Re: [ccp4bb] EM maps

[Christine Gee]

Hi,

I had a similar problem with a map crashing coot and pymol while it opened
fine in chimera. There was some kind of discrepancy in the file header and
the file size (slightly too small), but running through mapmask solved the
issue. I can't claim to have figured that out. James Holton showed me the
fix. If interested, the mapmask command is echo scale factor 1 | mapmask
mapin emdproblemmap.map mapout fixedemdproblemmap.map

Regards
Christine

On Fri, Mar 8, 2024 at 7:54 AM Paul Emsley 
wrote:

>
> On 08/03/2024 10:47, Dean Derbyshire wrote:
>
>
>
> Hi, I’m almost certain this has been addressed before so apologies… but is
> there a trick to import EM map files into COOT, it keeps crashing when I’ve
> tried.
>
>
>
>
> My guess is that your computer is running out of memory. A pint into a
> quart port? Sometime EM maps can be multi-gigs. And there was a memory leak
> that I discovered just last week in fact.
>
>
> It's somewhat disappointing that Coot crashes rather than giving you a
> useful error message. Are you using the latest and greatest in the 0.9.x
> series?
>
>
> (The patch has not been back-ported to the 0.9.x series. I should do that
> before the release of 0.9.8.94.)
>
>
> Regards,
>
> Paul.
>
>
>
> --
>
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Re: [ccp4bb] interesting map problem

[Christine Gee]

Hi Eleanor,

I wonder if in fact this is the problem. I of course didn't think properly
about it. The cell is the same, sort of, and I think you have put your
finger on my error. It is the same data more or less, I was reprocessing a
dataset, to slightly higher resolution using the same images as for the
reference .mtz. The reference dataset was output from aimless (or whatever
package they used) with the default a
wrote:

> Well - that should not happen!
> Are the cell dimensions the same for the new data and the reference set?
> E
>
> On Fri, 17 Dec 2021 at 22:04, Christine Gee  wrote:
>
>> Hi,
>>
>> I recently came across this strange issue. I was using aimless in CCP4 to
>> scale my data and apply an Rfree from a reference .mtz
>>
>> Neither the reference or the file I was working with had higher
>> resolution than 1.5
>> However aimless wrote out h, k, l and Rfree to 0.4. I did not click the
>> button to extend resolution by the way.
>>
>> No big deal right? Well Coot then assumed the resolution was 0.4 and
>> wrote out maps to super high resolution and everything took forever to
>> render, making coot basically unuseable.
>>
>> I could not find any global or local parameter in coot that seemed to
>> remedy this.
>>
>> Did anyone come across anything similar? What is the solution besides
>> editing the resolution of the .mtz file output from aimless and what
>> program woud you recommend for this?
>>
>> My simple solution for now was to use an .mtz file output from aimless
>> that a reference Rfree was not applied to.
>>
>> Regards
>> Christine
>>
>>
>> --
>>
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[ccp4bb] interesting map problem

[Christine Gee]

Hi,

I recently came across this strange issue. I was using aimless in CCP4 to
scale my data and apply an Rfree from a reference .mtz

Neither the reference or the file I was working with had higher resolution
than 1.5
However aimless wrote out h, k, l and Rfree to 0.4. I did not click the
button to extend resolution by the way.

No big deal right? Well Coot then assumed the resolution was 0.4 and wrote
out maps to super high resolution and everything took forever to render,
making coot basically unuseable.

I could not find any global or local parameter in coot that seemed to
remedy this.

Did anyone come across anything similar? What is the solution besides
editing the resolution of the .mtz file output from aimless and what
program woud you recommend for this?

My simple solution for now was to use an .mtz file output from aimless that
a reference Rfree was not applied to.

Regards
Christine



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[ccp4bb] post-doc position

[Christine Gee]

Dear all,

The Kuriyan Lab at UC Berkeley is looking for a post-doc interested in
using Next Generation Sequencing and deep mutagenesis to investigate
function and allostery. The job posting can be found here.
https://www.nature.com/naturecareers/job/postdoctoral-associate-kuriyan-lab-howard-hughes-medical-institute-hhmi-744080
If you know a suitable candidate please forward them the information.

Regards
Christine



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Re: [ccp4bb] cation-aromatic database

[Christine Gee]

Hi Stephan,

It seems to be online at the following

http://cmm.osdd.net/gnsmmg/databases/cad/

Regards
Christine


On Tue, Apr 20, 2021 at 12:27 PM stephen.c...@rc-harwell.ac.uk <
stephen.c...@rc-harwell.ac.uk> wrote:

> Dear BB,
>
> Does anyone know if the cation-aromatic database (Reddy, 2007, Prot Sci)
> is still available?  The link listed in the manuscript (
> http://203.199.182.73/gnsmmg/databases/cad/) no longer appears to work.
>
> Thanks,
> Steve
>
> Dr Stephen Carr
> Research Complex at Harwell (RCaH)
> Rutherford Appleton Laboratory
> Harwell Oxford
> Didcot
> Oxon OX11 0FA
> United Kingdom
> Email stephen.c...@rc-harwell.ac.uk
> tel 01235 567717
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Re: [ccp4bb] Linux Distro for setting up workstations - Is CentOS still a good choice?

[Christine Gee]

Hi all,

We use Debian and SBGRID. We have coot and pymol running in stereo with 3D 
vision glasses. 
If that’s helpful. 

Regards
Christine. 

Sent from my iPad

> On Feb 20, 2021, at 7:57 AM, Paul Emsley  wrote:
> 
> FWIW, looks like somebody at ETH Zurich is (or had been) trying to bring 
> Coot into the OS:
> 
> http://phd-sid.ethz.ch/debian/coot/coot-0.9.2/
> 
> Hello! Let me know if I can help.
> 
> Paul.
> 
> 
>> On 20/02/2021 15:35, Tim Gruene wrote:
>> Hi Matthias,
>> 
>> I have been using Debian for more than a decade. Every stable release
>> is supported for at least 5 years.
>> Many crystallographic libraries and some programs are part of the
>> standard repository, like raster3d, pymol, shelxle, libccp4,
>> libclipper, ...
>> 
>> Debian is particularly stable, and requires little maintenance.
>> 
>> Cheers,
>> Tim
>> 
>> On Fri, 19 Feb 2021 21:35:46 +0100
>> Matthias Zeug  wrote:
>> 
>>> Hi all,
>>> 
>>> 
>>> 
>>> I just came across the (already quite old) news that Red-Hat switches
>>> their support-policy for CentOS to a rolling preview model (replacing
>>> CentOS Linux by CentOS Stream):
>>> 
>>> https://www.zdnet.com/article/why-red-hat-dumped-centos-for-centos-stream/
>>> 
>>> https://www.enterpriseai.news/2021/01/22/red-hats-disruption-of-centos-unlea
>>> shes-storm-of-dissent/
>>> 
>>> 
>>> 
>>> I wondered if that has any implications for the community, as
>>> scientific programs - maybe except the big ones like coot, Phenix,
>>> and ccp4 - are often not *that* well maintained for an extended
>>> period. I had the impression CentOS was liked especially for its
>>> "unbreakability,"  and it seems to be the main developing platform
>>> for some widely used smaller programs (e.g., adxv).
>>> 
>>> 
>>> 
>>> Do you think it would be advisable to switch to a Ubuntu-distro when
>>> setting up new workstations in the future, or is it safe to stick to
>>> CentOS?
>>> 
>>> 
>>> 
>>> Please let me know what you think :-)
>>> 
>>> 
>>> 
>>> Best,
>>> 
>>> 
>>> 
>>> Matthias
>>> 
>>> 
>>> 
>>> 
>>> 
>>> Matthias Zeug
>>> 
>>> Buchmann Institute of Molecular Life Sciences
>>> 
>>> Goethe University Frankfurt
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
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>> 
> 
> 
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Re: [ccp4bb] Tyr pushed out during refinement

[Christine Gee]

Dear Michael
I would carefully check the backbone region around the tyrosine and make sure 
it’s correct as errors there might be the issue.
Regards
Christine 

Sent from my iPhone

> On Oct 19, 2020, at 11:52 AM, Boniecki, Michal  
> wrote:
> 
> 
> Hello,
> I have a problem during refining with one of the Tyr residues. It is 
> constantly pushed out of the position during refinement in all 4 chains in 
> ASU.
> I have tried to exclude it from refinement in phenix but it is refined anyway 
> out of the position with wrong geometry. Is there a possibility to fix it 
> during refinement?
> The closest contact it has, is 2.4A between hydroxyl group and C=O of Pro, 
> but Tyr itself is inside hydrophobic cleft (Ile,Pro,Leu)
> Thank You for all help. Stay safe,
> Michal
> 
> 
> 
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Re: [ccp4bb] [Off-Topic] 3D Vision stereo with Ubuntu 18.04

[Christine Gee]

Hi Chris
We have it working with the Mate desktop. Composite disabled. Let me know if 
you would like more details
Regards
Christine. 

Sent from my iPad

> On Nov 8, 2019, at 4:18 AM, Chris Richardson  
> wrote:
> 
> Apologies for the only slightly relevant question.
> 
> Does anyone know the correct incantations to get nVidia 3D Vision glasses and 
> emitter working with Ubuntu 18.04?
> 
> None of the tricks that work with 16.04 are helping with the new release.  In 
> particular, disabling composite in the extensions makes the display blank 
> while X11 restarts itself every few seconds.
> 
> Thanks in advance,
> 
> Chris
> -- 
> Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk
> 
> 
> 
> 
> 
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
> Limited by Guarantee, Registered in England under Company No. 534147 with its 
> Registered Office at 123 Old Brompton Road, London SW7 3RP.
> 
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> 
> 
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Re: [ccp4bb] ORCID being mandatory for PDB depositions

[Christine Gee]

Hi all,

I just submitted a PDB deposition where two of the deposition authors did
not have an ORCID and it went through fine. As long as the corresponding
author (ie the person submitting the PDB) and the PI has the ID I think it
will work.

Regards
Christine



On Tue, Apr 9, 2019 at 8:34 AM Mark J van Raaij 
wrote:

> to be honest, I would want to be an author on the paper (especially in a
> "glossy" :-)), but perhaps not on all the database entries...only the ones
> I actively contributed to.
> I agree being on the paper involves accepting responsibility for all the
> work, and often it is impossible to really be fully responsible, because it
> would imply checking (i.e. redoing) much of it, but at least in the paper
> byline it should say who did what, giving some "safety" if something turns
> out wrong with the omics or the mice, but the structure(s) being fine.
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij
> Section Editor of Acta Crystallographica F, Structural Biology
> Communications
> http://journals.iucr.org/f/
>
>
> On 9 Apr 2019, at 17:22, Phoebe A. Rice  wrote:
>
> Very good point, and a good argument against the current trend of
> publications in the glossies including everything from mice to omics to
> structure all in one manuscript with one set of authors.  Especially since
> it is being pointed out more vociferously these days (as it should be) that
> accepting authorship implies accepting responsibility.
>
>- Phoebe
>
>
> *From: *CCP4 bulletin board  on behalf of Mark J
> van Raaij 
> *Reply-To: *Mark J van Raaij 
> *Date: *Tuesday, April 9, 2019 at 9:32 AM
> *To: *"CCP4BB@JISCMAIL.AC.UK" 
> *Subject: *Re: [ccp4bb] ORCID being mandatory for PDB depositions
>
> There is something to be said for not everyone being an author of the PDB
> entry anyway.
> If I were a non structural biologist who for example had made and tested
> some essential knock-out mice for the paper, I might prefer not to be an
> author of the PDB entry in case there was something wrong with it (which I
> might not necessarily be able to judge).
> Similarly, as a structural biologist I might prefer not to be on the
> knock-out mice database entry in case there was something wrong or
> unethical in the way the mice were made...
>
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://wwwuser.cnb.csic.es/~mjvanraaij
> Section Editor of Acta Crystallographica F, Structural Biology
> Communications
> http://journals.iucr.org/f/
>
>
> On 9 Apr 2019, at 14:49, Robbie Joosten 
> wrote:
>
> Than it is easy enough. You mustn't create an ORCid for others, this could
> indeed get you into GDPR trouble as you are sharing personal data without
> consent.
>
> So that leaves the practical bit. If deposition requires an ORCid and a
> collaborator does not have an ORCid despite your requests, then that
> collaborator cannot be a depositor. Let the record show that this is not
> your fault as your hands are tied here.
>
> HTH,
> Robbie
>
> On Apr 9, 2019 14:33, V F  wrote:
>
> On 09/04/2019, Mark J van Raaij  wrote:
> > Perhaps the poster is referring to the legality of creating an ORCID on
> > behalf of the collaborator?
>
> Yes that is what I meant. (English not my first language)!
>
> > That is how I interpreted it - but perhaps I over-interpreted...
> >
> > Another thing that came to my mind, not everyone has to be an author of
> the
> > PDB structure. Often all the authors of the corresponding paper are also
> on
> > the PDB entry, and there is nothing wrong with that, but if a
> > (non-crystallographer?) collaborator really doesn't want an ORCID, he or
> she
> > doesn't have to be an author of the PDB entry.
> >
> >
> > Mark J van Raaij
> > Dpto de Estructura de Macromoleculas
> > Centro Nacional de Biotecnologia - CSIC
> > calle Darwin 3
> > E-28049 Madrid, Spain
> > tel. (+34) 91 585 4616
> > http://wwwuser.cnb.csic.es/~mjvanraaij
> > Section Editor of Acta Crystallographica F, Structural Biology
> > Communications
> > http://journals.iucr.org/f/
> >
> >
> >> On 9 Apr 2019, at 14:20, Anastassis Perrakis  wrote:
>
> >>
> >> I am wondering, are there any arguments that would suggest that ORCID is
>
> >> not in line with GDPR requirements? You are disclosing your name etc to
>
> >> the PDB anyway, does it matter if its through ORCID or not?
> >>
> >> Tassos
> >>
> >>
> >>> On Apr 9, 2019, at 14:04, V F  wrote:
> >>>
> >>> Dear all,
> >>> Did anyone observe that oneDep from EBI made ORCID mandatory for
> >>> deposition? What am I supposed to do if my collaborators do not want
> >>> to create ORCID? (especially with GDPR I do not want to create ORCID)
> >>> Just posting here so that some one will respond? my mails are going to
>
> >>> /dev/null?
> 

Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

[Christine Gee]

Hi Adarsh,

As others have commented, you need your IR emitter to be connected to the
P4000 graphics card through the 3 pin connector to get stereo with the
vision 2 glasses unless you have a screen with a built in emitter. We
recently set up a system using a Quadro P4000 and the additional 3 pin
connector (which we bought with the P4000).
If it helps, we also use the MATE instead of GNOME desktop. And in the
/etc/X11/xorg.conf file you will need to add set the stereo option to 10,
at least we did with our ASUS ROG PG278QR monitor and we also set composite
to disable. Please reach out if you would like any more information.
Regards
Christine



On Thu, Dec 20, 2018 at 12:46 PM Adarsh Kumar 
wrote:

> Hello everyone
>
> We have just purchased a Dell workstation for crystallography data
> analysis. We were trying to use Nvidia 3D vision 2 glasses with it, but
> failed to do so. Please help me out with this one. Some relevant
> information is as follows:
> OS: Ubuntu 16.04 LTS
> Graphics : Quadro P4000 (unfortunately doesn't have a 3-pin DIN socket)
> Monitor: Asus VG248QE
>
> Thanks and regards
> Adarsh Kumar
> Suo Lab
> Florida State University College of Medicine
>
> 
>
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Re: [ccp4bb] suggestions for cryoprotectant

[Christine Gee]

Dear Fridous

Have a look at https://www.ncbi.nlm.nih.gov/pubmed/14646118
Malonate as a cryoprotectant

Or https://www.ncbi.nlm.nih.gov/pubmed/20606259

Regards
Christine

On Fri, Oct 19, 2018 at 2:57 PM Firdous Tarique 
wrote:

> Dear members
>
> I have got beautiful crystal hits in SaltRx screens which are not
> diffracting to a good resoultion. All of them are salt based condition and
> I am not able to formulate a good cryoprotectant for these crystals. I also
> think that in my case the poor resolution is due to a poor cryoprotectant
> selection.
>
> The conditions are as follows:
>
> 1> 4M Ammonium Acetate 100mM Bis Tris Propane pH 7.0
> 2>0.5M KCN 100mM Tris pH8.5
> 3>1.5M LiSo4 100mM Bris Tris Propane pH 7.0
> 4>4M Sodium Nitrate 100mM Tris pH8.5
> 5>1.5M Sodium Nitrate 100mM Sodium acetate pH 4.6
>
> There are few more conditions but so far not able to see good diffraction
> with using lower peg and glycerol based cryoprotectants.
>
> Can anybody suggest me good cryos conditions for salt based
> crystallization conditions or anything good for SaltRx crystallization hits.
>
> Thanks
>
> Firdous
>
> --
>
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[ccp4bb] 3D stereo and pymol

[Christine Gee]

Hi,

I have looked in the archive for posts about this, but there hasn't been
one for about a year. Can anyone comment on whether they have managed to
get a linux flavor and GeForce cards to work with pymol and/or coot 3D
stereo? Geforce cards supposedly support openGL, but posts from October
last year on the BB suggests that it only works in windows unless you have
a monitor with a built in emitter. I would appreciate any feedback.

Regards
Christine

Re: [ccp4bb] Stable Refinement as Low(ish) resolution

[Christine Gee]

Hi Rhys,

In Refmac, you can change the weighting of the Xray terms vs the geometry
restraints rather than use what is automatically assigned. Have you tried
this? In Phenix you can use secondary structure restraints (probably you
can do this in Refmac too, but I haven't tried) and try checking the box
optimize stereochemistry/Xray weight. This will probably help if your over
fitting is moving things into density but making the geometry sub optimal.

Regards
Christine

On Wed, Jul 12, 2017 at 4:17 PM, Rhys Grinter 
wrote:

> Dear All,
>
> I'm currently in the process of refining a low(ish) resolution structure
> at 3.2 Ang, with a fair level of anisotropy. I processed the data through
> the anisotropy server (https://services.mbi.ucla.edu/anisoscale/), which
> elliptically truncated the data to 4.0, 3.8 and 3.2 Ang. This really
> improved the maps and allowed me to trace the majority of the chain and
> build most side chains.
>
> The R-factors are reasonable (0.29 work and 0.35 free respectively). but
> I'm having trouble with over fitting in refinement as I continue to refine.
> What parameters/restraints would the community generally use when refining
> this kind of structure? Additionally Refmac doesn't seem to read the
> structure factors from the anisotropy server output file properly, giving
> vastly inflated R values and strange looking maps.
>
> Cheers,
>
> Rhys
>
> --
> Dr Rhys Grinter
> Sir Henry Wellcome Fellow
> Monash University
> +61 (0)3 9902 9213 <+61%203%209902%209213>
> +61 (0)403 896 767 <+61%20403%20896%20767>
>

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Christine Gee]

Hi Xiao,

I can confirm you need to buy an active adapter if you want to convert the 
display port on the graphics card to DVI. The one that they supply with the 
graphics card is passive and won't work. I was in the same boat about a year 
ago. I bought a USB powered active adapter which allowed 120htz. My monitor 
only had DVI input so I didn't try a direct display port connection. I can't 
comment on why that didn't work. 

Cheers
Christine


Sent from my iPhone

> On Jan 30, 2017, at 4:25 PM, Takaaki Fukami  
> wrote:
> 
> Dear Xiao,
>  
> You need an active converter from DP to DVI.  You can't get 120Hz if you use 
> a passive converter, even with a DVI dual link cable.  If you used an adapter 
> come with the board, it's probably passive.
>  
> Taka
>  
>  
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Xiao Lei
> Sent: Tuesday, January 31, 2017 9:10 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under 
> Windows 10
>  
> Dear All,
>  
> I tried to make Coot and Pymol 3D working for a HP Workstation with Quadro 
> M4000 graphics card, the card has four displayport. I also has a Asus 24 inch 
> 3D monitor. I tried to connect  the graphics card with the monitor through 
> displayport to displayport connection and displayport to DVI-D dual link 
> connection but failed to set the monitor run on 120Hz. It seems I have to 
> follow the old way of using  DVI-D dual link connection for both graphic card 
> and monitor, but the problem is that the graphics card does not have a DVI-D 
> dual link socket, it only have displayport.
>  
> I appreciate any suggestions.
>  
>  

Re: [ccp4bb] non-specific disulfide bonds in crystal structures

[Christine Gee]

Hi Todd,

I used to work on PNMT which also is supposedly monomeric and formed a 
disulfide between monomers in the crystals.  See 
http://www.sciencedirect.com/science/article/pii/S1570963905000968?via=ihub
We showed that it was irrelevant to activity.

Cheers
Christine

Sent from my iPad

 On 20 Dec 2014, at 9:52 am, Todd Jason Green tgr...@uab.edu wrote:
 
 Hello All-
 
 I have recently determined a domain structure of a larger protein. The 
 structure shows a clear disulfide bond between two monomers in the asymmetric 
 unit. I'm trying to figure out if this is an artifact of the crystal packing 
 or has biological relevance. The protein has been reported to function as a 
 monomer. If I look at the pool of protein on a SDS-PAGE gel under 
 non-reducing conditions, I see that a smaller percentage (~15-20%) of the 
 protein runs as a dimer. In the structure, the association has 2-fold 
 symmetry with about 29% of the monomeric surface area buried between the 
 dimer. Can anyone point me in the direction of a paper describing a 
 non-specific disulfide in a crystal, or perhaps a criteria for assessing 
 specificity? I will do some functional studies, but I'm looking for some info 
 on a lazy saturday.
 
 Thanks in advance. Best-
 Todd

[ccp4bb] Job opportunity at the Australian Synchrotron

[Christine Gee]

Dear CCP4 readers
There is currently an opening on the MX beamlines at the Australian 
Synchrotron.  For the full job information consult the link below.
Regards
Christine

http://www.synchrotron.org.au/index.php/about-us/working-at-the-synchrotron/employment-opportunities/699-science-research-officer

[ccp4bb] Post-doctoral position in macromolecular crystallography at the Australian Synchrotron

[Christine Gee]

Dear all,
A two year post-doctoral position associated with the macromolecular
crystallography group at the Australian Synchrotron is currently open for
applications.
To read the position description and application instructions please go to
http://www.synchrotron.org.au/index.php/about-us/working-at-the-synchrotron/employment-opportunities
Regards
Christine

Re: [ccp4bb] Homology modelling

[Christine Gee]

You might want to have a look at consurf, which maps conservation from an 
alignment onto a structure.
http://consurf.tau.ac.il/
On 23/06/2011, at 6:42 PM, Simon Kolstoe wrote:

 Dear ccp4bb,
 
 One of my colleagues is interested in how a certain protein differs between 
 species. He's done a blast search, collected all the aligned sequences, and 
 emailed them to the crystallographer to tell him the implications of the 
 sequence changes. 
 
 Although I am not at all confident that I can predict any implications based 
 upon sequence differences, I thought I could at least have a try by mapping 
 the different species sequences onto the existing structure and then 
 regularising it just to see what happens (and then perhaps looking at buried 
 surface area, electrostatics, subunit interfaces etc.).
 
 I know the program chainsaw can mutate the sequence based on an alignment, 
 however I can't stop it pruning non-conserved residues. Does anyone know of 
 another program that I could use to do this step?
 
 Similarly if anyone knows other software tools/methods I could use to try and 
 work out the implications of sequence changes I would be grateful for advice.
 
 Thanks,
 
 Simon

Re: [ccp4bb] Cryoprotection in 3M ammonium sulfate

[Christine Gee]

Dear Brenda

Check out malonate
http://www.ncbi.nlm.nih.gov/pubmed/14646118? 
ordinalpos=2itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubm 
ed_DefaultReportPanel.Pubmed_RVDocSum


Malonate: a versatile cryoprotectant and stabilizing solution for  
salt-grown macromolecular crystals.

Holyoak T, Fenn TD, Wilson MA, Moulin AG, Ringe D, Petsko GA.

Regards
Christine


On 19/08/2009, at 9:18 AM, Schulman, Brenda wrote:


Hello!

I would be grateful for suggestions on cryoprotectants for crystals  
growing

in  3M ammonium sulfate.

Thanks!

Brenda


Email Disclaimer:  www.stjude.org/emaildisclaimer

Re: [ccp4bb] Problem with different map when ligand refinement

[Christine Gee]

Dear TriNigo
I would put waters in all the other difference density first (there  
are several obvious waters even in the section of map you sent with  
your email), without the substrate, and see if you see any more clues  
as to what's going on.  Do you expect something to be added on the  
substrate in the reaction?  Could you be looking at product?

Regards
Christine


Dear ccp4 experts,
I am trying to solve the structure of one esterase with its  
substrate. The structure was solved by MR to the resolution 2.2 A.  
In the active site, I can see clearly the different density map of  
the substrate (S- methyl hydroxy isobutyrate). After puting the  
substrate into that density map, I use Refmac to run restrain  
refinement at 0.1 weighting term.
Even though the substrate fits to the different map very well, a  
big different map appears at one end of the substrate after Refmac  
refinement. I attach the image so that it's easy to  see the problem.
I tried to put water or Na (because the crystallization contains:  
1M sodium citrate, 100mM Na Cacodylate, 20% glycerol) but it didn't  
work.
I tried to use CNS instead of Refmac, however the result is worse  
since the R-free is increased and the different map is still there.  
Because I am new with CNS so I don't know which parameters I should  
adjust.
Do you have any suggestion to solve this problem? Thank you very  
much for all of your helpful advice!


My best regards,
TriNgo,
PhD student,
Sungkyunkwan University, Koreaesterase_mut_S_ligand.png