   A   O  821 OC  2.006 X,Y,Z   0.40
> 7.51
>
>
>
>  Z  402 ZN   A   H   80 ND1  A  2.033 X,Y,Z   1.00
> 8.94
>
>  Z  402 ZN   A   H  135 NE2  A  2.032 X,Y,Z   1.00
> 8.70
>
>  Z  402 ZN   A   D  139 OD2  A  2.024 X,Y,Z   1.00
> 8.70
>
>  Z  402 ZN   A   Z  601 O2   A  2.131 X,Y,Z   0.60
> 11.05
>
>  Z  402 ZN   A   O  821 OC  1.829 X,Y,Z   0.40
> 7.81
>
>
>
>  Z  403 ZN   A   H  145 NE2  A  2.027 X,Y,Z   1.00
> 10.50
>
>  Z  403 ZN   A   H  168 NE2  A  2.030 X,Y,Z   1.00
> 10.19
>
>  Z  403 ZN   A   D  172 OD2  A  2.062 X,Y,Z   1.00
> 12.66
>
>  Z  403 ZN   A   Z  601 O3   A  1.953 X,Y,Z   0.60
> 11.54
>
>  Z  403 ZN   A   O  820 OC  2.207 X,Y,Z   0.20
> 9.09
>
>  Z  403 ZN   A   O  822 OC  2.059 X,Y,Z   0.40
> 13.79
>
>
>
>  Z  401 ZN   A   Z  402 ZN   A  3.349 X,Y,Z   1.00
> 8.73
>
>
>
>
>
>  Z  401 ZN   B   W   21 NB  2.099 X,Y,Z   1.00
> 9.22
>
>  Z  401 ZN   B   W   21 OB  2.184 X,Y,Z   1.00
> 8.91
>
>  Z  401 ZN   B   H   26 NE2  B  2.009 X,Y,Z   1.00
> 8.79
>
>  Z  401 ZN   B   D  139 OD1  B  2.069 X,Y,Z   1.00
> 8.76
>
>  Z  401 ZN   B   Z  601 O3   B  1.981 X,Y,Z   0.70
> 9.31
>
>
>
>  Z  402 ZN   B   H   80 ND1  B  2.032 X,Y,Z   1.00
> 9.49
>
>  Z  402 ZN   B   H  135 NE2  B  2.024 X,Y,Z   1.00
> 9.22
>
>  Z  402 ZN   B   D  139 OD2  B  2.032 X,Y,Z   1.00
> 9.70
>
>  Z  402 ZN   B   Z  601 O3   B  1.973 X,Y,Z   0.70
> 9.58
>
>
>
>  Z  403 ZN   B   H  145 NE2  B  2.027 X,Y,Z   1.00
> 10.80
>
>  Z  403 ZN   B   H  168 NE2  B  2.029 X,Y,Z   1.00
> 10.65
>
>  Z  403 ZN   B   D  172 OD2  B  2.089 X,Y,Z   1.00
> 13.12
>
>  Z  403 ZN   B   Z  601 O4   B  1.938 X,Y,Z   0.70
> 14.10
>
>  Z  403 ZN   B   O  825 OC  2.322 X,Y,Z   0.20
> 10.61
>
> ~
>
>
>
>
> On Tue, 8 Sep 2020 at 10:47, Garib Murshudov 
> wrote:
>
> Hi Robbie

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

2020-09-08 Thread Oganesyan, Vaheh

Hi Jan,

They hold nice because of high occupancy or because you have very high 
resolution and no restraints are necessary at all (even for protein part)?

Thank you

Vaheh

From: CCP4 bulletin board  On Behalf Of Jan Dohnalek
Sent: Tuesday, September 8, 2020 8:01 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] metal coordination at low resolution - restraints

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 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 
mailto:ga...@mrc-lmb.cam.ac.uk>> 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.

Regards
Garib



On 8 Sep 2020, at 11:11, Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>> wrote:

Hmm - here is my problem - a list of ZN contacts for the two molecules..
residue 602 is a phosphate, and there possibly should be a few more waters ..
No idea how best to tackle it..
E


 Z  401 ZN   A   W   21 NA  2.057 X,Y,Z   1.008.73
 Z  401 ZN   A   W   21 OA  2.220 X,Y,Z   1.008.76
 Z  401 ZN   A   H   26 NE2  A  2.000 X,Y,Z   1.008.39
 Z  401 ZN   A   D  139 OD1  A  2.085 X,Y,Z   1.008.61
 Z  401 ZN   A   Z  601 O2   A  1.927 X,Y,Z   0.60   10.74
 Z  401 ZN   A   O  821 OC  2.006 X,Y,Z   0.407.51

 Z  402 ZN   A   H   80 ND1  A  2.033 X,Y,Z   1.008.94
 Z  402 ZN   A   H  135 NE2  A  2.032 X,Y,Z   1.008.70
 Z  402 ZN   A   D  139 OD2  A  2.024 X,Y,Z   1.008.70
 Z  402 ZN   A   Z  601 O2   A  2.131 X,Y,Z   0.60   11.05
 Z  402 ZN   A   O  821 OC  1.829 X,Y,Z   0.407.81

 Z  403 ZN   A   H  145 NE2  A  2.027 X,Y,Z   1.00   10.50
 Z  403 ZN   A   H  168 NE2  A  2.030 X,Y,Z   1.00   10.19
 Z  403 ZN   A   D  172 OD2  A  2.062 X,Y,Z   1.00   12.66
 Z  403 ZN   A   Z  601 O3   A  1.953 X,Y,Z   0.60   11.54
 Z  403 ZN   A   O  820 OC  2.207 X,Y,Z   0.209.09
 Z  403 ZN   A   O  822 OC  2.059 X,Y,Z   0.40   13.79

 Z  401 ZN   A   Z  402 ZN   A  3.349 X,Y,Z   1.008.73


 Z  401 ZN   B   W   21 NB  2.099 X,Y,Z   1.009.22
 Z  401 ZN   B   W   21 OB  2.184 X,Y,Z   1.008.91
 Z  401 ZN   B   H   26 NE2  B  2.009 X,Y,Z   1.008.79
 Z  401 ZN   B   D  139 OD1  B  2.069 X,Y,Z   1.008.76
 Z  401 ZN   B   Z  601 O3   B  1.981 X,Y,Z   0.709.31

 Z  402 ZN   B   H   80 ND1  B  2.032 X,Y,Z   1.009.49
 Z  402 ZN   B   H  135 NE2  B  2.024 X,Y,Z   1.009.22
 Z  402 ZN   B   D  139 OD2  B  2.032 X,Y,Z   1.009.70
 Z  402 ZN   B   Z  601 O3   B  1.973 X,Y,Z   0.709.58

 Z  403 ZN   B   H  145 NE2  B  2.027 X,Y,Z   1.00   10.80
 Z  403 ZN   B   H  168 NE2  B  2.029 X,Y,Z   1.00   10.65
 Z  403 ZN   B   D  172 OD2  B  2.089 X,Y,Z   1.00   13.12
 Z  403 ZN   B   Z  601 O4   B  1.938 X,Y,Z   0.70   14.10
 Z  403 ZN   B   O  825 OC  2.322 X,Y,Z   0.20   10.61
~

On Tue, 8 Sep 2020 at 10:47, Garib Murshudov 
mailto:ga...@mrc-lmb.cam.ac.uk>> wrote:
Hi Robbie and Eleanor

There are links for Zn-His and Zn-Cys. They meant to be used automatically, 
obviously something is not entirely right.

Link names are:
ZN-CYS

It has a bond between Zn and S as well as an angle:
ZN-CYS   1 ZN  2 SG  2 CB  109.0003.000

This also removes H of Cys to make covalent bond between Zn and Cys.

Similar links are available for Zn and His ND1 and Zn - HIS NE2
Link names are:

ZN-HISND
ZN-HISNE

Again these links have angles between Zn and atoms of His.

Angle centred at Zn is missing. But these distances and angles defined in the 
link it

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

2020-09-08 Thread Jan Dohnalek

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.
>
> Regards
> Garib
>
>
> On 8 Sep 2020, at 11:11, Eleanor Dodson  wrote:
>
> Hmm - here is my problem - a list of ZN contacts for the two molecules..
> residue 602 is a phosphate, and there possibly should be a few more waters
> ..
> No idea how best to tackle it..
> E
>
>
>  Z  401 ZN   A   W   21 NA  2.057 X,Y,Z   1.00
> 8.73
>  Z  401 ZN   A   W   21 OA  2.220 X,Y,Z   1.00
> 8.76
>  Z  401 ZN   A   H   26 NE2  A  2.000 X,Y,Z   1.00
> 8.39
>  Z  401 ZN   A   D  139 OD1  A  2.085 X,Y,Z   1.00
> 8.61
>  Z  401 ZN   A   Z  601 O2   A  1.927 X,Y,Z   0.60
> 10.74
>  Z  401 ZN   A   O  821 OC  2.006 X,Y,Z   0.40
> 7.51
>
>  Z  402 ZN   A   H   80 ND1  A  2.033 X,Y,Z   1.00
> 8.94
>  Z  402 ZN   A   H  135 NE2  A  2.032 X,Y,Z   1.00
> 8.70
>  Z  402 ZN   A   D  139 OD2  A  2.024 X,Y,Z   1.00
> 8.70
>  Z  402 ZN   A   Z  601 O2   A  2.131 X,Y,Z   0.60
> 11.05
>  Z  402 ZN   A   O  821 OC  1.829 X,Y,Z   0.40
> 7.81
>
>  Z  403 ZN   A   H  145 NE2  A  2.027 X,Y,Z   1.00
> 10.50
>  Z  403 ZN   A   H  168 NE2  A  2.030 X,Y,Z   1.00
> 10.19
>  Z  403 ZN   A   D  172 OD2  A  2.062 X,Y,Z   1.00
> 12.66
>  Z  403 ZN   A   Z  601 O3   A  1.953 X,Y,Z   0.60
> 11.54
>  Z  403 ZN   A   O  820 OC  2.207 X,Y,Z   0.20
> 9.09
>  Z  403 ZN   A   O  822 OC  2.059 X,Y,Z   0.40
> 13.79
>
>  Z  401 ZN   A   Z  402 ZN   A  3.349 X,Y,Z   1.00
> 8.73
>
>
>  Z  401 ZN   B   W   21 NB  2.099 X,Y,Z   1.00
> 9.22
>  Z  401 ZN   B   W   21 OB  2.184 X,Y,Z   1.00
> 8.91
>  Z  401 ZN   B   H   26 NE2  B  2.009 X,Y,Z   1.00
> 8.79
>  Z  401 ZN   B   D  139 OD1  B  2.069 X,Y,Z   1.00
> 8.76
>  Z  401 ZN   B   Z  601 O3   B  1.981 X,Y,Z   0.70
> 9.31
>
>  Z  402 ZN   B   H   80 ND1  B  2.032 X,Y,Z   1.00
> 9.49
>  Z  402 ZN   B   H  135 NE2  B  2.024 X,Y,Z   1.00
> 9.22
>  Z  402 ZN   B   D  139 OD2  B  2.032 X,Y,Z   1.00
> 9.70
>  Z  402 ZN   B   Z  601 O3   B  1.973 X,Y,Z   0.70
> 9.58
>
>  Z  403 ZN   B   H  145 NE2  B  2.027 X,Y,Z   1.00
> 10.80
>  Z  403 ZN   B   H  168 NE2  B  2.029 X,Y,Z   1.00
> 10.65
>  Z  403 ZN   B   D  172 OD2  B  2.089 X,Y,Z   1.00
> 13.12
>  Z  403 ZN   B   Z  601 O4   B  1.938 X,Y,Z   0.70
> 14.10
>  Z  403 ZN   B   O  825 OC  2.322 X,Y,Z   0.20
> 10.61
> ~
>
>
> On Tue, 8 Sep 2020 at 10:47, Garib Murshudov 
> wrote:
>
>> Hi Robbie and Eleanor
>>
>> There are links for Zn-His and Zn-Cys. They meant to be used
>> automatically, obviously something is not entirely right.
>>
>> Link names are:
>> ZN-CYS
>>
>> It has a bond between Zn and S as well as an angle:
>> ZN-CYS   1 ZN  2 SG  2 CB  109.0003.000
>>
>> This also removes H of Cys to make covalent bond between Zn and Cys.
>>
>> Similar links are available for Zn and His ND1 and Zn - HIS NE2
>> Link names are:
>>
>> ZN-HISND
>> ZN-HISNE
>>
>> Again these links have angles between Zn and atoms of His.
>>
>> Angle centred at Zn is missing. But these distances and angles defined in
>> the link it should work fine.
>>
>> Regards
>> Garib
>>
>>
>>
>> On 8 Sep 2020, at 10:40, Robbie Joosten 
>> wrote:
>>
>> Hi Elanor,
>>
>> The distances are in the dictionaries but the angles involve three
>> different residues so these cannot be in the current dictionary. We could
>> add the program that generates these restraints to CCP4

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

Yes, and the Zn is tetrahedral with a vacancy which makes then angles a bit 
more open. It's a good thing insulin makes nice crystals 

Cheers,
Robbie

> -Original Message-
> From: Eleanor Dodson 
> Sent: Tuesday, September 8, 2020 12:59
> To: Robbie Joosten 
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] metal coordination at low resolution - restraints
> 
> I guess I have lived with Zn since I first learnt what a crystal was - ZN is 
> part
> of insulin secretion and whether it is or is not present is fundamental to the
> biochemistry..
> 
> I agree things have to be handled case by case - For insulin the three HIS are
> generated by symmetry and that causes horrible headaches for any restraint
> dictionary..
> And for Jan's case the resolution is excellent and the main links very clear. 
> (In
> fact they were not restrained but all distances finish up near to 2A as
> expected.) However maybe something can be learnt from this structure
> which would help the query which started us off!
> Eleanor
> 
> On Tue, 8 Sep 2020 at 11:49, Robbie Joosten   > wrote:
> 
> 
>   Hi Jan,
> 
>   If you want targets for your metal site you could have a look at
> MetalPDB (http://metalweb.cerm.unifi.it/). That has good tools to find
> similar sites and get some statistics you can use to generate case-specific
> restraints.
> 
>   Cheers,
>   Robbie
> 
>   > -Original Message-
>   > From: CCP4 bulletin board   > On Behalf Of Garib
>   > Murshudov
>   > Sent: Tuesday, September 8, 2020 12:44
>   > To: CCP4BB@JISCMAIL.AC.UK 
>   > Subject: Re: [ccp4bb] metal coordination at low resolution -
> restraints
>   >
>   > Hi Jan,
>   >
>   >
>   >
>   >
>   >   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 form the active site of our enzyme.
>   >
>   >
>   > So,are they  involved in reaction?
>   >
>   >
>   >   Normally there is no need to restrain these, they "behave".
>   >
>   >   But in general having such standard "restraint angles" available
>   > would be of use, I agree.
>   >
>   >
>   >
>   > For tetrahedral Zn we do have “bonds” and “angles” between Zn
> and
>   > coordinating residues. For general solution we need a bit different
> approach
>   > (e.g. coordination analysis).
>   >
>   >
>   >
>   > Regards
>   > Garib
>   >
>   >
>   >
>   >
>   >   Jan
>   >
>   >
>   >   On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov> lmb.cam.ac.uk    lmb.cam.ac.uk  > > 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.
>   >
>   >   Regards
>   >   Garib
>   >
>   >
>   >
>   >   On 8 Sep 2020, at 11:11, Eleanor Dodson
>   >      > > wrote:
>   >
>   >   Hmm - here is my problem - a list of ZN 
> contacts for
>   > the two molecules..
>   >   residue 602 is a phosphate, and there possibly 
> should
>   > be a few more waters ..
>   >   No idea how best to tackle it..
>   >   E
>   >
>   >
>   >Z  401 ZN   A   W   21 NA  2.057 X,Y,Z
>   > 1.008.73
>   >Z  401 ZN   A   W   21 OA  2.220 X,Y,Z
>   > 1.008.76
>   >Z  401 ZN   A   H   26 NE2  A  2.000 X,Y,Z
>   > 1.008.39
>   >Z  401 ZN   A   D  139 OD1  A  2.085 X,Y,Z
>   > 1.008.61
>   >Z  401 ZN   A   Z  601 O2   A  1.927 X,Y,Z
>   > 0.60   10.74
>   >

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

I guess I have lived with Zn since I first learnt what a crystal was - ZN
is part of insulin secretion and whether it is or is not present is
fundamental to the biochemistry..

I agree things have to be handled case by case - For insulin the three HIS
are generated by symmetry and that causes horrible headaches for any
restraint dictionary..
And for Jan's case the resolution is excellent and the main links very
clear. (In fact they were not restrained but all distances finish up near
to 2A as expected.)
However maybe something can be learnt from this structure which would help
the query which started us off!
Eleanor

On Tue, 8 Sep 2020 at 11:49, Robbie Joosten 
wrote:

> Hi Jan,
>
> If you want targets for your metal site you could have a look at MetalPDB (
> http://metalweb.cerm.unifi.it/). That has good tools to find similar
> sites and get some statistics you can use to generate case-specific
> restraints.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board  On Behalf Of Garib
> > Murshudov
> > Sent: Tuesday, September 8, 2020 12:44
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] metal coordination at low resolution - restraints
> >
> > Hi Jan,
> >
> >
> >
> >
> >   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 form the active site of our enzyme.
> >
> >
> > So,are they  involved in reaction?
> >
> >
> >   Normally there is no need to restrain these, they "behave".
> >
> >   But in general having such standard "restraint angles" available
> > would be of use, I agree.
> >
> >
> >
> > For tetrahedral Zn we do have “bonds” and “angles” between Zn and
> > coordinating residues. For general solution we need a bit different
> approach
> > (e.g. coordination analysis).
> >
> >
> >
> > Regards
> > Garib
> >
> >
> >
> >
> >   Jan
> >
> >
> >   On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov  > lmb.cam.ac.uk  > 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.
> >
> >   Regards
> >   Garib
> >
> >
> >
> >   On 8 Sep 2020, at 11:11, Eleanor Dodson
> > mailto:eleanor.dod...@york.ac.uk> > wrote:
> >
> >   Hmm - here is my problem - a list of ZN contacts
> for
> > the two molecules..
> >   residue 602 is a phosphate, and there possibly
> should
> > be a few more waters ..
> >   No idea how best to tackle it..
> >   E
> >
> >
> >Z  401 ZN   A   W   21 NA  2.057 X,Y,Z
> > 1.008.73
> >Z  401 ZN   A   W   21 OA  2.220 X,Y,Z
> > 1.008.76
> >Z  401 ZN   A   H   26 NE2  A  2.000 X,Y,Z
> > 1.008.39
> >Z  401 ZN   A   D  139 OD1  A  2.085 X,Y,Z
> > 1.008.61
> >Z  401 ZN   A   Z  601 O2   A  1.927 X,Y,Z
> > 0.60   10.74
> >Z  401 ZN   A   O  821 OC  2.006 X,Y,Z
> > 0.407.51
> >
> >
> >Z  402 ZN   A   H   80 ND1  A  2.033 X,Y,Z
> > 1.008.94
> >Z  402 ZN   A   H  135 NE2  A  2.032 X,Y,Z
> > 1.008.70
> >Z  402 ZN   A   D  139 OD2  A  2.024 X,Y,Z
> > 1.008.70
> >Z  402 ZN   A   Z  601 O2   A  2.131 X,Y,Z
> > 0.60   11.05
> >Z  402 ZN   A   O  821 OC  1.829 X,Y,Z
> > 0.407.81
> >
> >
> >Z  403 ZN   A   H  145 NE2  A  2.027 X,Y,Z
> > 1.00   10.50
> >Z  403 ZN   A   H  168 NE2  A  2.030 X,Y,Z
> > 1.00   10.19
> >Z  403 ZN   A   D  172 OD2  A  2.062 X,Y,Z
> > 1.00   12.66
> >Z  403 ZN   A   Z  601 O3   A  1.953 X,Y,Z
> > 0.60   11.54
> >Z  403 ZN   A   O  820 OC  2.207 X,Y,Z
> > 0.209.09
> >Z  403 ZN   A   O  822 OC  2.059 X,Y,Z
> > 0.40   13.79
> >
> >
> >Z  401 ZN   A   Z  402 ZN   A  3.349 X,Y,Z
> > 1.008.73
> >
> >
> >
> >
> >Z  401 ZN   B   W   21 NB  2.099 X,Y,Z
> > 1.009.22
> >

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

Hi Jan,

If you want targets for your metal site you could have a look at MetalPDB 
(http://metalweb.cerm.unifi.it/). That has good tools to find similar sites and 
get some statistics you can use to generate case-specific restraints.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Garib
> Murshudov
> Sent: Tuesday, September 8, 2020 12:44
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] metal coordination at low resolution - restraints
> 
> Hi Jan,
> 
> 
> 
> 
>   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 form the active site of our enzyme.
> 
> 
> So,are they  involved in reaction?
> 
> 
>   Normally there is no need to restrain these, they "behave".
> 
>   But in general having such standard "restraint angles" available
> would be of use, I agree.
> 
> 
> 
> For tetrahedral Zn we do have “bonds” and “angles” between Zn and
> coordinating residues. For general solution we need a bit different approach
> (e.g. coordination analysis).
> 
> 
> 
> Regards
> Garib
> 
> 
> 
> 
>   Jan
> 
> 
>   On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov  lmb.cam.ac.uk  > 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.
> 
>   Regards
>   Garib
> 
> 
> 
>   On 8 Sep 2020, at 11:11, Eleanor Dodson
> mailto:eleanor.dod...@york.ac.uk> > wrote:
> 
>   Hmm - here is my problem - a list of ZN contacts for
> the two molecules..
>   residue 602 is a phosphate, and there possibly should
> be a few more waters ..
>   No idea how best to tackle it..
>   E
> 
> 
>Z  401 ZN   A   W   21 NA  2.057 X,Y,Z
> 1.008.73
>Z  401 ZN   A   W   21 OA  2.220 X,Y,Z
> 1.008.76
>Z  401 ZN   A   H   26 NE2  A  2.000 X,Y,Z
> 1.008.39
>Z  401 ZN   A   D  139 OD1  A  2.085 X,Y,Z
> 1.008.61
>Z  401 ZN   A   Z  601 O2   A  1.927 X,Y,Z
> 0.60   10.74
>Z  401 ZN   A   O  821 OC  2.006 X,Y,Z
> 0.407.51
> 
> 
>Z  402 ZN   A   H   80 ND1  A  2.033 X,Y,Z
> 1.008.94
>Z  402 ZN   A   H  135 NE2  A  2.032 X,Y,Z
> 1.008.70
>Z  402 ZN   A   D  139 OD2  A  2.024 X,Y,Z
> 1.008.70
>Z  402 ZN   A   Z  601 O2   A  2.131 X,Y,Z
> 0.60   11.05
>Z  402 ZN   A   O  821 OC  1.829 X,Y,Z
> 0.407.81
> 
> 
>Z  403 ZN   A   H  145 NE2  A  2.027 X,Y,Z
> 1.00   10.50
>Z  403 ZN   A   H  168 NE2  A  2.030 X,Y,Z
> 1.00   10.19
>Z  403 ZN   A   D  172 OD2  A  2.062 X,Y,Z
> 1.00   12.66
>Z  403 ZN   A   Z  601 O3   A  1.953 X,Y,Z
> 0.60   11.54
>Z  403 ZN   A   O  820 OC  2.207 X,Y,Z
> 0.209.09
>Z  403 ZN   A   O  822 OC  2.059 X,Y,Z
> 0.40   13.79
> 
> 
>Z  401 ZN   A   Z  402 ZN   A  3.349 X,Y,Z
> 1.008.73
> 
> 
> 
> 
>Z  401 ZN   B   W   21 NB  2.099 X,Y,Z
> 1.009.22
>Z  401 ZN   B   W   21 OB  2.184 X,Y,Z
> 1.008.91
>Z  401 ZN   B   H   26 NE2  B  2.009 X,Y,Z
> 1.008.79
>Z  401 ZN   B   D  139 OD1  B  2.069 X,Y,Z
> 1.008.76
>Z  401 ZN   B   Z  601 O3   B  1.981 X,Y,Z
> 0.709.31
> 
> 
>Z  402 ZN   B   H   80 ND1  B  2.032 X,Y,Z
> 1.009.49
>Z  402 ZN   B   H  135 NE2  B  2.024 X,Y,Z
> 1.009.22
>Z  402 ZN   B   D  139 OD2  B  2.032 X,Y,Z
> 1.009.70
>Z  402 ZN   B   Z  601 O3   B  1.973 X,Y,Z
> 0.709.58
> 
> 
>Z  403 ZN   B   H  145 NE2  B  2.027 X,Y,Z
> 1.00   10.80
>Z  403 ZN   B   H  168 NE2  B  2.029 X,Y,Z
> 1.00   10.65
>Z  403 ZN   B

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

Hi Jan,



> 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 form the active site of our enzyme.

So,are they  involved in reaction?

> Normally there is no need to restrain these, they "behave".
> 
> But in general having such standard "restraint angles" available would be of 
> use, I agree.


For tetrahedral Zn we do have “bonds” and “angles” between Zn and coordinating 
residues. For general solution we need a bit different approach (e.g. 
coordination analysis). 



Regards
Garib


> 
> 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.
> 
> Regards
> Garib
> 
> 
>> On 8 Sep 2020, at 11:11, Eleanor Dodson > > wrote:
>> 
>> Hmm - here is my problem - a list of ZN contacts for the two molecules..
>> residue 602 is a phosphate, and there possibly should be a few more waters 
>> .. 
>> No idea how best to tackle it..
>> E
>> 
>> 
>>  Z  401 ZN   A   W   21 NA  2.057 X,Y,Z   1.00
>> 8.73
>>  Z  401 ZN   A   W   21 OA  2.220 X,Y,Z   1.00
>> 8.76
>>  Z  401 ZN   A   H   26 NE2  A  2.000 X,Y,Z   1.00
>> 8.39
>>  Z  401 ZN   A   D  139 OD1  A  2.085 X,Y,Z   1.00
>> 8.61
>>  Z  401 ZN   A   Z  601 O2   A  1.927 X,Y,Z   0.60   
>> 10.74
>>  Z  401 ZN   A   O  821 OC  2.006 X,Y,Z   0.40
>> 7.51
>> 
>>  Z  402 ZN   A   H   80 ND1  A  2.033 X,Y,Z   1.00
>> 8.94
>>  Z  402 ZN   A   H  135 NE2  A  2.032 X,Y,Z   1.00
>> 8.70
>>  Z  402 ZN   A   D  139 OD2  A  2.024 X,Y,Z   1.00
>> 8.70
>>  Z  402 ZN   A   Z  601 O2   A  2.131 X,Y,Z   0.60   
>> 11.05
>>  Z  402 ZN   A   O  821 OC  1.829 X,Y,Z   0.40
>> 7.81
>> 
>>  Z  403 ZN   A   H  145 NE2  A  2.027 X,Y,Z   1.00   
>> 10.50
>>  Z  403 ZN   A   H  168 NE2  A  2.030 X,Y,Z   1.00   
>> 10.19
>>  Z  403 ZN   A   D  172 OD2  A  2.062 X,Y,Z   1.00   
>> 12.66
>>  Z  403 ZN   A   Z  601 O3   A  1.953 X,Y,Z   0.60   
>> 11.54
>>  Z  403 ZN   A   O  820 OC  2.207 X,Y,Z   0.20
>> 9.09
>>  Z  403 ZN   A   O  822 OC  2.059 X,Y,Z   0.40   
>> 13.79
>> 
>>  Z  401 ZN   A   Z  402 ZN   A  3.349 X,Y,Z   1.00
>> 8.73
>> 
>> 
>>  Z  401 ZN   B   W   21 NB  2.099 X,Y,Z   1.00
>> 9.22
>>  Z  401 ZN   B   W   21 OB  2.184 X,Y,Z   1.00
>> 8.91
>>  Z  401 ZN   B   H   26 NE2  B  2.009 X,Y,Z   1.00
>> 8.79
>>  Z  401 ZN   B   D  139 OD1  B  2.069 X,Y,Z   1.00
>> 8.76
>>  Z  401 ZN   B   Z  601 O3   B  1.981 X,Y,Z   0.70
>> 9.31
>> 
>>  Z  402 ZN   B   H   80 ND1  B  2.032 X,Y,Z   1.00
>> 9.49
>>  Z  402 ZN   B   H  135 NE2  B  2.024 X,Y,Z   1.00
>> 9.22
>>  Z  402 ZN   B   D  139 OD2  B  2.032 X,Y,Z   1.00
>> 9.70
>>  Z  402 ZN   B   Z  601 O3   B  1.973 X,Y,Z   0.70
>> 9.58
>> 
>>  Z  403 ZN   B   H  145 NE2  B  2.027 X,Y,Z   1.00   
>> 10.80
>>  Z  403 ZN   B   H  168 NE2  B  2.029 X,Y,Z   1.00   
>> 10.65
>>  Z  403 ZN   B   D  172 OD2  B  2.089 X,Y,Z   1.00   
>> 13.12
>>  Z  403 ZN   B   Z  601 O4   B  1.938 X,Y,Z   0.70   
>> 14.10
>>  Z  403 ZN   B   O  825 OC  2.322 X,Y,Z   0.20   
>> 10.61
>> ~
>>   
>> 
>> On Tue, 8 Sep 2020 at 10:47, Garib Murshudov > > wrote:
>> Hi Robbie and Eleanor
>> 
>> There are links for Zn-His and Zn-Cys. They meant to be used automatically, 
>> obviously something is not entirely right.
>> 
>> Link names are:
>> ZN-CYS
>> 
>> It has a bond between Zn and S as well as an angle:  
>> ZN-CYS   1 ZN  2 SG  2 CB  109.0003.000
>> 
>> This also removes H of Cys to make covalent bond between Zn and Cys.
>> 
>> Similar links are available for Zn and His ND1 and Zn - HIS NE2

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

2020-09-08 Thread Jan Dohnalek

These are structural.
They form the active site of our enzyme.
Normally there is no need to restrain these, they "behave".

But in general having such standard "restraint angles" available would be
of use, I agree.

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.
>
> Regards
> Garib
>
>
> On 8 Sep 2020, at 11:11, Eleanor Dodson  wrote:
>
> Hmm - here is my problem - a list of ZN contacts for the two molecules..
> residue 602 is a phosphate, and there possibly should be a few more waters
> ..
> No idea how best to tackle it..
> E
>
>
>  Z  401 ZN   A   W   21 NA  2.057 X,Y,Z   1.00
> 8.73
>  Z  401 ZN   A   W   21 OA  2.220 X,Y,Z   1.00
> 8.76
>  Z  401 ZN   A   H   26 NE2  A  2.000 X,Y,Z   1.00
> 8.39
>  Z  401 ZN   A   D  139 OD1  A  2.085 X,Y,Z   1.00
> 8.61
>  Z  401 ZN   A   Z  601 O2   A  1.927 X,Y,Z   0.60
> 10.74
>  Z  401 ZN   A   O  821 OC  2.006 X,Y,Z   0.40
> 7.51
>
>  Z  402 ZN   A   H   80 ND1  A  2.033 X,Y,Z   1.00
> 8.94
>  Z  402 ZN   A   H  135 NE2  A  2.032 X,Y,Z   1.00
> 8.70
>  Z  402 ZN   A   D  139 OD2  A  2.024 X,Y,Z   1.00
> 8.70
>  Z  402 ZN   A   Z  601 O2   A  2.131 X,Y,Z   0.60
> 11.05
>  Z  402 ZN   A   O  821 OC  1.829 X,Y,Z   0.40
> 7.81
>
>  Z  403 ZN   A   H  145 NE2  A  2.027 X,Y,Z   1.00
> 10.50
>  Z  403 ZN   A   H  168 NE2  A  2.030 X,Y,Z   1.00
> 10.19
>  Z  403 ZN   A   D  172 OD2  A  2.062 X,Y,Z   1.00
> 12.66
>  Z  403 ZN   A   Z  601 O3   A  1.953 X,Y,Z   0.60
> 11.54
>  Z  403 ZN   A   O  820 OC  2.207 X,Y,Z   0.20
> 9.09
>  Z  403 ZN   A   O  822 OC  2.059 X,Y,Z   0.40
> 13.79
>
>  Z  401 ZN   A   Z  402 ZN   A  3.349 X,Y,Z   1.00
> 8.73
>
>
>  Z  401 ZN   B   W   21 NB  2.099 X,Y,Z   1.00
> 9.22
>  Z  401 ZN   B   W   21 OB  2.184 X,Y,Z   1.00
> 8.91
>  Z  401 ZN   B   H   26 NE2  B  2.009 X,Y,Z   1.00
> 8.79
>  Z  401 ZN   B   D  139 OD1  B  2.069 X,Y,Z   1.00
> 8.76
>  Z  401 ZN   B   Z  601 O3   B  1.981 X,Y,Z   0.70
> 9.31
>
>  Z  402 ZN   B   H   80 ND1  B  2.032 X,Y,Z   1.00
> 9.49
>  Z  402 ZN   B   H  135 NE2  B  2.024 X,Y,Z   1.00
> 9.22
>  Z  402 ZN   B   D  139 OD2  B  2.032 X,Y,Z   1.00
> 9.70
>  Z  402 ZN   B   Z  601 O3   B  1.973 X,Y,Z   0.70
> 9.58
>
>  Z  403 ZN   B   H  145 NE2  B  2.027 X,Y,Z   1.00
> 10.80
>  Z  403 ZN   B   H  168 NE2  B  2.029 X,Y,Z   1.00
> 10.65
>  Z  403 ZN   B   D  172 OD2  B  2.089 X,Y,Z   1.00
> 13.12
>  Z  403 ZN   B   Z  601 O4   B  1.938 X,Y,Z   0.70
> 14.10
>  Z  403 ZN   B   O  825 OC  2.322 X,Y,Z   0.20
> 10.61
> ~
>
>
> On Tue, 8 Sep 2020 at 10:47, Garib Murshudov 
> wrote:
>
>> Hi Robbie and Eleanor
>>
>> There are links for Zn-His and Zn-Cys. They meant to be used
>> automatically, obviously something is not entirely right.
>>
>> Link names are:
>> ZN-CYS
>>
>> It has a bond between Zn and S as well as an angle:
>> ZN-CYS   1 ZN  2 SG  2 CB  109.0003.000
>>
>> This also removes H of Cys to make covalent bond between Zn and Cys.
>>
>> Similar links are available for Zn and His ND1 and Zn - HIS NE2
>> Link names are:
>>
>> ZN-HISND
>> ZN-HISNE
>>
>> Again these links have angles between Zn and atoms of His.
>>
>> Angle centred at Zn is missing. But these distances and angles defined in
>> the link it should work fine.
>>
>> Regards
>> Garib
>>
>>
>>
>> On 8 Sep 2020, at 10:40, Robbie Joosten 
>> wrote:
>>
>> Hi Elanor,
>>
>> The distances are in the dictionaries but the angles involve three
>> different residues so these cannot be in the current dictionary. We could
>> add the program that generates these restraints to CCP4 though.
>>
>> Cheers,
>> Robbie
>>
>> -Original Message-
>> From: Eleanor Dodson 
>> Sent: Tuesday, September 8, 2020 11:38
>> To: Robbie Joosten ; Garib N Murshudov
>> 
>> Cc: CCP4BB@JISCMAIL.AC.UK; Robert Nicholls > lmb.cam.ac.uk>
>> Subject: Re: [ccp4bb] metal coordination at low resolution - restraints
>>
>> Robbie - could

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

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.

Regards
Garib


> On 8 Sep 2020, at 11:11, Eleanor Dodson  wrote:
> 
> Hmm - here is my problem - a list of ZN contacts for the two molecules..
> residue 602 is a phosphate, and there possibly should be a few more waters .. 
> No idea how best to tackle it..
> E
> 
> 
>  Z  401 ZN   A   W   21 NA  2.057 X,Y,Z   1.008.73
>  Z  401 ZN   A   W   21 OA  2.220 X,Y,Z   1.008.76
>  Z  401 ZN   A   H   26 NE2  A  2.000 X,Y,Z   1.008.39
>  Z  401 ZN   A   D  139 OD1  A  2.085 X,Y,Z   1.008.61
>  Z  401 ZN   A   Z  601 O2   A  1.927 X,Y,Z   0.60   10.74
>  Z  401 ZN   A   O  821 OC  2.006 X,Y,Z   0.407.51
> 
>  Z  402 ZN   A   H   80 ND1  A  2.033 X,Y,Z   1.008.94
>  Z  402 ZN   A   H  135 NE2  A  2.032 X,Y,Z   1.008.70
>  Z  402 ZN   A   D  139 OD2  A  2.024 X,Y,Z   1.008.70
>  Z  402 ZN   A   Z  601 O2   A  2.131 X,Y,Z   0.60   11.05
>  Z  402 ZN   A   O  821 OC  1.829 X,Y,Z   0.407.81
> 
>  Z  403 ZN   A   H  145 NE2  A  2.027 X,Y,Z   1.00   10.50
>  Z  403 ZN   A   H  168 NE2  A  2.030 X,Y,Z   1.00   10.19
>  Z  403 ZN   A   D  172 OD2  A  2.062 X,Y,Z   1.00   12.66
>  Z  403 ZN   A   Z  601 O3   A  1.953 X,Y,Z   0.60   11.54
>  Z  403 ZN   A   O  820 OC  2.207 X,Y,Z   0.209.09
>  Z  403 ZN   A   O  822 OC  2.059 X,Y,Z   0.40   13.79
> 
>  Z  401 ZN   A   Z  402 ZN   A  3.349 X,Y,Z   1.008.73
> 
> 
>  Z  401 ZN   B   W   21 NB  2.099 X,Y,Z   1.009.22
>  Z  401 ZN   B   W   21 OB  2.184 X,Y,Z   1.008.91
>  Z  401 ZN   B   H   26 NE2  B  2.009 X,Y,Z   1.008.79
>  Z  401 ZN   B   D  139 OD1  B  2.069 X,Y,Z   1.008.76
>  Z  401 ZN   B   Z  601 O3   B  1.981 X,Y,Z   0.709.31
> 
>  Z  402 ZN   B   H   80 ND1  B  2.032 X,Y,Z   1.009.49
>  Z  402 ZN   B   H  135 NE2  B  2.024 X,Y,Z   1.009.22
>  Z  402 ZN   B   D  139 OD2  B  2.032 X,Y,Z   1.009.70
>  Z  402 ZN   B   Z  601 O3   B  1.973 X,Y,Z   0.709.58
> 
>  Z  403 ZN   B   H  145 NE2  B  2.027 X,Y,Z   1.00   10.80
>  Z  403 ZN   B   H  168 NE2  B  2.029 X,Y,Z   1.00   10.65
>  Z  403 ZN   B   D  172 OD2  B  2.089 X,Y,Z   1.00   13.12
>  Z  403 ZN   B   Z  601 O4   B  1.938 X,Y,Z   0.70   14.10
>  Z  403 ZN   B   O  825 OC  2.322 X,Y,Z   0.20   10.61
> ~ 
>  
> 
> On Tue, 8 Sep 2020 at 10:47, Garib Murshudov  > wrote:
> Hi Robbie and Eleanor
> 
> There are links for Zn-His and Zn-Cys. They meant to be used automatically, 
> obviously something is not entirely right.
> 
> Link names are:
> ZN-CYS
> 
> It has a bond between Zn and S as well as an angle:  
> ZN-CYS   1 ZN  2 SG  2 CB  109.0003.000
> 
> This also removes H of Cys to make covalent bond between Zn and Cys.
> 
> Similar links are available for Zn and His ND1 and Zn - HIS NE2
> Link names are:
> 
> ZN-HISND
> ZN-HISNE
> 
> Again these links have angles between Zn and atoms of His.
> 
> Angle centred at Zn is missing. But these distances and angles defined in the 
> link it should work fine.
> 
> Regards
> Garib
> 
> 
> 
>> On 8 Sep 2020, at 10:40, Robbie Joosten > > wrote:
>> 
>> Hi Elanor,
>> 
>> The distances are in the dictionaries but the angles involve three different 
>> residues so these cannot be in the current dictionary. We could add the 
>> program that generates these restraints to CCP4 though.
>> 
>> Cheers,
>> Robbie
>> 
>>> -Original Message-
>>> From: Eleanor Dodson >> >
>>> Sent: Tuesday, September 8, 2020 11:38
>>> To: Robbie Joosten >> >; Garib N Murshudov
>>> mailto:ga...@mrc-lmb.cam.ac.uk>>
>>> Cc: CCP4BB@JISCMAIL.AC.UK ; Robert Nicholls 
>>> >> lmb.cam.ac.uk >
>>> Subject: Re: [ccp4bb] metal coordination at

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

Hmm - here is my problem - a list of ZN contacts for the two molecules..
residue 602 is a phosphate, and there possibly should be a few more waters
..
No idea how best to tackle it..
E


 Z  401 ZN   A   W   21 NA  2.057 X,Y,Z   1.00
8.73

 Z  401 ZN   A   W   21 OA  2.220 X,Y,Z   1.00
8.76

 Z  401 ZN   A   H   26 NE2  A  2.000 X,Y,Z   1.00
8.39

 Z  401 ZN   A   D  139 OD1  A  2.085 X,Y,Z   1.00
8.61

 Z  401 ZN   A   Z  601 O2   A  1.927 X,Y,Z   0.60
10.74

 Z  401 ZN   A   O  821 OC  2.006 X,Y,Z   0.40
7.51


 Z  402 ZN   A   H   80 ND1  A  2.033 X,Y,Z   1.00
8.94

 Z  402 ZN   A   H  135 NE2  A  2.032 X,Y,Z   1.00
8.70

 Z  402 ZN   A   D  139 OD2  A  2.024 X,Y,Z   1.00
8.70

 Z  402 ZN   A   Z  601 O2   A  2.131 X,Y,Z   0.60
11.05

 Z  402 ZN   A   O  821 OC  1.829 X,Y,Z   0.40
7.81


 Z  403 ZN   A   H  145 NE2  A  2.027 X,Y,Z   1.00
10.50

 Z  403 ZN   A   H  168 NE2  A  2.030 X,Y,Z   1.00
10.19

 Z  403 ZN   A   D  172 OD2  A  2.062 X,Y,Z   1.00
12.66

 Z  403 ZN   A   Z  601 O3   A  1.953 X,Y,Z   0.60
11.54

 Z  403 ZN   A   O  820 OC  2.207 X,Y,Z   0.20
9.09

 Z  403 ZN   A   O  822 OC  2.059 X,Y,Z   0.40
13.79


 Z  401 ZN   A   Z  402 ZN   A  3.349 X,Y,Z   1.00
8.73



 Z  401 ZN   B   W   21 NB  2.099 X,Y,Z   1.00
9.22

 Z  401 ZN   B   W   21 OB  2.184 X,Y,Z   1.00
8.91

 Z  401 ZN   B   H   26 NE2  B  2.009 X,Y,Z   1.00
8.79

 Z  401 ZN   B   D  139 OD1  B  2.069 X,Y,Z   1.00
8.76

 Z  401 ZN   B   Z  601 O3   B  1.981 X,Y,Z   0.70
9.31


 Z  402 ZN   B   H   80 ND1  B  2.032 X,Y,Z   1.00
9.49

 Z  402 ZN   B   H  135 NE2  B  2.024 X,Y,Z   1.00
9.22

 Z  402 ZN   B   D  139 OD2  B  2.032 X,Y,Z   1.00
9.70

 Z  402 ZN   B   Z  601 O3   B  1.973 X,Y,Z   0.70
9.58


 Z  403 ZN   B   H  145 NE2  B  2.027 X,Y,Z   1.00
10.80

 Z  403 ZN   B   H  168 NE2  B  2.029 X,Y,Z   1.00
10.65

 Z  403 ZN   B   D  172 OD2  B  2.089 X,Y,Z   1.00
13.12

 Z  403 ZN   B   Z  601 O4   B  1.938 X,Y,Z   0.70
14.10

 Z  403 ZN   B   O  825 OC  2.322 X,Y,Z   0.20
10.61

~


On Tue, 8 Sep 2020 at 10:47, Garib Murshudov 
wrote:

> Hi Robbie and Eleanor
>
> There are links for Zn-His and Zn-Cys. They meant to be used
> automatically, obviously something is not entirely right.
>
> Link names are:
> ZN-CYS
>
> It has a bond between Zn and S as well as an angle:
> ZN-CYS   1 ZN  2 SG  2 CB  109.0003.000
>
> This also removes H of Cys to make covalent bond between Zn and Cys.
>
> Similar links are available for Zn and His ND1 and Zn - HIS NE2
> Link names are:
>
> ZN-HISND
> ZN-HISNE
>
> Again these links have angles between Zn and atoms of His.
>
> Angle centred at Zn is missing. But these distances and angles defined in
> the link it should work fine.
>
> Regards
> Garib
>
>
>
> On 8 Sep 2020, at 10:40, Robbie Joosten 
> wrote:
>
> Hi Elanor,
>
> The distances are in the dictionaries but the angles involve three
> different residues so these cannot be in the current dictionary. We could
> add the program that generates these restraints to CCP4 though.
>
> Cheers,
> Robbie
>
> -Original Message-
> From: Eleanor Dodson 
> Sent: Tuesday, September 8, 2020 11:38
> To: Robbie Joosten ; Garib N Murshudov
> 
> Cc: CCP4BB@JISCMAIL.AC.UK; Robert Nicholls  lmb.cam.ac.uk>
> Subject: Re: [ccp4bb] metal coordination at low resolution - restraints
>
> Robbie - could that be added to the distributed dictionaries? Zn binding is
> common and at low resolution distance restraints are not enough..
> Eleanor
>
> On Tue, 8 Sep 2020 at 10:33, Robbie Joosten   > wrote:
>
>
> Hi Anna,
>
> Yes you can do this in Refmac by adding external restraints. If you
> have structural Zinc sites (Zn coordinated by 4 histidines or cysteines)
>  you
> can also use PDB-REDO to generate the restraints automatically. The
> restraints are written to the output so you can continue using them in
> Refmac.
>
> HTH,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board   > On Behalf Of anna
> > anna
> > Sent: Tuesday, September 8, 2020 11:28
> > To: CCP4BB@JISCMAIL.AC.UK  >
> > Subject: [ccp4bb] metal coordination at low resolution - restraints
> >
> > Dear all,
> >
> > quickly: is there a way to restrain metal coordination geometry
> (even angles)
> > in refmac?
>

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

Hi Robbie and Eleanor

There are links for Zn-His and Zn-Cys. They meant to be used automatically, 
obviously something is not entirely right.

Link names are:
ZN-CYS

It has a bond between Zn and S as well as an angle:  
ZN-CYS   1 ZN  2 SG  2 CB  109.0003.000

This also removes H of Cys to make covalent bond between Zn and Cys.

Similar links are available for Zn and His ND1 and Zn - HIS NE2
Link names are:

ZN-HISND
ZN-HISNE

Again these links have angles between Zn and atoms of His.

Angle centred at Zn is missing. But these distances and angles defined in the 
link it should work fine.

Regards
Garib



> On 8 Sep 2020, at 10:40, Robbie Joosten  wrote:
> 
> Hi Elanor,
> 
> The distances are in the dictionaries but the angles involve three different 
> residues so these cannot be in the current dictionary. We could add the 
> program that generates these restraints to CCP4 though.
> 
> Cheers,
> Robbie
> 
>> -Original Message-
>> From: Eleanor Dodson 
>> Sent: Tuesday, September 8, 2020 11:38
>> To: Robbie Joosten ; Garib N Murshudov
>> 
>> Cc: CCP4BB@JISCMAIL.AC.UK; Robert Nicholls > lmb.cam.ac.uk>
>> Subject: Re: [ccp4bb] metal coordination at low resolution - restraints
>> 
>> Robbie - could that be added to the distributed dictionaries? Zn binding is
>> common and at low resolution distance restraints are not enough..
>> Eleanor
>> 
>> On Tue, 8 Sep 2020 at 10:33, Robbie Joosten >  > wrote:
>> 
>> 
>>  Hi Anna,
>> 
>>  Yes you can do this in Refmac by adding external restraints. If you
>> have structural Zinc sites (Zn coordinated by 4 histidines or cysteines)  you
>> can also use PDB-REDO to generate the restraints automatically. The
>> restraints are written to the output so you can continue using them in
>> Refmac.
>> 
>>  HTH,
>>  Robbie
>> 
>>  > -Original Message-
>>  > From: CCP4 bulletin board >  > On Behalf Of anna
>>  > anna
>>  > Sent: Tuesday, September 8, 2020 11:28
>>  > To: CCP4BB@JISCMAIL.AC.UK 
>>  > Subject: [ccp4bb] metal coordination at low resolution - restraints
>>  >
>>  > Dear all,
>>  >
>>  > quickly: is there a way to restrain metal coordination geometry
>> (even angles)
>>  > in refmac?
>>  >
>>  > I am refining a low resolution structure (3.3A) with 2 zinc binding
>> sites.
>>  > I am pretty sure about metal position (strong anomalous signal)
>> and what
>>  > are the residues involved in coordination since I solved the apo-
>> structure at
>>  > good resolution and Zn-binding does not induce huge structural
>> variations.
>>  > However, as you can imagine, electron density is poorly defined
>> and Refmac
>>  > gives a very distorted coordination geometry.
>>  > I noticed that in phenix it is possible to generate restraints with
>> readyset but
>>  > I'd like to work with refmac.
>>  >
>>  > Many thanks for your suggestions.
>>  >
>>  > Cheers,
>>  > Anna
>>  >
>>  > 
>>  >
>>  >
>>  > To unsubscribe from the CCP4BB list, click the following link:
>>  > https://www.jiscmail.ac.uk/cgi-bin/WA-
>> JISC.exe?SUBED1=CCP4BB=1
>> 
>> 
>>  
>> 
>> 
>>  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
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>> 
> 




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

That seems an excellent idea - I have been struggling with a Zn complex in
a ineffectual way and something like that would help,
Eleanor

On Tue, 8 Sep 2020 at 10:40, Robbie Joosten 
wrote:

> Hi Elanor,
>
> The distances are in the dictionaries but the angles involve three
> different residues so these cannot be in the current dictionary. We could
> add the program that generates these restraints to CCP4 though.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: Eleanor Dodson 
> > Sent: Tuesday, September 8, 2020 11:38
> > To: Robbie Joosten ; Garib N Murshudov
> > 
> > Cc: CCP4BB@JISCMAIL.AC.UK; Robert Nicholls  > lmb.cam.ac.uk>
> > Subject: Re: [ccp4bb] metal coordination at low resolution - restraints
> >
> > Robbie - could that be added to the distributed dictionaries? Zn binding
> is
> > common and at low resolution distance restraints are not enough..
> > Eleanor
> >
> > On Tue, 8 Sep 2020 at 10:33, Robbie Joosten  >  > wrote:
> >
> >
> >   Hi Anna,
> >
> >   Yes you can do this in Refmac by adding external restraints. If you
> > have structural Zinc sites (Zn coordinated by 4 histidines or
> cysteines)  you
> > can also use PDB-REDO to generate the restraints automatically. The
> > restraints are written to the output so you can continue using them in
> > Refmac.
> >
> >   HTH,
> >   Robbie
> >
> >   > -Original Message-
> >   > From: CCP4 bulletin board  >  > On Behalf Of anna
> >   > anna
> >   > Sent: Tuesday, September 8, 2020 11:28
> >   > To: CCP4BB@JISCMAIL.AC.UK 
> >   > Subject: [ccp4bb] metal coordination at low resolution -
> restraints
> >   >
> >   > Dear all,
> >   >
> >   > quickly: is there a way to restrain metal coordination geometry
> > (even angles)
> >   > in refmac?
> >   >
> >   > I am refining a low resolution structure (3.3A) with 2 zinc
> binding
> > sites.
> >   > I am pretty sure about metal position (strong anomalous signal)
> > and what
> >   > are the residues involved in coordination since I solved the apo-
> > structure at
> >   > good resolution and Zn-binding does not induce huge structural
> > variations.
> >   > However, as you can imagine, electron density is poorly defined
> > and Refmac
> >   > gives a very distorted coordination geometry.
> >   > I noticed that in phenix it is possible to generate restraints
> with
> > readyset but
> >   > I'd like to work with refmac.
> >   >
> >   > Many thanks for your suggestions.
> >   >
> >   > Cheers,
> >   > Anna
> >   >
> >   > 
> >   >
> >   >
> >   > To unsubscribe from the CCP4BB list, click the following link:
> >   > https://www.jiscmail.ac.uk/cgi-bin/WA-
> > JISC.exe?SUBED1=CCP4BB=1
> >
> >
> >   
> > 
> >
> >   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
> > available at https://www.jiscmail.ac.uk/policyandsecurity/
> >
>
>



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Re: [ccp4bb] Going back to Coot 0.8

2020-09-08 Thread V F

Dear Paul,
Sorry to re-open old thread (staycatation...)

glad for you listening to the feedback - much appreciated.

> I think the situation has arisen because Coot users are bringing previous
> experience of using RSR into their
> use of 0.9. Because the movement of the non-dragged atoms in 0.8.x was
> rather unsophisticated, many people
> learnt (I discovered, rather late in the day) to "flick" the dragged atom
> with a large and fast movement to
> get over a local energy barrier. (Needless to say, I hadn't intended for

This +1 (everyone using coot, that I know does it)



> For myself, by using eigen-flip and jiggle fit beforehand and then by
> combining pepflip, JED Flip and
> backrub rotamer during RSR I often don't even need to pull on the atoms. By


Do you mean in the new version: instead of simple "drag - large and
fast movement to  get over a local energy barrier" - you recommend to
do this above multiple steps? Sadly, it would be a great decrease in
usability.

Best regards,
Vero

PS: I still have not used the new version.




> adding in interactive contact
> dots, I can see what it is that's causing Coot to not move the atom to where
> I'm trying to drag it (the NBCs
> have been re-paramaterized and up-weighted in the 0.9.x rewrite). I have,
> from time to time in the past
> year, used Coot 0.8.x and to me it now feels painfully crippled. RSR in Coot
> 0.9.x is joyfully expeditious
> and pleasingly animated.
>
> For now (which is to say, before Coot 0.9.1 is available) I suggest keeping
> an eye out for unsatisfied atom
> pull restraints, and using the "Clear Pull Restraints" at moments of
> confusion. Also, use less flick and
> more smoothness when dragging atoms. For example, a 180 degree rotation of
> the ribose from the Coot tutorial
> would be difficult, if not impossible using 0.8.x, but in 0.9.x one can pull
> on the hydrogen atom of the O5'
> to rotate it in a few seconds. I have added a (rather poor) video of me
> doing just that to my channel (I
> should make a better video).
>
> With all that said, I am still listening - I will add a change shortly that
> will make the pull atom
> restraints more obvious by making them fatter, pinker and more opaque. If
> there are still problems and you
> could somehow make a screencast available to me that illustrates the
> problem, then I would be very
> interested to view it.
>
> Regards,
>
> Paul.
>
>
> On 04/09/2020 10:05, Schreuder, Herman /DE wrote:
>> Dear Paul,
>>
>> Here I fully agree with Eike. With the real space refinement in the new
>> coot the ligand often goes
>> everywhere, except where it should go. Changing the Xray weight helps
>> sometimes, but not always. In many
>> cases I do not real-space refine and leave it to Buster to do the
>> refinement. It would be very good if the
>> old behavior could be reinstalled.
>>
>> Best regards,
>>
>> Herman
>>
>> *Von:*CCP4 bulletin board  *Im Auftrag von *Schulz,
>> Eike-Christian
>> *Gesendet:* Freitag, 4. September 2020 10:36
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* [EXTERNAL] [ccp4bb] Going back to Coot 0.8
>>
>> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
>> 
>>
>> Dear Paul,
>>
>> I have been working with coot for over 10 years now with little reason to
>> complain.
>>
>> However, in spite of trying for a few months now, I am not getting warm
>> with coot 0.9.
>>
>> I like the new eye-candy, and the more organized menus. But fitting
>> residues and ligands into ED, has never
>> before been so difficult, and frankly it annoys me that previously simple
>> tasks have become an effort. It
>> seems as if coot and I see different minima and we always disagree where
>> to put the residue. At the moment
>> all my data are at convenient resolutions of 1.7Å or better, so there is
>> little ambiguity on that side.
>>
>> I am using all default settings, but maybe there is something that needs
>> to be changed?
>>
>>   * Is there a way to go back to the old (0.8-style) fitting functions in
>> coot 0.9? If so how?
>>   * If not, which of the last coot versions
>>
>> (https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/
>>
>> )
>> would you recommend?
>>
>> With best regards,
>>
>> Eike
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>

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

Hi Elanor,

The distances are in the dictionaries but the angles involve three different 
residues so these cannot be in the current dictionary. We could add the program 
that generates these restraints to CCP4 though.

Cheers,
Robbie

> -Original Message-
> From: Eleanor Dodson 
> Sent: Tuesday, September 8, 2020 11:38
> To: Robbie Joosten ; Garib N Murshudov
> 
> Cc: CCP4BB@JISCMAIL.AC.UK; Robert Nicholls  lmb.cam.ac.uk>
> Subject: Re: [ccp4bb] metal coordination at low resolution - restraints
> 
> Robbie - could that be added to the distributed dictionaries? Zn binding is
> common and at low resolution distance restraints are not enough..
> Eleanor
> 
> On Tue, 8 Sep 2020 at 10:33, Robbie Joosten   > wrote:
> 
> 
>   Hi Anna,
> 
>   Yes you can do this in Refmac by adding external restraints. If you
> have structural Zinc sites (Zn coordinated by 4 histidines or cysteines)  you
> can also use PDB-REDO to generate the restraints automatically. The
> restraints are written to the output so you can continue using them in
> Refmac.
> 
>   HTH,
>   Robbie
> 
>   > -Original Message-
>   > From: CCP4 bulletin board   > On Behalf Of anna
>   > anna
>   > Sent: Tuesday, September 8, 2020 11:28
>   > To: CCP4BB@JISCMAIL.AC.UK 
>   > Subject: [ccp4bb] metal coordination at low resolution - restraints
>   >
>   > Dear all,
>   >
>   > quickly: is there a way to restrain metal coordination geometry
> (even angles)
>   > in refmac?
>   >
>   > I am refining a low resolution structure (3.3A) with 2 zinc binding
> sites.
>   > I am pretty sure about metal position (strong anomalous signal)
> and what
>   > are the residues involved in coordination since I solved the apo-
> structure at
>   > good resolution and Zn-binding does not induce huge structural
> variations.
>   > However, as you can imagine, electron density is poorly defined
> and Refmac
>   > gives a very distorted coordination geometry.
>   > I noticed that in phenix it is possible to generate restraints with
> readyset but
>   > I'd like to work with refmac.
>   >
>   > Many thanks for your suggestions.
>   >
>   > Cheers,
>   > Anna
>   >
>   > 
>   >
>   >
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> 
>   
> 
> 
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Re: [ccp4bb] metal coordination at low resolution - restraints

Robbie - could that be added to the distributed dictionaries? Zn binding is
common and at low resolution distance restraints are not enough..
Eleanor

On Tue, 8 Sep 2020 at 10:33, Robbie Joosten 
wrote:

> Hi Anna,
>
> Yes you can do this in Refmac by adding external restraints. If you have
> structural Zinc sites (Zn coordinated by 4 histidines or cysteines)  you
> can also use PDB-REDO to generate the restraints automatically. The
> restraints are written to the output so you can continue using them in
> Refmac.
>
> HTH,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board  On Behalf Of anna
> > anna
> > Sent: Tuesday, September 8, 2020 11:28
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] metal coordination at low resolution - restraints
> >
> > Dear all,
> >
> > quickly: is there a way to restrain metal coordination geometry (even
> angles)
> > in refmac?
> >
> > I am refining a low resolution structure (3.3A) with 2 zinc binding
> sites.
> > I am pretty sure about metal position (strong anomalous signal) and what
> > are the residues involved in coordination since I solved the
> apo-structure at
> > good resolution and Zn-binding does not induce huge structural
> variations.
> > However, as you can imagine, electron density is poorly defined and
> Refmac
> > gives a very distorted coordination geometry.
> > I noticed that in phenix it is possible to generate restraints with
> readyset but
> > I'd like to work with refmac.
> >
> > Many thanks for your suggestions.
> >
> > Cheers,
> > Anna
> >
> > 
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] metal coordination at low resolution - restraints