[ccp4bb] Fwd: [ccp4bb] Crystal vacuum cleaner

2009-03-27 Thread Patrick Loll
Pretty cool, but the examples shown are all gigantic. Having just spent a frustrating several hours chasing 5 um crystals, I'd give half my kingdom for a simple way to catch THOSE little buggers (damn you, surface tension!). Begin forwarded message: From: Patrick Shaw Stewart Date: March

[ccp4bb] Fwd: more about low order reflections

2009-02-21 Thread Richard Gillilan
Since Sacha is having trouble posting directly the list I will forward his latest message since It addresses my second set of questions: Begin forwarded message: From: Alexandre OURJOUMTSEV Thank you, Richard, for your questions ! Unfortunately, I failed to pass my mail to the CCP4bb - I

[ccp4bb] Fwd: [ccp4bb] dry shipper & FedEx

2009-02-02 Thread Aleksander Roszak
Hi Uli, When we send our dry shipper from UK to ESRF, Grenoble, via FedEx we place a following note on the box: DRY SHIPPER, Non-hazardous, non-toxic, non-flammable, non- restricted. Conforms with the IATA regulations Special Provision A800 We write the same in the Contents place of the I

Re: [ccp4bb] Fwd: Twinning

2009-01-18 Thread Peter Cherepanov
Dear Andreas and all, refining multiple models together would sound like the most straightforward solution in a case like that. But (please correct me if I am wrong), generally, such trick can only work in P1: obviously, any symmetry operation (but lattice translation) applied to the sh

Re: [ccp4bb] Fwd: Twinning

2009-01-07 Thread Andreas Förster
Hey Stephen, how about simply putting three models, separated by 16A, into your original unit cell and refining them together. You'd have to guess their fractional occupancies from the heights of the Patterson peaks (and make them add up to one, obviously). This approach (in contrast to cor

Re: [ccp4bb] Fwd: Twinning

2009-01-07 Thread Isupov, Michail
wishes Misha Isupov University of Exeter From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Stephen Hare [s.h...@mail.cryst.bbk.ac.uk] Sent: 06 January 2009 16:35 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: Twinning Dear All, We are

Re: [ccp4bb] Fwd: Twinning

2009-01-06 Thread Lijun Liu
This is an interesting case but your description lacked the diffraction part. Assuming no Heavy Atom sites in the native structure. Based on your description, another possibility may be Lattice Translocation. - Ref: J. Wang, S. Kamtekar, A. J. Berman and T. A. Steitz. Correctio

Re: [ccp4bb] Fwd: Twinning

2009-01-06 Thread Ethan Merritt
On Tuesday 06 January 2009 08:35:19 Stephen Hare wrote: > Dear All, > > We are currently working on a structure of apparent P21 symmetry which > has been solved by molecular replacement. The data are to 2.7Å but the > Rfree will not drop below 30%. The density is clear for the model we > hav

[ccp4bb] Fwd: Twinning

2009-01-06 Thread Stephen Hare
Dear All, We are currently working on a structure of apparent P21 symmetry which has been solved by molecular replacement. The data are to 2.7Å but the Rfree will not drop below 30%. The density is clear for the model we have, however there is extra density that suggests a shift of the st

Re: [ccp4bb] Fwd: [ccp4bb] site mutation evaluation

2008-12-03 Thread Juergen Bosch
And this is what I call just in time publication: Davis et al. RosettaLigand Docking with Full Ligand and Receptor Flexibility. J Mol Biol (2008) pp. available online today. Jürgen On 3 Dec 2008, at 01:47, David Briggs wrote: Hi there Assuming you have a model of the complex you are inte

[ccp4bb] Fwd: REMINDER: Workshop BioOrbit associated to the 4th SOLEIL Users' Meeting - On-line registration

2008-12-03 Thread Valerie Biou
Satellite Workshop “BioOrbit: coupling methods for exploring structures of increasing complexity from molecules to tissues” on Monday 19th (afternoon) & Tuesday 20th January, 2009 Auditorium Bloch at CEA L'Orme des Merisiers (next to SOLEIL), Saint Aubin (France) ***

[ccp4bb] Fwd: [ccp4bb] site mutation evaluation

2008-12-03 Thread David Briggs
Hi there Assuming you have a model of the complex you are interested in tinkering with, try submitting it to the Rosetta Alanine Scanning servery thing. http://robetta.bakerlab.org/alascansubmit.jsp By default, it mutates each residue in the interface to ala, does some local minimisation (side ch

Re: [ccp4bb] Fwd: [ccp4bb] X-Ray versus NMR Structure

2008-11-16 Thread mesters
Charlie, This is not a good comparison because combining NMR and X-ray data is like having higher resolution again (i.e. more constraints). Further, the informations are much more of a "redundant nature" than "profoundly complementary" as they stem from the same molecule. More resolution would

[ccp4bb] Fwd: [ccp4bb] X-Ray versus NMR Structure

2008-11-15 Thread Charles W. Carter Jr.
Begin forwarded message: From: "Charles W. Carter Jr." <[EMAIL PROTECTED]> Date: November 15, 2008 9:51:36 AM EST To: Boaz Shaanan <[EMAIL PROTECTED]> Subject: Re: [ccp4bb] X-Ray versus NMR Structure Boaz: I have always and still fee that this paper is a landmark, because it shows that nei

[ccp4bb] Fwd: [ccp4bb] crystallization of proteins with His-tag and/or c-myc tags

2008-11-12 Thread Kathleen Frey
Returning to the previous discussion, we've had luck crystallizing several proteins with a His-tag. We've used both N-terminal and C-terminal his tags, and have had success with both of them. In one of our structures, the his tag actually formed an interface for crystal packing. We have also tried

[ccp4bb] Fwd: [ccp4bb] Radius of Gyration

2008-10-29 Thread Nathan Cowieson
I know it's not CCP4 but I use moleman2 for this, http://xray.bmc.uu.se/usf/xutil.html . You read your pdb into moleman and choose the STatistics option, it outputs Rg among lots of other things. It can all be scripted too if you wanted to say charge through the whole PDB and get Rg for ever

[ccp4bb] Fwd: [ccp4bb] Spooky, moving crystals

2008-07-21 Thread Richard Gillilan
I recently had exactly this problem only I caught the crystal frozen in the act of being catapulted out of the loop. I was using a thicker- than usual oil for cryoprotectant and kept seeing empty loops with what looked like long clear hairs attached. Finally, one loop had a graceful arc of f

[ccp4bb] Fwd: DNA/RNA base stacking restraint add-on to CNS avaliable.

2008-07-14 Thread William Scott
Date: Mon, 14 Jul 2008 15:22:52 -0700 (PDT) From: Martin.Laurberg <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Cc: CCP4BB@JISCMAIL.AC.UK Subject: DNA/RNA base stacking restraint add-on to CNS avaliable. Dear all, A DNA/RNA base stacking restraint add-on to CNS version 1.21 is avaliable for downlo

[ccp4bb] [Fwd: Re: [ccp4bb] CCP4 & Coot on Ubuntu]

2008-06-10 Thread Martyn Winn
I now have Hardy Heron on my EM64T machine, and ccp4 works fine. For bltwish, I'm still using the version I compiled from source ages ago, as described on my page. Did you try that? Martyn Forwarded Message > From: Tim Gruene <[EMAIL PROTECTED]> > Reply-To: Tim Gruene <[EMAIL P

[ccp4bb] Fwd: [ccp4bb] HEK293S

2008-06-06 Thread A. Radu Aricescu
Dear Vaheh, I'm not aware of a commercial or cell bank source, but you can get these cells from HG Khorana's lab at MIT. Best wishes, radu -- A. Radu Aricescu, PhD University of Oxford Wellcome Trust Centre for Human Genetics Division of Structural Biolo

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation and mosaicity

2008-06-06 Thread R.M. Garavito
Tommi, The question has been asked and answered not by protein crystallography, but by cyroelectron microscopy and EM freeze etch research. Even as far back as the early 1960's, people noticed that liq. N2 was really slow at cooling. Read the cyroEM work on the bacteriorhodopsin photocyc

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation and mosaicity

2008-06-05 Thread Tommi Kajander
according to literature,see below and references http://www.px.nsls.bnl.gov/courses/papers/ZD_EG_papers.html, it is not clear that liq. propane plunged item would cool faster. (whilst i havent tested this)... Would anyone have actual experimental data with protein crystals on the hyperquenchin

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation and mosaicity

2008-06-05 Thread Edward Berry
I think the important thing here is that liquid nitrogen in the lab tends to be exactly at its boiling point, since the temperature is maintained by continuously boiling off some of the N2. This means the only mechanism for heat absorption is through vaporization, depending on the latent heat of

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation and mosaicity

2008-06-05 Thread Petr Leiman
yes you are right, but I assumed if people see a cloud of condensed fog over their LN2 bath they should remove that by a) filling up the bowl completely e.g. some LN2 drips out of the bowl b) blow the fog away before you dip I think the original poster meant the relatively low heat conduction of

[ccp4bb] Fwd: [ccp4bb] crystallisation and mosaicity

2008-06-05 Thread Patrick Loll
Hi Charlie, yes you are right, but I assumed if people see a cloud of condensed fog over their LN2 bath they should remove that by a) filling up the bowl completely e.g. some LN2 drips out of the bowl b) blow the fog away before you dip True; this has been demonstrated quite rigorously:

[ccp4bb] Fwd: Right terminal residues for constructs.

2008-05-20 Thread Jayashankar
-- Forwarded message -- From: Jayashankar <[EMAIL PROTECTED]> Date: Tue, May 20, 2008 at 7:34 PM Subject: Right terminal residues for constructs. To: CCP4BB@jiscmail.ac.uk Dear friends and scientists, (A pre-Structural biological question.) I Have a multidomain protein , I know

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

2008-04-15 Thread Jochen Muller-Dieckmann
ary 18, 2008 2:20 AM To: <mailto:CCP4BB@JISCMAIL.AC.UK>CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: [ccp4bb] crystallisation robot One thing that people often overlook is that quite a lot of protein can be lost by denaturation on the surface of the drop. This is more significant for smaller drops.

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

2008-04-15 Thread Stephen McMahon
EMAIL PROTECTED] ** ** Headington, Oxford OX3 7BNhttp://www.oppf.ox.ac.uk ** Original message Date: Mon, 14 Apr 2008 17:10:26 -0400 From: JOE CRYSTAL <[EMAIL PROTECTED]> Subject: Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

2008-04-15 Thread Tom Walter
87547 ** ** Roosevelt Drive [EMAIL PROTECTED] ** ** Headington, Oxford OX3 7BNhttp://www.oppf.ox.ac.uk ** Original message >Date: Mon, 14 Apr 2008 17:10:26 -0400 >From: JOE CRYSTAL <[EMAIL PROTECTED]> >Subject: Re: [

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

2008-04-15 Thread Yusuke Yamada
Thanks Leo for your introduction. However, the link is broken. Please look at the following page. http://pfweis.kek.jp/protein/Robot/PXS/index-e.html Best regards, Yusuke --- Yusuke Yamada, Ph.D. Photon Factory High Energy Accelerator Research Organi

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

2008-04-14 Thread Frank von Delft
B@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot Hi, Does anyone have information about how long it takes to set up a 96-well tray for the crystallization robots available? Besides cost per tray and maintenance cost, another important feature we consider is the time

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

2008-04-14 Thread Chavas Leo
Dear Joe -- Does anyone have information about how long it takes to set up a 96- well tray for the crystallization robots available? Besides cost per tray and maintenance cost, another important feature we consider is the time for setting up a 96-well tray. It is an important factor sinc

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

2008-04-14 Thread Artem Evdokimov
board [mailto:[EMAIL PROTECTED] On Behalf Of JOE CRYSTAL Sent: Monday, April 14, 2008 5:10 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot Hi, Does anyone have information about how long it takes to set up a 96-well tray for the crystallization robots

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

2008-04-14 Thread Janet Newman
CP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot Hi, Does anyone have information about how long it takes to set up a 96-well tray for the crystallization robots available? Besides cost per tray and maintenance cost, another important feature we consider is the time for se

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

2008-04-14 Thread Andreas Forster
gt; -- > > > Lisa A. Nagy, Ph.D. > > > University of Alabama-Birmingham > > > [EMAIL PROTECTED] > > > > > > -Original Message- > > > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of > > > Patrick Shaw Stewart >

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

2008-04-14 Thread William Scott
ilto:[EMAIL PROTECTED] On Behalf Of Patrick Shaw Stewart Sent: Friday, January 18, 2008 2:20 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: [ccp4bb] crystallisation robot One thing that people often overlook is that quite a lot of protein can be lost by denaturation on the surface of the drop. T

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

2008-04-14 Thread JOE CRYSTAL
aw Stewart > Sent: Friday, January 18, 2008 2:20 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Fwd: [ccp4bb] crystallisation robot > > One thing that people often overlook is that quite a lot of protein > can be lost by denaturation on the surface of the drop. This is more > s

[ccp4bb] [Fwd: Re: Summary of Thermofluor]

2008-03-31 Thread mesters
Dear [EMAIL PROTECTED], I have to correct my earlier statement in an previous email to the bulletin board (see below): One of the detection channels of the AB StepOne is in the right detection range and the signal is strong! Our lab just purchased the new AB StepOne RT-PCR machine for conduct

Re: [ccp4bb] Fwd: Re: [ccp4bb] Glu+Arg solutions for solubility

2008-03-03 Thread Stephen Prince
from the horses mouth .. - Forwarded message from [EMAIL PROTECTED] - Date: Mon, 03 Mar 2008 10:16:41 + From: Alexander Golovanov <[EMAIL PROTECTED]> Reply-To: Alexander Golovanov <[EMAIL PROTECTED]> Subject: Re: Fwd: Re: [ccp4bb] Glu+Arg solutions for solubility To: St

[ccp4bb] Fwd: [ccp4bb] Calculate dipole moment of ligands from their coordinates

2008-01-28 Thread Miguel Ortiz-Lombardía
Hi all, For those interested, this script can be downloaded from: http://www.ysbl.york.ac.uk/~mol/scripts.html There is a short description as well. It works with proteins and molecules for which you can generate partial charges in a force field su

[ccp4bb] Fwd: [ccp4bb] Summary solvent-resistant Micro-Bridges

2008-01-25 Thread Mark J. van Raaij
Dear All, Please note that I stand corrected and that http://www.crystalmicrosystems.co.uk/ DO sell polypropylene microbridges and that they have distributors in the USA (Hampton Research) and Japan (Ieda Trading Corporation). greetings, Mark PS if anyone knows of solvent-resistant Terazaki

Re: [ccp4bb] Fwd: [ccp4bb] crystallisation robot

2008-01-18 Thread Lisa A Nagy
ECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Patrick Shaw Stewart Sent: Friday, January 18, 2008 2:20 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: [ccp4bb] crystallisation robot One thing that people often overlook is that quite a lot of protei

[ccp4bb] Fwd: [ccp4bb] crystallisation robot

2008-01-18 Thread Patrick Shaw Stewart
One thing that people often overlook is that quite a lot of protein can be lost by denaturation on the surface of the drop. This is more significant for smaller drops. Two suggestions: (1) increase the proportion of protein in the - technical term - teeny drop to say two thirds and (2) cover the

[ccp4bb] Fwd: Web Address

2008-01-02 Thread Charles Ballard
Here is the web address for the streaming http:// extrplay.dl.ac.uk/ Stuart Stuart Eyres Media Services Daresbury Laboratory Tel: 01925 603344

Re: [ccp4bb] [Fwd: Re: [ccp4bb] Expired Crystallization Screening? - what about to freeze ?]

2007-12-27 Thread Janet Newman
2:22 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] [Fwd: Re: [ccp4bb] Expired Crystallization Screening? - what about to freeze ?] We used to freeze screens in 96-well deep blocks and plates - with no apparent issues :-) Some stuff crystallizes out but usually goes right back into solution.

Re: [ccp4bb] [Fwd: Re: [ccp4bb] Expired Crystallization Screening? - what about to freeze ?]

2007-12-27 Thread Artem Evdokimov
:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] [Fwd: Re: [ccp4bb] Expired Crystallization Screening? - what about to freeze ?] Dear all, I was about to write something quite related, but as the topic has just started ... I had better add my comments. I am just establishing a

[ccp4bb] [Fwd: Re: [ccp4bb] Expired Crystallization Screening? - what about to freeze ?]

2007-12-27 Thread iulek
Dear all, I was about to write something quite related, but as the topic has just started ... I had better add my comments. I am just establishing a crystallization facility, but currently in my lab proteins to crystallize will be a rare opportunity (hopefully to increase the number duri

Re: [ccp4bb] Fwd: [ccp4bb] Occupancy refinement of substrate using refmac5

2007-12-18 Thread Edward Berry
Zheng Zhou wrote: Hi, Ed I am dealing the similar problem. I checked CNS qindividual.inp. But how do I refine one compound with two or more possible conformations (mainly due to one bond rotation), each of wihich has a different occupancy? Thanks in advance. Hi Zheng, Others can answer bet

Re: [ccp4bb] Fwd: [ccp4bb] Occupancy refinement of substrate using refmac5

2007-12-18 Thread Zheng Zhou
Hi, Ed I am dealing the similar problem. I checked CNS qindividual.inp. But how do I refine one compound with two or more possible conformations (mainly due to one bond rotation), each of wihich has a different occupancy? Thanks in advance. Joe On Dec 17, 2007 2:24 PM, Edward Berry <[EMAIL PROTE

Re: [ccp4bb] Fwd: [ccp4bb] Occupancy refinement of substrate using refmac5

2007-12-17 Thread Gerard DVD Kleywegt
I thought that I would never have to disagree with both Eleanor and Tassos in the same email, let alone risk being burnt at a stake as a heretic for doubting the Gospel according to Kleywegt, but in my but ... but ... i haven't even said anything! i'm innocent! my name is being used in vain!

Re: [ccp4bb] Fwd: [ccp4bb] Occupancy refinement of substrate using refmac5

2007-12-17 Thread Edward Berry
I think the correlation between occupancy and B-factor depends also on the size of the ligand (relative to resolution). Bob Stroud, I think, has estimated occupancy by comparing the integrated electron density of the ligand with that of a well-defined, isolated water (assumed to be at unit occuanc

Re: [ccp4bb] Fwd: [ccp4bb] Occupancy refinement of substrate using refmac5

2007-12-17 Thread Anastassis Perrakis
In the danger of getting corrected by George twice in the same time (burning stakes excluded...) I am not doubting at all if its doable, but if the final result will be more accurate / useful. Thinking about it, with 1.5 A data it is very likely to be more accurate than manual handling, but

Re: [ccp4bb] Fwd: [ccp4bb] Occupancy refinement of substrate using refmac5

2007-12-17 Thread Santarsiero, Bernard D.
I would also ask what is the actual goal in refining the occupancy of the ligand? While I agree wholeheartedly with George, the B-factors will adequately model a lower ligand occupancy. Usually the question you want to resolve is "Is the ligand really bound in the active site, or is this an artif

Re: [ccp4bb] Fwd: [ccp4bb] Occupancy refinement of substrate using refmac5

2007-12-17 Thread George M. Sheldrick
I thought that I would never have to disagree with both Eleanor and Tassos in the same email, let alone risk being burnt at a stake as a heretic for doubting the Gospel according to Kleywegt, but in my experience, given the very fortunate position that you have data to 1.5A, the refinement of o

Re: [ccp4bb] Fwd: [ccp4bb] Occupancy refinement of substrate using refmac5

2007-12-17 Thread Anastassis Perrakis
I have already changed occupancies as Eleanor mentioned, and got approximate values. But my hope is to try to get much precise ones if possible. I never expected to preach the 'Kleywegt Gospel' in the ccp4bb, but in this case what you need is more accurate answers, not more precise ones (or be

[ccp4bb] Fwd: [ccp4bb] Occupancy refinement of substrate using refmac5

2007-12-17 Thread nkamiya
Dear Profs. Eleanor and Isaac, Thank you for your quick and kind replies. I have already changed occupancies as Eleanor mentioned, and got approximate values. But my hope is to try to get much precise ones if possible. I have heard from my colleague SHELX can refine occupancies, and got its lic

Re: [ccp4bb] [Fwd: [ccp4]: iso - anisotropic B factor refinement on Refmac5]

2007-12-06 Thread Garib Murshudov
This result means that you need to use TLS refinement and it may improve your statistics considerable. Garib On 6 Dec 2007, at 11:27, Ronan Keegan wrote: From: Rafael Couñago <[EMAIL PROTECTED]> Date: 6 December 2007 04:58:51 GMT To: <[EMAIL PROTECTED]> Subject: [ccp4]: iso - anisotropic

[ccp4bb] [Fwd: [ccp4]: iso - anisotropic B factor refinement on Refmac5]

2007-12-06 Thread Ronan Keegan
--- Begin Message --- Hi, I had a very curious result when doing a round of isotropic B factor refinement on Refmac5. After iso B my R is 19.2 and Rf 24.3. My resolution is 1.95, what does not justify anisotropic b-factor refinement. However I did it by mistake and it dropped my R to 17.8

[ccp4bb] Fwd: Re: [ccp4bb] Protein powder diffraction (fwd)

2007-11-14 Thread Jonathan Wright
-- Forwarded message -- Date: Wed, 14 Nov 2007 14:36:32 +0100 From: Margiolaki Rena <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Subject: Fwd: Re: [ccp4bb] Protein powder diffraction Dear Marius, Here are some notes from us, we would welcome news from anyone else. One of our most

Re: [ccp4bb] Fwd: [ccp4bb] CCP4i and modeller integration

2007-11-03 Thread Winn, MD (Martyn)
: Fri 11/2/2007 10:57 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] CCP4i and modeller integration Jayashankar wrote: > Dear friends and scientists, > > I want to ask about for an integration of modeller in the ccp4i > interface. The interface in ccp4i is designed

Re: [ccp4bb] Fwd: [ccp4bb] CCP4i and modeller integration

2007-11-02 Thread Ben Webb
Jayashankar wrote: Dear friends and scientists, I want to ask about for an integration of modeller in the ccp4i interface. The interface in ccp4i is designed for modeller Version 6.2, we have by now modeller 9.2 , which is a lot different. Nevertheless I tried to enter the necessary data i

[ccp4bb] [Fwd: Re: [ccp4bb]: self rotation function matrix & NCS matrix]

2007-08-22 Thread weikai
Hi Eleanor and others: This is a little too late to follow up on this thread. But here is a similar question concerning MR and self-rotation. Without going into the translational part of MR, is it possible to tell the orientation of a 2-fold axis directly from the cross-rotation peaks? e.g. I ha

[ccp4bb] [Fwd: [ccp4bb] accessible surface area of PISA at EBI]

2007-07-17 Thread Hyunchul Kim
Dear all, I understood what they mean. ASA -> Solvent accessible surface area BSA -> Buried area among Solvent accessible surface area when it make interaction Sorry for self-questioning and -answering. Best, Hyunchul Kim Forwarded Message > From: Hyunchul Kim <[EMAIL PROTECTED

[ccp4bb] Fwd: problem with Scala in intel CCP4-6.0.2

2007-07-15 Thread Sheena McGowan
Begin forwarded message: From: Sheena McGowan <[EMAIL PROTECTED]> Date: 16 July 2007 4:11:47 PM To: [EMAIL PROTECTED] Subject: problem with Scala in intel CCP4-6.0.2 Hi I have run into a problem running Scala after Mosflm in CCP4i (CCP4-6.0.2) on an intel Mac. I have copied the error mess

[ccp4bb] Fwd: extend resolution in refmac

2007-07-14 Thread JOE CRYSTAL
Dear all, I am refining a structure in Refmac at 2.3 A and I set resolution range to 2.2 A to extend the resolution. However, Refmac seemed to ignore my setting and still refined structure at 2.3 A. Thank you in advance for your any helpful suggestions. Best, Joe

[ccp4bb] [Fwd: Re: [ccp4bb] Flat Screen and Stereo]

2007-06-22 Thread zach powers
Adding the following commands to my xorg.conf file "fixed" my problem: Section "Extensions" Option "Composite" "Disable" EndSection The screen now makes an attempt to run stereo: it will draw two sets of lines and the eDimensional glasses now work. But the flickering is unbearable

[ccp4bb] Fwd: Re: [ccp4bb] (bigger) fragment identification of limited proteolysis w/ mass-spec

2007-04-01 Thread Paul Kraft
Certainly you can seperate these fragments by SDS-PAGE, cut the bands out, redo the proteolysis and throw them into the MS again... Note: forwarded message attached. - Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo!

[ccp4bb] [Fwd: Re: [ccp4bb] question about redundancy]

2007-03-20 Thread Bart Hazes
Hi Li, There is nothing wrong with your opinion the expected redundancy is indeed 4 because, as you say, each reflection intersects the Ewald sphere twice, once through the top and once through the bottom (redundancy will actually be a bit less due to the missing cusp region). Bart yang li wrot

Re: [ccp4bb] Fwd: [ccp4bb] Swiss humour - no laughing matter? (Re: [ccp4bb] process SeMet labelled data)

2007-03-05 Thread Andreas Forster
Hello Klaus, I think you should give Gerard some "Hofnarrenfreiheit". (That's a fine German word for you to figure out, Gerard.) He is certainly not an evil racist at heart. Andreas Klaus Piontek wrote: Greetings (or in "correct" Swiss German "Grüezi wohl", with Umlaut=vowel mutation) t

[ccp4bb] Fwd: [ccp4bb] Swiss humour - no laughing matter? (Re: [ccp4bb] process SeMet labelled data)

2007-03-01 Thread Klaus Piontek
Greetings (or in "correct" Swiss German "Grüezi wohl", with Umlaut=vowel mutation) to all CCP4BB subscribers, being a CCP4BB reader (and sometimes writer) since something like 15 years, I realized today that the comment of Gerard was the first one I read since then containing a side-swipe r

[ccp4bb] [Fwd: Re: [ccp4bb] how many stuck datasets are actually twinned?]

2007-02-21 Thread Santarsiero, Bernard D.
- It's very possible with any overlap of lattice points, even in the lower symmetry space groups. To extend Eleanor's list: For example, I once had a structure with the unit cell relationship 3c cos(beta) = -a. In cases like that, it's not really a c

[ccp4bb] Fwd: [ccp4bb] pseudotranslation and dyads in NCS

2007-02-19 Thread Daniel Adams
-- Forwarded message -- From: Daniel Adams <[EMAIL PROTECTED]> Date: Feb 16, 2007 12:29 PM Subject: Re: [ccp4bb] pseudotranslation and dyads in NCS To: [EMAIL PROTECTED] My apology for not mentioning unit cell, The P1 unit cell is 74 91 116 109 105 90 Any suggestions or comments

[ccp4bb] Fwd: Re: [ccp4bb] AKTA prime

2007-02-14 Thread Frank Lee
"David R. Cooper" <[EMAIL PROTECTED]> wrote: From: "David R. Cooper" <[EMAIL PROTECTED]> Subject: Re: [ccp4bb] AKTA prime To: Frank Lee <[EMAIL PROTECTED]> Date: Wed, 14 Feb 2007 15:13:18 -0500 Hello, Frank. I seem to be having trouble posting directly to the bulletin board. Perhaps you c

[ccp4bb] [Fwd: [ccp4bb] relation between wavelength and inter-atomic distances]

2007-01-25 Thread Carlos Frazao
Carlos Frazao wrote: Hi, I have once heard and recently read that "the diffraction event results from the fact that both the X-rays wavelength and the atomic distances are of the same magnitude". Although such a relation seems appealing I am unsure if this is not a mere coincidence. Could som

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