Re: [ccp4bb] How to determine ligand binding from diffraction pat tern?

[Schubert, Carsten [PRDUS]]

Aha Dr. Palm 

Tough to generalize this, but if the ligand is weak or the site only
partially occupied you need to refine almost to completion. Since you seem
to be doing something akin to fragment screening I can only pass on my
experience. I had plenty of cases where the Rfree was ~35 after a rigid body
refinement and the ligand density was practically indistinguishable from
bound water. Refinement to an Rfree of ~25 with waterpicking/pruning
resulted in clear enough density to place the ligand. This is probably
overkill for very tight binders but necessary for weak binders.
phenix works pretty well for this since one can do rigid body refinement,
individual positional refinement and B-refinement all in one shot. 

Ciao 

Carsten


> -Original Message-
> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of
> Palm
> Sent: Tuesday, May 29, 2007 4:25 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] How to determine ligand binding from diffraction
> pattern?
> 
> 
> I would like to expand on the question and answer below and compare 
> your experiences: Looking for ligands in many different soaks 
> / cocrystals 
> of your protein of interest, you still should do molecular 
> replacement 
> and a bit of refinement. I agree with Steve, but how much refinement 
> is necessary and enough? 
> 
> We have a specific case with a 24 kDa protein crystallizing in P6522 
> with resolution of 2.5 - 3 A, which should be comparable to most 
> cases. The ligands have 10 - 20 non-hydrogen atoms (most of the time 
> we don't know, we are actually screening for them). How far should 
> we refine to see if we have only water molecules or a ligand bound 
> - to an Rfree of 0.45 or 0.40 or 0.35?
> greetings 
>Gottfried
> 
> 
> Dear all,
> 
> Is there a simple way to determine whether ligand is bound or not 
> by comparing the diffraction patterns between ligand-free (structure 
> known) and ligand-soaked protein crystals?  I would like to solve 
> the ligand bound protein structure, but before I do so, I have to 
> find out if the ligand is actually bound.  Thank you very much!
> 
> Best,
> 
> Joe
> 
> Having done this a few hundred times, I would strongly suggest that 
> you just collect the data and solve the structure.  Since you already 
> have the apo structure solved, then it really isn't that much work 
> to do an MR solution on the complex.  Be aware that quite frequently 
> there is enough non-isomorphism to necessitate partial refinement 
> of the "complex" structure before recognizable density will appear 
> for the ligand.  The definitive answer can only be obtained with 
> a full data set, so go for it.
>  
> Good luck-
>  
> Steve
> 
> 
> 
> 
> ===
> WEB-Mailer der Uni-Greifswald ( http://www.uni-greifswald.de/ )
> ===
> 

Re: [ccp4bb] coot in stereo

[Schubert, Carsten [PRDUS]]

Paul:

that is a problem with the NVIDIA hardware. In some old release notes 2 years 
ago they spoke
of some instabilities of the GPU with regards to stereo. This happens more 
under linux than under windows, which points to a driver issue. To my knowledge 
there is not much you can do. 

May be somebody else has more insight?

Carsten


> -Original Message-
> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of
> Paul D. Cook
> Sent: Tuesday, August 14, 2007 9:22 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] coot in stereo
> 
> 
> Hello,  I'm running stereocoot on linux (centos) machines with nvidia 
> video cards and stereographics emitters and glasses.  The 
> setup seems to 
> work fine most of the time, but the stereo will invert every 
> now and then
> (the right eye is shown the left image and vice versa).  This 
> seems to 
> happen especially after a computation such as realspace refine is 
> performed.  The stereo will usually spontaneously correct itself, but 
> sometimes I have to minimize the window and restore it.  This 
> is occuring 
> on three machines with the above configuration.  Swapping 
> emitters and 
> glasses seems to do nothing.  Has anyone had such a problem?
> 
> Thanks,
> Paul D. Cook
> 

Re: [ccp4bb] insoluble ligand

[Schubert, Carsten [PRDUS]]

Simon,

solubilize your ligand in DMSO so it is maximally concentrated, 100mM works 
fine. Add enough compound to achieve 2-3 fold excess to your protein, mix and 
set up. Make sure your final DMSO concentration is ~3%, otherwise chances are 
you might harm your protein. If you cannot achieve a high enough stock 
concentration of DMSO to be below the 3% threshold, dilute you protein in the 
storage buffer to ~1mg/ml. Add compound to 2-3 fold access, incubate and 
co-concentrate to the desired concentration. That way you avoid the DMSO shock.

Alternatively you could incubate the concentrated protein with the compound 
solubilized in water for 24-48hr and hope it is soluble and potent enough to 
get taken up by the protein and then set up your trays.

HTH

Carsten



> -Original Message-
> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED]
> Behalf Of Yue Li
> Sent: Tuesday, December 11, 2007 11:55 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] insoluble ligand
>
>
> Hi all,
>
> I have one ligand which is insoluble in water, and I would like to
> co-crystallize it with my protein. Is there any other method
> except for
> dissolving it in DMSO ?
>
> Thanks
>
> Simon
>
> 

Re: [ccp4bb] coot question for any/all?

[Schubert, Carsten [PRDUS]]

David,

check if your personal environment (login scripts, paths, etc...) is the same 
on your home machine and the other machines. Looks as if there might be a 
difference. What does the coot console say, any error messages or hints? 

HTH

Carsten

> -Original Message-
> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of
> David Roberts
> Sent: Wednesday, March 05, 2008 2:39 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] coot question for any/all?
> 
> 
> Hello,
> 
> So sorry to post this here but I'm at wits end and am just 
> hoping that 
> somebody here has had a similar problem (and subsequent fix). 
>  Here goes.
> 
> I have 7 systems, close to identical, all running FC7.  For 
> all, I used 
> the autobuild script on the ccp4 website to generate the entire ccp4 
> package (including coot0.3.1).  As I don't want to deal with network 
> problems, I install the programs on every computer following the same 
> build methods.  I know I could do this differently, but for 
> now I don't 
> want to change methods.
> 
> Now, everything appears to be running normally with no 
> issues.  However, 
> I just recently tried building a model from scratch, using the 
> baton-mode and then CAatoms - > mainchain button.  One one computer, 
> this works great, and I can build, combine fragments, renumber, blah 
> blah blah and get a structure.  For the other 6 machines, I 
> can do the 
> baton mode (and it seems to work), but when I hit the CA - > 
> mainchain 
> button, nothing happens (it just spins for a few seconds then 
> appears to 
> work but there are no new atoms on the screen).
> 
> I tried downloading the newest ccp4 with no luck, and also the newest 
> coot (from the coot website).  They seem to run fine, but again get 
> stalled when I try to do what I state above.  It just doesn't work 
> (though coot appears to be working normally - I can display 
> molecules/maps and move things around and such).
> 
> The problem is, I don't even know where to start here.  I 
> would gladly 
> replace/uninstall/reinstall, but what is it that is broken and needs 
> fixing?  Like I said, I tried several different reinstalls 
> today with no 
> luck at all (even the new coot gave the same problem).  I went to the 
> coot faq and did the soft-link of the reference-libraries 
> (which is an 
> old fix but you never know) and it had no effect. 
> 
> I will say the one machine that is working is my one at home, 
> and so I 
> can't simply share that directory via nfs and see if it works on the 
> other machines (not trivial).  All were built the same way, but 
> obviously I missed a file/link or something that is not allowing this 
> important part of the program to work.
> 
> Any helpful tips?
> 
> Thanks so much.
> 
> Dave Roberts
> [EMAIL PROTECTED]
> 
> 

Re: [ccp4bb] 96-well block storage

[Schubert, Carsten [PRDUS]]

Brian,

We use a PlateLoc Thermal Microplate sealer from Agilent. Works very
well, pricey though ...

Cheers,

Carsten

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Brian Mark
> Sent: Tuesday, June 14, 2011 5:19 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] 96-well block storage
> 
> Hi all,
> 
> Considering the popularity of 96-well deep well block format for
> purchasing and storing protein crystallization conditions, I'm
> surprised that a better re-sealing system has not been invented to
> prevent evaporation from the blocks when they are stored.  We
typically
> don't consume our blocks fast enough to avoid this issue.  There must
> be a better way to re-seal these blocks other than using peel and
stick
> foil tape over and over again...
> 
> Would anyone like to share their optimal method for storing 96-wells
> blocks that avoids (or a least minimizes) evaporation?
> 
> Cheers,
> 
> Brian Mark

Re: [ccp4bb] pymol python and cctbx

[Schubert, Carsten [PRDUS]]

Tim,

I'm shooting from the hip here, but I think the problem is that cctbx
comes with its own python, which you would need to run both pymol and
numpy under. According to Ralf it is at least not trivial to utilize the
system python to run cctbx. So I think you need to compile/install pymol
against cctbx.python and install it as a module under cctbx.python.
Similar deal for numpy, which may already be available in cctbx, if not
installation should be straightforward.

These broad steps may work (again shooting from the hip...)
-Install cctbx
-link cctbx.python to python and make sure its first in your path (may
be optional)
-install numpy under cctbx.python (if not already present)
-compile and install open.pymol against the cctbx.python, either via the
renaming trick 
 above or calling cctbx.python setup.py (build/install)

Good luck, let us know how it works...

Carsten



> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> Tim Gruene
> Sent: Wednesday, June 23, 2010 8:35 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] pymol python and cctbx
> 
> Dear all,
> 
> I've been trying to install the SuperSym module for pymol (svn trunk
> version of pymol as of today, 1.3.x). Upon restart the console says
> "Ooops!  SuperSym requires cctbx and numeric python to function.
Please
> install these."
> 
> The system is i7 with Debian Testing 64bit with python2.5 (although
> python2.6 is also installed but not the default). cctbx was installed
> using cctbx_fedora8_x86_64_py265_inc.selfx and the installation output
> did not imply any issues, e.g. about the wrong python version (and I
> did only find cctbx packages for python 2.6.5 on their web site).
> 
> python-numpy is install which I believe is the "numeric python" the
> module output complains about.
> 
> Would anyone be so kind to direct someone who despises python (phyuuu,
> that
> helped...) to how to get the SuperSym module to work with pymol? A
> start would be if the module would tell me whether it complains about
> missing numeric python or cctbx or both.
> 
> Do I have to compile pymol with python2.6? Just starting pymol with
> python2.6 did not change anything.
> 
> Thanks a lot, Tim
> 
> 
> --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A

Re: [ccp4bb] Problem with getting protein-inhibitor complex structure

[Schubert, Carsten [PRDUS]]

Hi Xiaopeng,

In addition to what has been suggested:

Make sure to understand that your 'inhibitors' are really inhibitors and
not just general destabilizers of proteins. A binding assay like ITC or
Thermofluor like assay is useful to establish that your inhibitors are
actually binding to the protein and not just unfolding it. Destabilizers
tend not to show up in crystal structures.
Accessibility of the active site is also key to success. Check for any
intrusions of symmetry mates into the putative binding pocket. This is a
common problem for proteases for instance. If so, you would need to
screen for a different apo-crystal form or try co-crystallization. 
Try soaking in cryo-protectant with excess ligand present for a couple
of days. Solubilizing additives like 3% DMSO or cyclodextrane may also
help. If your protein crystallizes in high salt, you can try to switch
soaking in higher PEG concentrations, that sometimes improves things.

Good luck

Carsten




> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> ???
> Sent: Saturday, August 28, 2010 1:40 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Problem with getting protein-inhibitor complex
> structure
> 
> Dear all,
> We are working on protein-inhibitor complex crystal structures,
> although we did get nice crystals and soaked them with inhibitor for
> several days, all structures we obtained were empty!!There are nothing
> at the active site. For several crystals. their color turned very
> clearly from colorless to yellow the color of the inhibitors, nothing
> found either.
> These inhibitors work very well in enzyme assay. We, especially
our
> students, are very depressed...
> Any suggestions will be really appreciated!
> 
> 
> 
> 
> Xiaopeng Hu, D.Sc.,
> School of Pharmaceutical Sciences
> Sun Yat-sen University,
> Higher Education Mega Center
> Guangzhou, Guangdong, China 510006
> Tel. +86 020 39943032

Re: [ccp4bb] Graphics for notebook

[Schubert, Carsten [PRDUS]]

Eric, 

if you want to use stereo on a notebook you have very limited options. I have 
stereo running using a Lenovo T61p with a Nvidia Quadro FX570M under XP, not 
tried Linux yet. Officially this card is not even supported by Nvidia for 3D 
application, but works anyway in conjunction with a docking station, which has 
a DVI adaptor. Don't go with a Quadro NV series, they did not work in our 
hands. 

HTH

Carsten



> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> 
> Sent: Sunday, September 19, 2010 11:46 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Graphics for notebook
> 
> Dear all,
> 
> I wanted to know which type of graphics card is more suitable for a
> notebook which is going to be used for structural biology. Integrated
> or dedicated? ATI or NVIDIA? At the moment I have to choose between an
> integrated Intel HD Graphics or a dedicated NVIDIA NVS 3100M Graphics.
> Any suggestions are highly appreciated.
> 
> Thanks!
> 
> Eric

Re: [ccp4bb] Graphics card for Nvidia 3D vision

[Schubert, Carsten [PRDUS]]

Andreas,

I can only second what Chris was saying. We have the same setup (FX3800
with separate riser for stereo connection) used in all of our machines
and it works very well. In terms of monitor I would recommend to spend a
bit more money and go with an Alienware or Asus 3D LCD, both are running
at 1920x1080, vs. 1680x1050. There may be newer ones out there with the
same capabilities, but you need to make sure the driver supports the
newer monitors. Initially the ASUS monitors were not supported in the
195.xx.xx series of drivers, but it worked after updating to the latest
drivers. I personally prefer the Alienware since it has a matte finish,
but the quality on both is excellent. 

As for the kit, I ran into the issue were the 3D vision kit was bundled
with the Asus monitors and they were missing the stereo cables, I
suppose they were bundled for the European market. NVIDIA support was
unwilling to send me the missing cables even though we are using quite a
bit of their hardware, so much for customer support... So beware when
you are buying the cheaper bundles. The Nvidia website has a list of the
Kits, which include the stereo cable. Also another thing to watch out
for is not to confuse the newer 3D Vision Pro line with the older
consumer grade line. The Pro line emitter work on RF vs. the older grade
emitters work on IR. As far as I know they are not compatible.

You can even run stereo in dual-monitor mode. That's how I reuse old
LCDs. One LCD for stereo, the other adds more real-estate. Haven't found
a reliable way to get this to work from the get-go though. I suppose
it's is a problem with our outdated X-server, but can be overcome with
the nvidia-settings tool.

HTH

Carsten


> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Chris Richardson
> Sent: Tuesday, March 01, 2011 5:27 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Graphics card for Nvidia 3D vision
> 
> >>> Andreas Eichinger  03/01/11 9:24 AM >>>
> 
> > We are currently setting up a new 3D workstation with a Samsung
> > SyncMaster 2233RZ monitor and a Nvidia 3D vision glasses kit on a
> > Redhat Enterprise Linux box. According to Nvidia, a Quadro FX 4800,
> > Quadro FX 4600 or Quadro FX 3700 graphics card can be used for 3D on
> > Linux if it is connected via a 3-pin mini-DIN stereo connector. Has
> > somebody experience with such a setup?
> 
> The FX 3800 will also work, but it doesn't have a mini-DIN connector.
> You can buy a separate riser fitted with the connector, which mounts
in
> a spare slot next to the card and connects to it by a cable.  This is
> made by PNY, part number 900-50762--000.  In our experience, an FX
> 3800 and separate riser is a lot cheaper than a card with a built-in
> DIN connector.
> 
> When you buy the 3D Vision glasses kit, check that it contains the
> mini-DIN to emitter cable.  At one stage this was included in kits for
> the US market, but not in kits for Europe.  This may have changed.
> 
> We use the same monitor with an FX 3800 and 3D vision glasses kit on a
> couple of machines and are very impressed with the quality of the
> stereo.  The glasses are a lot nicer than the old models, and it's
nice
> being able to recharge them by USB rather than constantly swapping
> batteries because someone left the arms open and the glasses active
> overnight.
> 
> Regards,
> 
> Chris
> 
> 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.
> 
> This e-mail message is confidential and for use by the addressee only.
> If the message is received by anyone other than the addressee, please
> return the message to the sender by replying to it and then delete the
> message from your computer and network.

Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'

[Schubert, Carsten [PRDUS]]

Eric, Takaaki:

I just remembered that we ran into the same problem. If you are using Linux try 
launching 'nvidia-settings' and disable GPU scaling. That helped with some of 
our monitors, which exhibited the same problem. Not sure if that would be 
applicable to Windows though. 

HTH 

Carsten


-Original Message-
From: CCP4 bulletin board on behalf of Eric Bennett
Sent: Tue 5/10/2011 6:58 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
 
Nvidia lists that monitor on their list of supported hardware:
http://www.nvidia.com/object/3d-vision-requirements.html

They even sell some Acer monitors in their online store although they are 
labeled in conflicting ways.

I tried upgrading the driver yesterday to the 270.41.06 version but it didn't 
make any difference, still only 100 Hz.  Are you using Windows or Linux?  We're 
using the 64-bit Linux driver.   

-Eric



On May 9, 2011, at 4:26 AM, Takaaki Fukami wrote:

>> not seen a working 120 Hz stereo setup working on the Acer GD235 monitor.
>> if you ask the Nvidia driver or the monitor, it reports 100 Hz instead
> 
> This is what I encountered on Dell Alienware OptX AW2310 with Quadro FX3800,
> which has been fixed by nVIDIA Linux driver update (in 256.44).
> 
> I don't know if the Acer monitor is compatible or not, 
> it seems better to ask NVIDIA directly. see:
> http://twitter.com/#!/NVIDIAQuadro/status/65188179753435137
> 
> 
> Takaaki Fukami
> 
> -
> Discovery Platform Technology Dept. Gr.5
> Chugai Pharmaceutical Co.,Ltd.

Re: [ccp4bb] CONECT records

[Schubert, Carsten [PRDUS]]

Christina, 
 
phenix.elbow will generate the CONECT records for you.
 
HTH
 
Carsten

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of Christina Bourne
Sent: Thursday, October 02, 2008 12:33 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CONECT records


Hello all,

Probably a very basic question- where can I generate CONECT records in my pdb 
file for my ligand?  

Neither pdbset nor refmac did it for me.

I am trying to run this file through ligplot, but the ligand is not being 
recognized.  As compared to examples, a glaring difference is the lack of 
CONECT records in my file.  This structure has been refined with phenix.

Any help appreciated,
Christina Bourne
Oklahoma State University

Re: [ccp4bb] foam dewar usage ?

[Schubert, Carsten [PRDUS]]

Hmmm, that's funny. Our experience was quite the opposite. The first time we 
used one of the darker small dewars we ended up with a lot of burr in the LN2. 
Those got picked up by the cryo and we ended up with lilac particles embedded 
inside the cryo. You can imagine the reaction when these particles showed up in 
the mounting camera 
We also noticed that the LN2 in these dewars actually ices up more rapidly as 
compared to the glass dewars. We attribute this to the lower insulating 
capacity of the foam dewars, which causes a vigorous boiling action and the 
higher turbulence seems to suck in more ambient air. Needless to say the dewars 
did not make it past the first use...

Carsten



-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of
[EMAIL PROTECTED]
Sent: Thursday, October 09, 2008 8:50 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] foam dewar usage ?


Yes, we use them all the time and they're great. Stuff does not slip on
the bottom like it does in the glass Dewars and the formation of ice is
greatly reduced. Plus, they're much easier to dry.

Artem

> Does anyone in the biocrystallogaphy community use foam dewars for
> handly liquid nitrogen and freezing/manipulating frozen protein
> crystals ?

Re: [ccp4bb] foam dewar usage ?

[Schubert, Carsten [PRDUS]]

We are talking about the same containers. Actually, Jon Spear contacted me 
today and indicated that the burrs are probably left-overs from the milling 
process which were not cleaned out sufficiently. This explains the particles 
and the vigorous boiling action caused by the abundance of nuclei for the 
bubbles to form and not by lack of insulating capacity. 

Ours must have been an isolated incident, since everybody else seems to be 
quite happy with these vessels. So we may give them another shot 

Cheers

Carsten

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of Artem Evdokimov
Sent: Thursday, October 09, 2008 6:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] foam dewar usage ?


Maybe we're not talking about the same kind of container? We never had any kind 
of particles** in ours and with the use of a lid the ice does not appear for 
quite some time. We did not see 'vigorous boiling' either. If one leaves LN2 in 
the open it would eventually ice up regardless of the nature of storage 
container J
 
Artem
 
* calling foam LN2 container a 'Dewar' is a misnomer, James Dewar would not be 
happy.
** there is a scenario in which particulates may form - and that is if a wet 
container (i.e. not dried for long enough after previous use) is subjected to 
LN2. This would rapidly freeze the water inside the foam layer and bust up the 
pores, resulting in particulates.
 



From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Van Den Berg, 
Bert
Sent: Thursday, October 09, 2008 11:03 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] foam dewar usage ?
 
 
Funny indeed. Our experience has been as well that icing of the foam dewars 
seems to be reduced compared to the "classical" ones.

Bert



-Original Message-
From: CCP4 bulletin board on behalf of Schubert, Carsten [PRDUS]
Sent: Thu 10/9/2008 9:15 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] foam dewar usage ?

Hmmm, that's funny. Our experience was quite the opposite. The first time we 
used one of the darker small dewars we ended up with a lot of burr in the LN2. 
Those got picked up by the cryo and we ended up with lilac particles embedded 
inside the cryo. You can imagine the reaction when these particles showed up in 
the mounting camera 
We also noticed that the LN2 in these dewars actually ices up more rapidly as 
compared to the glass dewars. We attribute this to the lower insulating 
capacity of the foam dewars, which causes a vigorous boiling action and the 
higher turbulence seems to suck in more ambient air. Needless to say the dewars 
did not make it past the first use...

Carsten



-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of
[EMAIL PROTECTED]
Sent: Thursday, October 09, 2008 8:50 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] foam dewar usage ?


Yes, we use them all the time and they're great. Stuff does not slip on
the bottom like it does in the glass Dewars and the formation of ice is
greatly reduced. Plus, they're much easier to dry.

Artem

> Does anyone in the biocrystallogaphy community use foam dewars for
> handly liquid nitrogen and freezing/manipulating frozen protein
> crystals ?

Re: [ccp4bb] cryoloops for X-ray data collection from protein crystals at room temperature

[Schubert, Carsten [PRDUS]]

http://www.mitegen.com/
 
Cheers

Carsten

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk]on Behalf Of cedric 
bauvois
Sent: Friday, January 16, 2009 9:27 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] cryoloops for X-ray data collection from protein crystals at 
room temperature


Dear CCP4ers,

in their paper entitled " Using cryoloops for X-ray data collection from 
protein crystals at room temperature: A simple applicable method" (  
 Journal of Crystal 
Growth
Volume  

 281, Issues 2-4, 1 August 2005, Pages 592-595.), the authors present a way to 
mount crystals using "a cryoloop accompanied by a glass capillary cap" (see 
abstract below).
Do you know if any commercial version of such system are now available ?


Abstract: Although cryoloops are now routinely used for X-ray data collection 
from protein crystals in cryocooling condition, it is still necessary to 
collect X-ray diffraction data from protein crystals at room temperature under 
such circumstances as to find resolution limit and/or to avoid damage of 
protein crystals at cryogenic temperature (e.g. 100 K). Here, we show that a 
cryoloop, which is accompanied by a glass capillary cap to maintain humid 
environment of crystal in the cryoloop, can be used not only to examine protein 
or non-protein crystals but also to collect X-ray diffraction data for 
structural analysis from protein crystals at room temperature. The size of 
cryoloop should be carefully chosen so that the crystal does not move in the 
cryoloop. This crystal mounting method can be time-saving compared to the 
traditional method to mount a crystal in a glass capillary tube.




Many thanks 


-- 
Dr. Cedric Bauvois
Cristallographie des protéines
Institut de Recherches Microbiologiques JM Wiame -IRMW
Av E. Gryzon 1, 1070 Brussels (Belgium)  
tél: +32 (0)2 5273634
fax: +32 (0)2 5267273

Re: [ccp4bb] desktop models

[Schubert, Carsten [PRDUS]]

Chris,

For the laser-etched glass blocks have a look at:

http://www.bathsheba.com/

I have a couple of them and they look very good.

Cheers,

Carsten


> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> Christopher Rife
> Sent: Tuesday, May 05, 2009 2:42 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] desktop models
> 
> Hi,
> 
> I am looking to have a model produced from a PDB, i.e. something that
> we
> can put on the desk for everyone to admire :)
> 
> Googling for such a thing is rather challenging, so I'm curious if
> anyone
> has suggestions as to where I might get something like that made. So
> far,
> I have found two options:
> 1. Molecular Dimensions:
> http://www.moleculardimensions.com/us/merchant.ihtml?new_id=223&step=2
> (etching in a glass block)
> 
> 2. 3D Molecular Designs: http://www.3dmoleculardesigns.com/
> (nylon models)
> 
> I think #2 is more what we have in mind. Does anyone have any
> experience
> with their final product in terms of quality and durability?
> 
> Thanks very much.
> 
> Chris
> 
>
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Re: [ccp4bb] DSSP server

[Schubert, Carsten [PRDUS]]

Jane,

you could use ksDSSP, which is an OpenSource implementation of DSSP.
Requires some compiling though and I am not sure if OSX is supported.
You also need to compile the PDB record I/O libraries.

http://www.cgl.ucsf.edu/Overview/software.html

Cheers,

Carsten




> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> Jane Bailey
> Sent: Thursday, January 14, 2010 9:54 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] DSSP server
> 
> Hello all,
> 
> I am sorry for this off-topic question. I see it has been discussed
> many
> times, but somehow I got stuck in the very beginning.
> 
> I want to assign ss to my pdb file in DSSP, but I could not find a
> server to run it. Does anybody know a webserver where I could run this
> kind of tasks? I use iMAC.
> 
> Many thanks!
> 
> Jane

Re: [ccp4bb] Does the substrate has access to the active site?

[Schubert, Carsten [PRDUS]]

Paul,

couple things come to mind:

 -make sure your substrate is actually a binder and not an (unspecific)
inhibitor (ITC, Thermofluor, Biacore)
 -soak longer and at higher concentration. (3mM concentration from 100mM
stock in DMSO for a week or more)
 -Is there evidence that your protein needs to undergo substantial
rearrangement prohibited by the crystal 
  packing? Then you may be out of luck with soaking, try
co-crystallization.

The folks from GSK had a nice paper about some useful techniques for
ligand incorporation probably a worthwhile read: Acta Cryst. (2007).
D63, 72-79  (doi:10.1107/S0907444906047020)

HTH

Carsten


> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> Paul Lindblom
> Sent: Friday, April 09, 2010 5:15 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Does the substrate has access to the active site?
> 
> Dear Bulletin Board,
> 
> I am trying to soak substrate into crystals of an enzyme, but so far I
> can't see the substrate in the structure. Does anyone knows a program
> to ensure that the entrance to the central cavity is accessibly? I
> mean based on the whole crystal. I already checked the crystal packing
> manually and it seems that the way is free more or less, but I find it
> hard to interpret.
> 
> Thanks in advance,
> 
> P.