Re: [ccp4bb] Conserved water

[Andres Libreros]

Thanks everyone for the tips. Actually, I need this information to improve my 
analysis on drug/protein interaction.
Best regards:)

Gerardo A. Libreros
Universidade de São Paulo
Laboratório de Biologia Estrutural Aplicada

Sent from my iPhone

> On 7 Jun 2017, at 18:34, Jared Sampson  wrote:
> 
> Hi Gerardo - 
> 
> Something based on distance alone (and not e.g. H-bonding network) could be 
> done in a straightforward fashion in PyMOL:
> 
> select close_wats, (object1 and solvent) within 1 of (object2 and solvent)
> hide everything, solvent
> as nb_spheres, close_wats
> 
> This would give you only the waters in object 1, but you could expand this 
> logic and include the object2 waters as well.
> 
> select close_wats, close_wats or ((object2 and solvent) within 1 of 
> (object1 and solvent))
> 
> Hope that helps.
> 
> Cheers,
> Jared
> 
> 
>> On Jun 6, 2017, at 7:30 PM, gerardo andres 
>> <130afa955101-dmarc-requ...@jiscmail.ac.uk> wrote:
>> 
>> Hi everyone, does anyone know any strategy or program (besides pywater) to 
>> identify conserved waters in a protein?
>> 
>> Thanks, 
>> 
>> Gerardo
> 

Re: [ccp4bb] Conserved water

[Edward A. Berry]

Easiest way is to line up molecule pairs or chain pairs in COOT and see if 
there are equivalent waters.


If the number of waters is too large to inspect manually,
save the superposed structures to disk, grep out the waters from each into a 
separate files,
and use a program like http://www.cytbc1.com/berry/for/pdbdist3w.for
to compare files and write atoms closer than a specified threshold into a new 
pdb file

That program only compares two files, so you would have to do all possible 
pairs to get waters conserved
in at least 2 structures, or compare each file with the survivors from previous 
to get waters
conserved in all.
PS- It compiles with f77 (g77). May need touch-up for fortran90 (gfortran).
eab

On 06/07/2017 02:59 AM, Eleanor Dodson wrote:

Many years ago I wrote code to label waters with a code related to the 
residue/atom  they were Hbonded to , so then you could check whether all OH TYR 
227 in each chain  had an associated water.. But it used non-standard water 
naming ..

Easiest way is to line up molecule pairs or chain pairs in COOT and see if 
there are equivalent waters.

Eleanor

On 7 June 2017 at 00:30, gerardo andres <130afa955101-dmarc-requ...@jiscmail.ac.uk 
> wrote:

Hi everyone, does anyone know any strategy or program (besides pywater) to 
identify conserved waters in a protein?

Thanks,

Gerardo

Re: [ccp4bb] Conserved water

[benjamin bax]

How about 
WONKA and OOMMPPAA: analysis of protein–ligand interaction data to direct 
structure-based drug design?
Ben 



On 7 Jun 2017, at 07:59, Eleanor Dodson  wrote:

Many years ago I wrote code to label waters with a code related to the 
residue/atom  they were Hbonded to , so then you could check whether all OH TYR 
227 in each chain  had an associated water.. But it used non-standard water 
naming ..

Easiest way is to line up molecule pairs or chain pairs in COOT and see if 
there are equivalent waters.

Eleanor

On 7 June 2017 at 00:30, gerardo andres 
<130afa955101-dmarc-requ...@jiscmail.ac.uk 
> wrote:
Hi everyone, does anyone know any strategy or program (besides pywater) to 
identify conserved waters in a protein?

Thanks, 

Gerardo



Dr Ben Bax

York Structural Biology Laboratory, 
Department of Chemistry, 
University of York,
York YO10 5DD

ben.d.v@gmail.com

 

 

Re: [ccp4bb] Conserved water

[Eleanor Dodson]

Many years ago I wrote code to label waters with a code related to the
residue/atom  they were Hbonded to , so then you could check whether all OH
TYR 227 in each chain  had an associated water.. But it used non-standard
water naming ..

Easiest way is to line up molecule pairs or chain pairs in COOT and see if
there are equivalent waters.

Eleanor

On 7 June 2017 at 00:30, gerardo andres <
130afa955101-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi everyone, does anyone know any strategy or program (besides pywater) to
> identify conserved waters in a protein?
>
> Thanks,
>
> Gerardo
>

[ccp4bb] Conserved water

[gerardo andres]

Hi everyone, does anyone know any strategy or program (besides pywater) to 
identify conserved waters in a protein?
Thanks, 
Gerardo

[ccp4bb] Conserved water positions in low resolution refinement?

[Guenter Fritz]

Dear all,
and especially all of you involved in the development of refinement 
programs,
in low resolution refinement we always include structural information we 
actually do not see in the electron density (side chains, riding 
hydrogens) since we know that these atoms are there. But what about 
water molecules?
The inner shell water molecules are often tightly bound and reside on 
conserved positions.
I made a simple test and repeated a couple of refinement runs (refmac 
using the high res structure as ref model) with  or without water 
molecules. Indeed most water molecules stay almost at the same position 
and R factors using an input file with water molecules are significantly 
lower.


Shall we use such information in the future in low resolution refinement?

And if we decide to do so, are there already good tools to evaluate and 
find conserved water positions maybe even by comparison of closely 
related structures?


Best regards,
Guenter

Re: [ccp4bb] RE : [ccp4bb] Conserved water positions in low resolution refinement?

[Guenter Fritz]

Hi Sacha,
thanks a lot. I hadn't expected that the effect of missing  water 
molecules would be so severe.


Best, Guenter

Dear Guenter,

please look at at Fig. 7. It numerically confirms some of your worries.

Best regards,

Sacha

De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Guenter Fritz 
[guenter.fr...@uni-konstanz.de]
Date d'envoi : samedi 2 novembre 2013 16:04
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Conserved water positions in low resolution refinement?

Dear all,
and especially all of you involved in the development of refinement
programs,
in low resolution refinement we always include structural information we
actually do not see in the electron density (side chains, riding
hydrogens) since we know that these atoms are there. But what about
water molecules?