Re: [ccp4bb] How to calculate the contacts between the dimer-dimer interface
If you just want the residues involved in the interface, you can use the byres selection commands in Pymol. select contacts, (byres monA and (monB around 4)) which will show all the residues on monA that are within 4 Ang. of Mon B. Steve -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Xiaoyi Deng Sent: Thursday, September 20, 2007 1:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to calculate the contacts between the dimer-dimer interface Dear all: I used moleman2 to calculate the contacts between chain A and B. Can anyone suggest a program to calculate the contacts between the interface of dimer-dimer? Thank you, Xiaoyi Graduate student University of Nebraska Medical center -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [ccp4bb] centrosymm structure
oopss...Not science: Proteins: Structure, Function, and Genetics Volume 16, Issue 3 , Pages 301 - 305 (1993) -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Soisson, Stephen Michael Sent: Friday, August 24, 2007 10:59 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] centrosymm structure Jeremy Berg, Rubredoxin. In Science around 1995. Steve -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp Sent: Friday, August 24, 2007 10:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] centrosymm structure Dear All, there was a paper (quite) a while ago where someone made for the first time a racemic protein mixture, obtained a centrosymmetric structure and solved it (not the 2003 PNAS paper by the Eisenberg grp). Hints appreciated. Thx, br - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - People can be divided in three classes: The few who make things happen The many who watch things happen And the overwhelming majority who have no idea what is happening. - -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. -- -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. -- -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [ccp4bb] centrosymm structure
Jeremy Berg, Rubredoxin. In Science around 1995. Steve -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp Sent: Friday, August 24, 2007 10:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] centrosymm structure Dear All, there was a paper (quite) a while ago where someone made for the first time a racemic protein mixture, obtained a centrosymmetric structure and solved it (not the 2003 PNAS paper by the Eisenberg grp). Hints appreciated. Thx, br - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - People can be divided in three classes: The few who make things happen The many who watch things happen And the overwhelming majority who have no idea what is happening. - -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [ccp4bb] Combining MR and MAD phases
If you want to combine though, I use the molrep phases to get all heavy atoms in an anomalous fourier map, then go to SHARP with these sites and use the 'External phases' option in the SHARP gui. Works well for me. This has worked well for me too...I highly recommend SHARP. Good luck- Steve -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Anastassis Perrakis Sent: Tuesday, July 17, 2007 12:56 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Combining MR and MAD phases I would be tempted to say that you don't need to combine; with 1.7 A data, refinement should do it with no trouble. And, yes, of course ARP/wARP (7.0) would be the best way to do it ;-) If you want to combine though, I use the molrep phases to get all heavy atoms in an anomalous fourier map, then go to SHARP with these sites and use the 'External phases' option in the SHARP gui. Works well for me. I also recall that Phaser has an option for exactly do that, but with SAD data only. But, again, if you have 1.7 A data good old refinement and auto- building will (likely) do the job in a glance. Tassos PS If you dont want to install arp/warp locally why not try: http://cluster.embl-hamburg.de/ARPwARP/remote-http.html PS2 Apologies for the shameless promotion of ARP/wARP ;-) On 17 Jul 2007, at 18:22, Joe Batchelor wrote: Hi, I have a 1.7 A native dataset, a good MR solution for 2/3 of the protein, and MAD phases to 3 A. How should I combine the MR phases with the MAD phases? Thanks, Joe -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [ccp4bb] Eden SUSE linux libfftw.so.2
SuSE is a Mandrake derivative, so that is your best bet. It is likely that the Rehat RPM will work too. Make sure that the library goes to the right place after you install it (especially if you go Redhat) - you may have to put a symbolic link where the program in question is looking for this... Good luck- Steve -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Juergen J. Mueller Sent: Wednesday, June 13, 2007 9:08 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Eden SUSE linux libfftw.so.2 Dear all, trying to install electron density calculation program eden-5.3-1.2.el4.mok.i386.rpm under SUSE linux 9.3-10.1 the libfftw.so.2 is missing. Does anybody know which provider is so equivalent to SUSE that the programs can be mixed (fftw2 from REDHAT, MANDRAKE, ...)? Many thanks, Jürgen -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [ccp4bb] B-factor sharpening in CCP4 or Coot
Eleanor was kind enough to modify truncate years ago for me to do this - I would guess the feature is still there. Thanks again Eleanor! Steve -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jeff Lee Sent: Wednesday, June 13, 2007 1:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] B-factor sharpening in CCP4 or Coot Hi, I have a question for everyone. I wanted to up-weight my high resolution terms in my electron density map by applying a B-factor sharpening term. I have mtz files produced from DM and I usually use Coot to generate my electron density maps. I was wondering is there an easy way to apply a B-factor sharpening term in Coot? If not, is there a program in ccp4 where by I can set the B-sharp factor? Thanks Jeff -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [ccp4bb] B-factor sharpening in CCP4 or Coot
Senility is, in fact, setting in. It was a modified version of CAD! Sorry for the confusion. To further compound the confusion, I am not sure if my solution is what you are really looking for, although I suspect you should try it. What we did was use an overall negative B-factor to achieve a sharpening effect (Cell 119(3):393-405). Others had done this before (David Borhani comes to mind)anyway, it can be very, very useful. Steve -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Soisson, Stephen Michael Sent: Wednesday, June 13, 2007 1:23 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] B-factor sharpening in CCP4 or Coot Eleanor was kind enough to modify truncate years ago for me to do this - I would guess the feature is still there. Thanks again Eleanor! Steve -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jeff Lee Sent: Wednesday, June 13, 2007 1:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] B-factor sharpening in CCP4 or Coot Hi, I have a question for everyone. I wanted to up-weight my high resolution terms in my electron density map by applying a B-factor sharpening term. I have mtz files produced from DM and I usually use Coot to generate my electron density maps. I was wondering is there an easy way to apply a B-factor sharpening term in Coot? If not, is there a program in ccp4 where by I can set the B-sharp factor? Thanks Jeff -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. -- -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. -- -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [ccp4bb] How to determine ligand binding from diffraction pattern?
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 In my opinion, this is not easy to reduce to a single number since there are too many variables. True resolution and quality of the data, the actual non-isomorphism (and in particular conformational changes), B-factor of the ligand, etc. The coy answer would be enough refinement to convince yourself that it is or isn't there, but in all seriousness, it does boil down to a judgment call on when you have reached the point of diminishing returns. I think the problem is particularly complex with the fragment screening work you describe, since you may or may not know where the ligands are actually binding. Tricky stuff indeed. Steve -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [ccp4bb] How to determine ligand binding from diffraction pattern?
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 From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Joe Chen Sent: Monday, May 28, 2007 4:35 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to determine ligand binding from diffraction pattern? 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 -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [ccp4bb] A bit of history: John W Backus obit [Broadcast]
Regarding David Sayre, Ed Lattman once opined in a Sayre's Equation lecture to graduate students that if only David Sayre would focus his attention on macromolecular crystallography again, that perhaps the phase problem would be solved. Lofty praise indeed. Thanks for the anecdote Bob. Steve -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Robert Sweet Sent: Tuesday, March 20, 2007 11:15 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] A bit of history: John W Backus obit [Broadcast] I'm pretty sure that the crystallographer was David Sayre. I also believe (not documented well enough for wikipedia, but perhaps for here) that IBM were so pleased with this performance that they made David an IBM Fellow, which meant that he could do anything he wanted for the rest of his life. Here's what he decided to do: He's known in crystallography for the Sayre Equation, a fundamental relationship in direct methods. Also, maybe not so well known, he was a major driving force behind the method of visualizing single molecules or cells from diffraction patterns: J. Miao, H. N. Chapman, J. Kirz, D. Sayre and K. O. Hodgson, TTaking X-ray Diffraction to the Limit: Macromolecular Structures from Femtosecond X-ray Pulses and Diffraction Microscopy of Cells with Synchrotron Radiation, Annu. Rev. Biophys. Biomol. Struct. 33, 157-176 (2004). He and I used to use adjacent darkrooms at the NSLS for developing x-ray films (the '80's). I'd meet him on the long walk, ask what he was doing, and smile sympathetically when he said he was going to image single yeast cells. Well, they're essentially doing it now. One never want's to underestimate David Sayre's ability to find phases. When David retired from IBM and his adjunct appointment at SUNY Stony Brook one of his old buddies from the FORTRAN project spoke at the symposium. Perhaps it was Backus. They both said that the period of developing that language in a small team was one of the happiest times of their lives. Don't take this as fact, but this is what I remember. Bob On Tue, 20 Mar 2007, Bart Hazes wrote: The storey also made it to the CNN business page and they add... The Fortran programming language, which was a huge leap forward in easing the creation of computer software, was released in 1957, said the report. Backus launched his research project at IBM (Charts) four years earlier, assembling a diverse team of 10, including a chess wizard, a crystallographer and a cryptographer, said the Times. Full story @: http://money.cnn.com/2007/03/20/news/newsmakers/backus/index.htm?postver sion=2007032008 Bart P.Artymiuk wrote: A bit of history: NY Times obituary for John W. Backus, 82, developer of Fortran, without which CCP4 and much else would not have been possible. http://www.nytimes.com/2007/03/19/obituaries/20cnd-backus.html?ex=133204 3200en=adde3ee5a1875330ei=5124partner=permalinkexprod=permalink Pete A -- = Robert M. Sweet E-Dress: [EMAIL PROTECTED] Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) = -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [ccp4bb] electron density maps in Coot vs O / Pymol
I am guessing it is a difference in normalization, but I would love to hear a definitive answer from someone. Steve -Original Message- From: CCP4 bulletin board on behalf of mac minista Sent: Wed 2/14/2007 10:59 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] electron density maps in Coot vs O / Pymol Dear all, I have noticed that going from refmac 5 (script) to generate fo-fc and 2fo-fc maps in O / Pymol once and Coot in the other, the outcome is not exactly the same electron density maps-I mean some differences are seen. I have used the following columns in Coot (latest version): FOFCWT, PHFOFCWT and 2FOFCWT, PH2FOFCWT. The .o map file was generated using FFT, MAPMASK and MAPMAN. I want to know why I am not getting identical maps, and if there is a solution to avoid this problem then I would really appreciate your help. With regards Mac Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites http://farechase.yahoo.com/promo-generic-14795097;_ylc=X3oDMTFtNW45amVpBF9TAzk3NDA3NTg5BF9zAzI3MTk0ODEEcG9zAzEEc2VjA21haWx0YWdsaW5lBHNsawNxMS0wNw-- to find flight and hotel bargains. -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
