Re: [ccp4bb] Deposition of a BUSTER refined structure

[Robbie Joosten]

Dear Melanie,
 
To obtain a reasonable error estimate of R-free you could try to refine your 
structure against different sets of reflections. You can force the R-free set 
to be the reflections flagged with 1 or 2, etc. instead of 0 (at least in 
Refmac) and refine to convergence again. You should get similar (but not the 
same) R-free values. This will give you a good view of possible R-free values. 
I admit it is a lot of work (and probably totally over the top) but you can 
script this quite easily. I tried it a few times and the SD of R-free values is 
typically a few tenths of a percent(age point). 
 
Cheers,
Robbie Joosten


> Date: Tue, 2 Mar 2010 08:44:18 -0800
> From: merr...@u.washington.edu
> Subject: Re: [ccp4bb] Deposition of a BUSTER refined structure
> To: CCP4BB@JISCMAIL.AC.UK
>
> On Tuesday 02 March 2010 07:09:47 Melanie Vollmar wrote:
>> Hi all
>>
>> I did my first deposition of a BUSTER refined structure and I was very
>> surprised when I was asked for an "estimated error of free R value" and
>> "estimated error of bin free R value" as well an "ESD based on Luzzati Plot"
>> during the deposition process.
>
> These instructions are unfortunate, since the use of Luzzati plots
> to estimate error is at this point a historical remnant.
>
> The same 'problem' occurs when depositing structures refined with refmac.
> The error estimates output by the program are based either on the
> maximum likelihood statistics or on Cruickshank's DPI indicator.
>
> Bottom line: Just ignore the request for Luzzati plot esds.
>
> Ethan
>
>
>> I had a detailed look into the refinement log file and I tried the Buster 
>> documentation but I have absolutely no clue where I can find these values.
>>
>> Can someone give me a hint where I can find some information about this or 
>> where the values are in the log file? If they are not listed anywhere, in 
>> which way do they have to be estimated? And what is a Luzzati Plot? I have 
>> never heard of such a plot before...
>>
>>
>> Thank you very much.
>>
>> Cheers
>>
>> Melanie
>>
>
>
>
> --
> Ethan A Merritt
> Biomolecular Structure Center
> University of Washington, Seattle 98195-7742  
>   
_
New Windows 7: Find the right PC for you. Learn more.
http://windows.microsoft.com/shop

Re: [ccp4bb] homology modelling using sequence alignment

[Rotem Sertchook]

Very easy way is the Swiss-Model server via the alignment mode
Good luck

Rotem
On 4 Mar, 2010, at 0:59, Brett, Thomas wrote:


Dear all:
I am trying to create a homology model of a coiled-coil for use in  
molecular replacement. I have a template poly-ala coiled coil that  
I like to use, so that is fine. I want to thread my sequence onto  
the helix and am trying to find a server/easy program that will do  
this. I want to use a hand made alignment so that I can create 7  
models shifted by residue (to be complete). Really all this should  
need is a template pdb and the sequence alignment. What are peoples  
favorite servers/easy programs for this? I have been trying to use  
the WHAT IF server and the SCWRL3 server, but WHAT IF isn't working  
for me (it just spits out the template pdb with the original  
sidechains that were pruned to poly ala built back in- is it  
because I am using a mac?) and scwrl keeps crashing with python  
errors (has anyone got the scwrl server to work?). Apologies for  
the off topic. Thanks in advance,

-Tom


Tom J. Brett, PhD
Assistant Professor of Medicine
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110





 
---

Rotem Sertchook, Ph.D.
Bioinformatics Unit, Biological Services
Weizmann Institute of Science,
Rehovot 76100, Israel.

Phone:   +972-8-934-4315 (office)  |  +972-52-5304384 (mobile)
Email: rotem.sertch...@weizmann.ac.il
 

[ccp4bb] column labels for SIRAS/MIRAS

[Yogesh Gupta]

Hello,

My aim is to calculate SIRAS/MIRAS phases using PHENIX. Which should be the
correct column labels and associated "Differences" in the derivative data
one should select to calculate SIRAS phases? I am supplying both native and
derivative data and for the derivative data i am selecting F_HA, SigF_HA,
DANO_HA, SigDANO_HA as labels and 'Anomalous' as differences. Should the
differences not be 'Isomorphous+Anomalous' in case of SIRAS? If so, which
column label is the correct one if i choose Iso+Ano as differences?
Running SIRAS in SHARP requires Fs,DANOs, and ISYM for the derivative.
It seems that columns F_HA(+),SigF_HA(+),F_HA(-), and SigF(-) can also be
used for SIRAS as mentioned below, which confused me a little bit.
http://www.ccp4.ac.uk/HAPPy/docshow.php?doc=design/input.html#input

Could someone please clarify?

Thanks for your time and help.

Yogesh

Re: [ccp4bb] homology modelling using sequence alignment

[Sean Seaver]

>I am trying to create a homology model of a coiled-coil for use in
molecular >replacement. I have a template poly-ala coiled coil that I like
to use, so that is fine. >I want to thread my sequence onto the helix and am
trying to find a server/easy >program that will do this. 

As a starting point I put together a list of 27 homology servers:

http://bit.ly/KEMsT

Unfortunately, I have not used all of them so am unable to suggest the
easiest one for your situation, but hope it helps.

Sean

Re: [ccp4bb] Question about modeling SAM into a protein structure

[Paul Emsley]

Yuan Cheng wrote:
I am trying to model a S-adenosylmethionine (SAM) molecule into the 
active site of a protein using the SAH (exists in the crystal structure) 
as the template.


2)Coot: I tried to superpose SAM to SAH in coot. Bot SSM superpose and 
LSQ superpose didn't work. when I did SSM superpose, coot said "can't 
make graph for SAH structure".  when I did LSQ superpose, nothing 
happened after I run it.  I also tried Extensions> modeling> superpose 
ligands, nothing happened too. Does anyone know what's wrong here?
  


Finger fumble?

AFAICS if you are using Coot, Extensions> Modelling> Superpose 
Ligands... is indeed what you want.


I just did it myself, it looks fine.

http://www.biop.ox.ac.uk/coot/screenshots/Screenshot-Coot-SAM-SAH.png

(Using ligands from SBASE and LIBCHECK).


I know that I can probably manually move SAM to the position of SAH and 
change the bond angles to make SAM align to SAH. 


Bleugh.


(You are not the first to SSM superpose a ligand, I've improved the 
dialog to better explain what's needed - thanks.)


Paul.

Re: [ccp4bb] Deposition of a BUSTER refined structure

[John Badger]

I would echo Ethan on this metric being something of a relic and add a bit 
more data. 

Several years ago I tried to get a practical solution to the questions:
- when is a refinement finished?
- how to detect the correctable abnormalities (errors) in a structure so they 
can all be corrected during refinement and before deposition ?
- what is the 'quality' of a structure? 

The idea was that our in-company structure refinements would give high 
quality structures (at least no gross errors) that could be used by chemists 
and the refinement work would not just go on forever.

Anyway, if you consider a simple count of the number of residues with an 
identifiable problem (say, a grossly distorted geometry, a disallowed phi-psi, 
a 
very unlikely chi-1 angle, very short contacts, a really poor correlation with 
electron density, all defined is rather generous ways) as sensible proxy for a 
useful structure 'quality' then coordinate accuracy quantities like DPI (or its 
older relation, the Luzzati plot) turned out to be pretty much useless. 


For that matter, like the current PDB we initially used SFCHECK and PROCHECK 
in our standard validation system but ultimately found them not really robust 
enough for all cases and switched to direct use of REFMAC with 0 refinement 
cycles as a structure factor/map calculator and applied the Richardson's phi-
psi data to create more accurate Ramachandran metrics. 

Re: [ccp4bb] Question about modeling SAM into a protein structure

[Eric Larson]

Hi Yuan,

LSQ within Coot works quite well for superimposing similar ligands.  Are you 
sure you are selecting the appropriate chain IDs and residue numbers in the LSQ 
dialog box?  It is a rigid body superposition though so it will only get you in 
the neighborhood (i.e. the adenine and sugar rings should at least superimpose 
well and then you may have to manually adjust the rest).  If you have electron 
density for the SAH, the 2 ligands are similar enough that you could then use 
real space refinement to get the SAM to superimpose almost perfectly on SAH.  
You would have to read a restraint file for SAM (which can be obtained by 
uploading the SAM coordinates into the PRODRG server) into coot for this 
though. 

Good luck,
Eric

PS - SSM will not work for ligands, as you saw.
__
Eric Larson, PhD
MSGPP Consortium
Department of Biochemistry
Box 357742
University of Washington
Seattle, WA 98195

On Wed, 3 Mar 2010, Yuan Cheng wrote:

> Hi everyone,
>   I am trying to model a S-adenosylmethionine (SAM) molecule into the active 
> site of a protein using the SAH (exists in the crystal structure) as the 
> template.
>
> What I have already tried but failed so far are
> 1)Pymol: I loaded the pdbs of SAM and protein-SAH into pymol and copy SAH 
> into a separate object. Then I tried to align SAM to SAH, but it didn't work 
> and pymol said " Executivealign:Mobile selection must derive from one object 
> only". Does anyone know what this mean?
>
> 2)Coot: I tried to superpose SAM to SAH in coot. Bot SSM superpose and LSQ 
> superpose didn't work. when I did SSM superpose, coot said "can't make graph 
> for SAH structure".  when I did LSQ superpose, nothing happened after I run 
> it.  I also tried Extensions> modeling> superpose ligands, nothing happened 
> too. Does anyone know what's wrong here?
>
> I know that I can probably manually move SAM to the position of SAH and 
> change the bond angles to make SAM align to SAH. I am wondering if there is 
> any program that can help to perform ligand alignment without the need for 
> manual adjustment.
>
> Thank you very much for your suggestion!
>
> Yuan
>

[ccp4bb] homology modelling using sequence alignment

[Brett, Thomas]

Dear all:
I am trying to create a homology model of a coiled-coil for use in molecular 
replacement. I have a template poly-ala coiled coil that I like to use, so that 
is fine. I want to thread my sequence onto the helix and am trying to find a 
server/easy program that will do this. I want to use a hand made alignment so 
that I can create 7 models shifted by residue (to be complete). Really all this 
should need is a template pdb and the sequence alignment. What are peoples 
favorite servers/easy programs for this? I have been trying to use the WHAT IF 
server and the SCWRL3 server, but WHAT IF isn't working for me (it just spits 
out the template pdb with the original sidechains that were pruned to poly ala 
built back in- is it because I am using a mac?) and scwrl keeps crashing with 
python errors (has anyone got the scwrl server to work?). Apologies for the off 
topic. Thanks in advance,
-Tom


Tom J. Brett, PhD
Assistant Professor of Medicine 
Division of Pulmonary and Critical Care
Washington University School of Medicine
Campus Box 8052, 660 S. Euclid
Saint Louis, MO 63110

[ccp4bb] Question about modeling SAM into a protein structure

[Yuan Cheng]

Hi everyone,
   I am trying to model a S-adenosylmethionine (SAM) molecule into the 
active site of a protein using the SAH (exists in the crystal structure) 
as the template.


What I have already tried but failed so far are
1)Pymol: I loaded the pdbs of SAM and protein-SAH into pymol and copy 
SAH into a separate object. Then I tried to align SAM to SAH, but it 
didn't work and pymol said " Executivealign:Mobile selection must derive 
from one object only". Does anyone know what this mean?


2)Coot: I tried to superpose SAM to SAH in coot. Bot SSM superpose and 
LSQ superpose didn't work. when I did SSM superpose, coot said "can't 
make graph for SAH structure".  when I did LSQ superpose, nothing 
happened after I run it.  I also tried Extensions> modeling> superpose 
ligands, nothing happened too. Does anyone know what's wrong here?


I know that I can probably manually move SAM to the position of SAH and 
change the bond angles to make SAM align to SAH. I am wondering if there 
is any program that can help to perform ligand alignment without the 
need for manual adjustment.


Thank you very much for your suggestion!

Yuan

[ccp4bb] UTP binding site and druggability

[Eric Liu]

Hi All,

I have a question regarding developing inhibitor for UTP binding protein.
Since UTP is a common nucleotide substrate for a lot of glycoenzymes
similiar to ATP for kinases, developing potent inhibitor for UTP in vitro
may not  seem to be an impossible task, or at least it's technically
feasible by using fragment-based approach, however, I was told that it is
possible that UTP is so abundant in the cell that a potent inhibitor in
vitro may not be able to work as an inhibitor in vivo. I was trying to
search for evidence that a UTP inhibitor works in vivo but did not succeed.
I wonder if any one can help to provide some examples that a UTP inhibitor
works in vivo. This example would provide evidence for the druggability for
UTP binding site for many glycoenzymes.  Thanks a lot!

Eric

[ccp4bb] Director, Institute for Structural Biology

[Jason Rife]

Director, Institute for Structural Biology, Virginia Commonwealth University 
(VCU).  

VCU seeks an outstanding investigator in the field of structural biology to 
direct the VCU Institute for Structural Biology and Drug Discovery (ISBDD), 
which was established in 1995 as the nidus of structural studies at the Medical 
Center Campus and the University.  The Institute currently embraces twelve 
research groups engaged in X-ray crystallography, high field NMR, computational 
chemistry and molecular modeling. VCU recently committed to a major expansion 
of structural biology research, which will be overseen by the Director of 
ISBDD. The incumbent will be provided with resources to support his/her 
leadership, including an endowed chair. Because of the close relationship 
between the ISBDD and the NCI-designated VCU Massey Cancer Center, candidates 
with research programs directed at understanding key proteins involved in cell 
proliferation and survival, neoplasia and tumor progression, and the extension 
of such mechanistic studies to structure-based drug design are strongly 
preferred.  Candidates should have earned the Ph.D. and/or M.D. degree and 
currently be tenured at the Associate or Full Professor level. Candidates 
should also have demonstrated leadership skills, and should currently direct a 
high-impact, externally-funded research program.  Applications will be reviewed 
upon receipt until the position is filled.  

Please submit a letter of interest, a detailed curriculum vitae and names, 
telephone numbers and addresses of three professional references to: Cathleen 
A. Finnerty, Office of the Vice President for Research, Box 980568, Richmond, 
VA 23298-0568 (Street address: 800 E. Leigh Street, Suite 115, Richmond, VA 
23219) or by e-mail:  finne...@vcu.edu.  Applications which are not complete 
will not be considered. Review of applications will begin immediately and the 
position will remain open until filled.   
Virginia Commonwealth University is an Equal Opportunity/Affirmative Action 
Employer.
Women, minorities and persons with disabilities are encouraged to apply.

Re: [ccp4bb] crystallization of highly-glycosylated protein complex-avoid phase separation

[Nathaniel Clark]

Jerry,
One thing you might try is a combination of Endo F1, F3, and possibly
Endo H(might trim a little bit more).  This works for me on
glycoproteins expressed in insect cells which show little or no
sensitivity to PNGaseF and EndoH.  Depending on the host strain you
are using to express, the sensitivity to different glycosidases will
change.  Other approaches are to add kifunensin to the culture media,
which inhibits mannosidase trimming, resulting in high-mannose
carbohydrate that will be sensitive to PNGaseF and EndoH.  However,
one might assume that the protein will need some amount of
carbohydrate to be happy, so that may not improve you crystallization
(for one project the best crystals ended up being fully glycosylated).
 In one instance removing a single carbohydrate (1 out of 5 on a 50 kD
human glycoprotein)  though point-mutagenesis created a crystal
contact at that very site which allowed me to solve the structure.
Enzymatic deglycosylation with EndoF1 and F3 did not produce good
crystals.

If it is a mammalian expressed protien, you can use the EDEGLY kit
from sigma to sequentially remove the terminal sialic acids,
beta-galactose, and beta N-acetyl glucoses, at which point it should
be PNGaseF sensitive.  Or, you could use a mannosidase to get back to
a glucNac_2 carbohydrate.

We have had better success with material produced in insect cells, as
they only put on pauci-mannose carbohydrates, which are much smaller
and not charged like mammalian carbohydrates.  In fact we have seen
those glycans participate in favorable crystal contacts that would not
be possible with mammalian glycans.

So, there are ways to deglycosylate it and change the glycosylation,
or course it's not guaranteed to improve the crystals, but it's
something to try.  Hope that helps,

Nat

On Wed, Mar 3, 2010 at 10:59 AM, Jerry McCully
 wrote:
> Dear ALL:
>
>  Recently we've been trying hard to crystallize a highly glycosylated
> protein complex ( 30% percent of carbohydrate in the total 120KD molecular
> weight).
>
>IT is a high affinity protein complex. One component can be crystallized
> in high salt condition and the other can be crystallized in PEG.
>
> Through screening, we happened to get some very ugly crystals in PEG
> condition using gel-fil purified complex sample.
>
> The problem is that it is very hard to repeat the screening condition. In
> contrast, it is very
> easy to get phase separation in the drop although we tried to optimize the
> protein and precipitant concentration.
>
>   We tried to de-glycosylated using PNGase and EndoH but failed in
> non-denaturing condition.
>
> Hampton additive screen  did not help either. We tried seeding several times
> but so far we have not got any better luck.
>
>   Can anyone give some guidance here? Thanks a lot,
>
> Jerry McCully
>
>
>
>
>
> 
> Hotmail: Powerful Free email with security by Microsoft. Get it now.

Re: [ccp4bb] crystallization of highly-glycosylated protein complex-avoid phase separation

[Prince, D Bryan]

Dear Jerry, 

 

First of all, it will be hard to reproduce the conditions with the
glycosylated protein because by its nature, it is heterogeneous. One
thing I would try with the glycosylated protein is a detergent screen,
or if you don't have one, use a few NDSB's. Second, I would try setting
up a lower PEG condition concentration and seed into it with the phase
separated material, or with polystyrene nanobeads. Third, I would try
FID (Free Interface Diffusion- like Microlytic's Crystal Former-
www.microlytic.com) experiments, or use Enrico Sturza's technique with
the Granada (?) Crystallization Boxes. Have you tried shifts in
temperature? Start by warming up the protein to between 37-42C, then set
up the drops. Allow the plate to equilibrate at some temperature between
37-20C then transfer to 4C after 24H.

 

Something I suggest is that you go back to construct design and mutate
the amino acids being  glycosylated to something like GLY or ALA. If you
can, express the protein in a different system (if you used Ecoli, try
Insect cells or vice-versa). Alternately, you can use SGC's method of
dilute protease mixed with your protein prior to setting up the drops. I
have tried 1:1 dilution, but I think that is too weak. I would start
with 1:100 or so. 

 

Good Luck, and let us know how it turns out. 

 

Regards, 

Bryan Prince.

 

 

 

 

From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Jerry McCully
Sent: Wednesday, March 03, 2010 10:59 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] crystallization of highly-glycosylated protein
complex-avoid phase separation

 

Dear ALL:

 Recently we've been trying hard to crystallize a highly
glycosylated protein complex ( 30% percent of carbohydrate in the total
120KD molecular weight). 

   IT is a high affinity protein complex. One component can be
crystallized in high salt condition and the other can be crystallized in
PEG.  

Through screening, we happened to get some very ugly crystals in PEG
condition using gel-fil purified complex sample. 

The problem is that it is very hard to repeat the screening condition.
In contrast, it is very 
easy to get phase separation in the drop although we tried to optimize
the protein and precipitant concentration. 

  We tried to de-glycosylated using PNGase and EndoH but failed in
non-denaturing condition.

Hampton additive screen  did not help either. We tried seeding several
times but so far we have not got any better luck.

  Can anyone give some guidance here? Thanks a lot,

Jerry McCully



   



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Re: [ccp4bb] Nvidia 3D vision + 1920x1080 Desktop Displays

[David J. Schuller]

On Wed, 2010-03-03 at 08:45 -0800, Greg Warren wrote:
>  This is most likely a 3800 problem since the 3800 has 1 DVI and 2 HDMI 
> outputs instead of 2 DVI outputs.

Those are DisplayPort, not HDMI.

 --
 ===
 All Things Serve the Beam
 ===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

[ccp4bb] Trouble with P1 data

[José Trincão]

Dear all,
we have a protein isolated from mouse liver which crystallized in P1. The 
amount of protein was very little so we could not get better crystals. The 
protein expressed in E.coli did not yield any usable crystals.

We managed to collect data from 2 crystals after annealing at the beamline 
(before annealing the data was useless). The data is very anisotropic, useless 
for about 50º (split crystal), but looks ok on other orientations.
The data collected could only be processed in P1 with XDS - mosflm consistently 
crashes in autoindexing. 
The protein is ~150kDa - we could find 4 mol in the unit cell by MR.
Although the data is ~95% complete to ~3 A, it extends to >2.5 (~60% 
completeness, and the maps are significantly better if we include these). 
All the tests indicate twinning. Even then we could refine the structure to R 
~25% and Rfree ~33% but are stuck at this point. Only 55 waters could be found 
(for 5400 residues).
My questions are:
- is it possible to have twinning in P1? Can it be detwinned?
- if we can't get better crystals, will it ever be possible to convince a 
referee that the high Rfree is due to twinning and that the model is ok?

- apart from getting better crystals, is there anything we could try to improve 
our data, lower our Rfree? 

Thanks!

Jose Trincao
José Trincão, PhD   c...@fct-unl
2829-516 Caparica, Portugal

"It's very hard to make predictions... especially about the future" - Niels Bohr

Re: [ccp4bb] Nvidia 3D vision + 1920x1080 Desktop Displays

[Greg Warren]

I have Nvidia 3D vision running on the Samsung SyncMaster 2233.  One note of 
caution, for the Quadra FX3800 if you are using dual monitors I haven't found a 
way to get TwinView to work with the Nvidia 195.30 beta linux driver.  You can 
configure for 2 X-screens to drive the two screens as a work around.  This is 
most likely a 3800 problem since the 3800 has 1 DVI and 2 HDMI outputs instead 
of 2 DVI outputs.  If you are looking for a new graphics card as well and like 
dual monitors I would stay away from the Quadro FX1800 and FX3800.

The Nvidia 3D vision quality is better than Zalman but the Zalman glasses are 
much lighter if you do a lot of stereo.

Greg

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Christian 
Rausch
Sent: Wednesday, March 03, 2010 8:51 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Nvidia 3D vision + 1920x1080 Desktop Displays

Hello,

is someone using Nvidia 3D vision + a compatible 1920x1080 23.5" Desktop 
Display e.g.
ACER GD245HQ 120 Hz LCD display
OR
Alienware OptX AW2310 120 Hz LCD display?

Is it running nicely with Linux + Nvidia's Linux driver?

How is the stereo quality compared to Zalman's 3D-LCDs or the old 
CrystalEyes shutter glasses + CRT monitor?



Thank you,
Christian Rausch


-- 

Dr. Christian Rausch   rau...@wzw.tum.de
Lehrstuhl f. Biologische Chemie   Phone: +49 (0)8161 71-4050
Technische Universitaet MuenchenFax:   -4352
85350 Freising-Weihenstephan
Germany http://www.wzw.tum.de/bc

Re: [ccp4bb] Nvidia 3D vision + 1920x1080 Desktop Displays

[Sabuj Pattanayek]

No, and it has nothing to do with the monitor. It's the sync signal
from the nvidia emitter which isn't compatible with nuvision,
crystaleyes, or edimensional goggles.

On Wed, Mar 3, 2010 at 10:22 AM, Brick, Peter  wrote:
> A related question:
>
> Can one use the old Crystal Eyes glasses system with the new LCD displays? 
> And if not why not?

Re: [ccp4bb] Nvidia 3D vision + 1920x1080 Desktop Displays

[Brick, Peter]

A related question:

Can one use the old Crystal Eyes glasses system with the new LCD displays? And 
if not why not? 
 
Peter B.

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Christian 
Rausch
Sent: 03 March 2010 15:51
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Nvidia 3D vision + 1920x1080 Desktop Displays

Hello,

is someone using Nvidia 3D vision + a compatible 1920x1080 23.5" Desktop 
Display e.g.
ACER GD245HQ 120 Hz LCD display
OR
Alienware OptX AW2310 120 Hz LCD display?

Is it running nicely with Linux + Nvidia's Linux driver?

How is the stereo quality compared to Zalman's 3D-LCDs or the old 
CrystalEyes shutter glasses + CRT monitor?



Thank you,
Christian Rausch


-- 

Dr. Christian Rausch   rau...@wzw.tum.de
Lehrstuhl f. Biologische Chemie   Phone: +49 (0)8161 71-4050
Technische Universitaet MuenchenFax:   -4352
85350 Freising-Weihenstephan
Germany http://www.wzw.tum.de/bc

Re: [ccp4bb] Nvidia 3D vision + 1920x1080 Desktop Displays

[Ajit Datta]

I am using the combination you are asking for with alienware monitor. The 
driver I am using is 195.30 beta. It works very well.
Quality is much much better than Zalman and somewhat better than CRTs.

Hope it helps.

Ajit B.

- Original Message -
From: Christian Rausch 
Date: Wednesday, March 3, 2010 10:51 am
Subject: [ccp4bb] Nvidia 3D vision + 1920x1080 Desktop Displays
To: CCP4BB@JISCMAIL.AC.UK


> Hello,
> 
> is someone using Nvidia 3D vision + a compatible 1920x1080 23.5" 
> Desktop 
> Display e.g.
> ACER GD245HQ 120 Hz LCD display
> OR
> Alienware OptX AW2310 120 Hz LCD display?
> 
> Is it running nicely with Linux + Nvidia's Linux driver?
> 
> How is the stereo quality compared to Zalman's 3D-LCDs or the old 
> CrystalEyes shutter glasses + CRT monitor?
> 
> 
> 
> Thank you,
> Christian Rausch
> 
> 
> -- 
> 
> Dr. Christian Rausch   rau...@wzw.tum.de
> Lehrstuhl f. Biologische Chemie   Phone: +49 (0)8161 71-4050
> Technische Universitaet MuenchenFax:   -4352
> 85350 Freising-Weihenstephan
> Germany 
> 

[ccp4bb] crystallization of highly-glycosylated protein complex-avoid phase separation

[Jerry McCully]

Dear ALL:

 Recently we've been trying hard to crystallize a highly glycosylated 
protein complex ( 30% percent of carbohydrate in the total 120KD molecular 
weight). 

   IT is a high affinity protein complex. One component can be crystallized in 
high salt condition and the other can be crystallized in PEG.  

Through screening, we happened to get some very ugly crystals in PEG condition 
using gel-fil purified complex sample. 

The problem is that it is very hard to repeat the screening condition. In 
contrast, it is very 
easy to get phase separation in the drop
although we tried to optimize the protein and precipitant concentration. 

  We tried to de-glycosylated using PNGase and EndoH but failed in 
non-denaturing condition.

Hampton additive screen  did not help either. We tried seeding several times 
but so far we have not got any better luck.

  Can anyone give some guidance here? Thanks a lot,

Jerry McCully



   
  
_
Hotmail: Powerful Free email with security by Microsoft.
http://clk.atdmt.com/GBL/go/201469230/direct/01/

[ccp4bb] Nvidia 3D vision + 1920x1080 Desktop Displays

[Christian Rausch]

Hello,

is someone using Nvidia 3D vision + a compatible 1920x1080 23.5" Desktop 
Display e.g.

ACER GD245HQ 120 Hz LCD display
OR
Alienware OptX AW2310 120 Hz LCD display?

Is it running nicely with Linux + Nvidia's Linux driver?

How is the stereo quality compared to Zalman's 3D-LCDs or the old 
CrystalEyes shutter glasses + CRT monitor?




Thank you,
Christian Rausch


--

Dr. Christian Rausch   rau...@wzw.tum.de
Lehrstuhl f. Biologische Chemie   Phone: +49 (0)8161 71-4050
Technische Universitaet MuenchenFax:   -4352
85350 Freising-Weihenstephan
Germany http://www.wzw.tum.de/bc

[ccp4bb] density in LLG maps for heavy atoms sit on xtal axes?

[Francis E Reyes]

Is this a cause for concern? FOM's are over 0.5 and Phasing Power is over 2.0.
Thanks

FR

-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

Re: [ccp4bb] _diffrn.detail in PDB sf.cif releases

[Martyn Winn]

I'll update the CCP4 version of the dictionary
(ccp4/lib/data/cif_mm.dic). Thanks for the heads-up.

As you say, the workaround meanwhile is to edit the .cif file to
remove/change any offending lines. 

Martyn

On Wed, 2010-03-03 at 11:24 +, Thomas Womack wrote:
> I notice that a fair number of PDB-deposited sets of structure factors
> in sf.cif format (fourteen of them in the March 2 2010 release)
> contain an _diffrn.detail line; this comes to my attention because
> ccp4-6.1.2's cif2mtz falls over when it encounters such a line and I
> have to edit the CIF manually to get it to continue.
> 
> I have never observed this line to have a value other than '?'; is it
> known what software produces sf.cif files with this meaningless and
> problematic line in, and how to make it stop?
> 
> http://mmcif.rcsb.org/dictionaries/mmcif_pdbx.dic/Categories/diffrn.html
> 
> does not mention _diffrn.detail, although it offers an optional
> _diffrn.details line, and one example where that was used to describe
> a data-gathering protocol where exposure increased over time.
> 
> Tom
-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603634Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***

[ccp4bb] REMINDER: BEAMTIME ON THE ESRF Bio-SAXS BEAMLINE ID14-3

[David FLOT]

-

REMINDER: BEAMTIME ON THE ESRF Bio-SAXS BEAMLINE ID14-3

The Bio-SAXS beamline at ID14-3 at the ESRF ( 
http://www.esrf.fr/UsersAndScience/Experiments/MX/About_our_beamlines/ID14-3 
) has now been in operation for over a year.


Robotic sample loading is available on the beamline using a device 
constructed in a collaboration between the EMBL (Grenoble and Hamburg 
outstations) and the ESRF. Automated data analysis is also implemented 
following the model of the SAXS facility at X-33, EMBL Hamburg 
(processing and preliminary analysis).


The end-station can rapidly provide Users with standard data concerning 
the size (radius of gyration, maximum dimension and volume) and 
molecular weight of samples and allow on-the fly / /ab-inito// shape 
reconstruction in order to provide feedback enabling the data collection 
strategies to be optimized. Access to this Bio-SAXS facility for SANS 
users (small angle neutron scattering at the Institute Laue- Langevin) 
just after their neutron experiment is possible if required. The 
procedure is to first apply for the SANS experiment, specifying that 
access to ESRF beamtime is also requested.  The ILL will then indicate 
if an ESRF rolling proposal is to be completed. First Users using both 
facilities are expected this summer. The complementary information 
provided by neutron scattering (i.e. contrast variation) and X-ray 
scattering can be obtained in a single visit to the Grenoble site.


Application for beam-time on ID14-3 can be made via the rolling access 
mechanism at ANY time. Those who wish to apply should use the mechanism at:


http://www.esrf.fr/UsersAndScience/UserGuide/Applying/ProposalGuidelines/MXnon-BAGproposal 



where it must be clearly indicated in the title of the proposal that the 
application is for Bio-SAXS beamtime on ID14-3.  Please note that BAG 
members should also continue to apply using the rolling mechanism.  
However, in the next proposal round (September 2010) BAGs will also be 
able to apply through the BAG system.


--


Dr David FLOT
Beam-Line Operation Manager Tel : (+33) 4 76 88 17 63
Structural Biology GroupFax : (+33) 4 76 88 26 24
ESRF
B.P. 220, 6 rue Jules Horowitz  e-mail : david.f...@esrf.fr
F-38043 GRENOBLE CEDEX  http://www.esrf.eu

[ccp4bb] _diffrn.detail in PDB sf.cif releases

[Thomas Womack]

I notice that a fair number of PDB-deposited sets of structure factors in 
sf.cif format (fourteen of them in the March 2 2010 release) contain an 
_diffrn.detail line; this comes to my attention because ccp4-6.1.2's cif2mtz 
falls over when it encounters such a line and I have to edit the CIF manually 
to get it to continue.

I have never observed this line to have a value other than '?'; is it known 
what software produces sf.cif files with this meaningless and problematic line 
in, and how to make it stop?

http://mmcif.rcsb.org/dictionaries/mmcif_pdbx.dic/Categories/diffrn.html

does not mention _diffrn.detail, although it offers an optional _diffrn.details 
line, and one example where that was used to describe a data-gathering protocol 
where exposure increased over time.

Tom

Re: [ccp4bb] twin refinement

[Randy Read]

Hi,

You don't say whether you've considered the possibility that the true symmetry 
is higher than P61, e.g. P6122.  If there's higher symmetry consistent with 
your data, then either pointless or xtriage will tell you which space groups to 
consider for test refinements.  Another good test (if you haven't allowed 
NCS-related copies to diverge in the refinement in P61) is the R vs R test, to 
tell whether the apparent twin operator is really a symmetry operator in the 
model.

Note that the R-factors aren't the best indicator, as they tend to drop when 
you assume perfect twinning, even if it doesn't exist.  I think Garib has some 
of his talks on the web, giving some indication of what you can expect.

Regards,

Randy Read

On 3 Mar 2010, at 04:35, subhash C bihani wrote:

> Hi
> 
> i am refining a protein strucutre with space group P61. Intesity statistics
> doesnot suggest any twining but refmac and phenix xtriage suggest a twin
> operator  with fraction 0.48. when refined with this twin operator R factors
> come dowm by 3-5% and also map looks much better. but upon closer inspceion it
> seems that maps are heavily biased toward the model in both refmac and phenix 
> (
> I have mutated one lysine to his and it changed the map to cover his). my
> question is why twin refinement maps are biased and what are the ways to
> overcome this.
> 
> my second question is how to decide whether to use twin refinement or not. is 
> it
> depends on R factor statistics or we have to check some other parameters.
> 
> thanks in advance
> subhash bihani
> scientific officer
> Bhabha Atomic Research Centre
> Trombay-400085
> Mumbai(M.S.)
> India
> Ph. +912594688 (o)
> +919322191020
> subhash bihani
> scientific officer
> Bhabha Atomic Research Centre
> Trombay-400085
> Mumbai(M.S.)
> India
> Ph. +912594688 (o)
> +919322191020
> subhash bihani
> scientific officer
> Bhabha Atomic Research Centre
> Trombay-400085
> Mumbai(M.S.)
> India
> Ph. +912594688 (o)
> +919322191020
> 
> 
> 
> 
> 
> -

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk