[ccp4bb] Molecular replacement
Dear All,
I wanted to solve one of my new structures by molecular
replacement. I got three short search motifs from three
different structures available in the PDB. My question is, how
do I use all the search models to solve the structure.
With by best regards,
Sekar
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[ccp4bb] phaser ensemble xyz output
should i take it that when given > 1 .pdb in an ensemble, phaser will output only the first member of the ensemble, and its up to the user to tranform the others? if so, i gather there are no keywords to make phaser do that automatically? -bryan
Re: [ccp4bb] How to calculate the contacts between the dimer-dimer interface
Xiaoyi, When I'm interested in dimer interfaces, or protein ligand contacts I usually use Molprobity to define the interface. http://molprobity.biochem.duke.edu/ It is a bit of a process, but here's the rundown: Load your .pdb into molprobity Add hydrogens Visualize interface contacts Then select your two 'half-interfaces' and run probe One of the outputs from this is a list that has: residue from half 1 : residue from half 2 : contact type : details I usually will take this list of residues and display them in pymol, then add dashes for hydrogen bonds using the dist command -bob
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] How to calculate the contacts between the dimer-dimer interface
Hi, apart from the ccp4 "contact" it's also worth checking the following servers: pisa: http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html protein-protein interaction server: http://www.biochem.ucl.ac.uk/bsm/PP/server/index.html Cheers Nikos Xiaoyi Deng wrote: > 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 > > -- *** Nikos Pinotsis, PhD EMBL-Hamburg, c/o DESY Notkestr. 85, Geb. 25A 22603 Hamburg, Germany Phone : +49 40 89902144 Fax: +49 40 89902149 e-mail : [EMAIL PROTECTED] ***
Re: [ccp4bb] post-doc possibility in newcastle
You'd need quite a large French press or meat grinder to crack the cells and get the protein. William Scott wrote: On Thu, 20 Sep 2007 17:23:05 +0100 "R. J. Lewis" <[EMAIL PROTECTED]> wrote: a large signalling complex called the 'stressosome' from B. subtilis. - If you decide to go for the human form of this signalling complex, I am an over-producing strain. -- >> Andreas Förster << Imperial College London https://wasatch.biochem.utah.edu/~andreas
[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
Re: [ccp4bb] post-doc possibility in newcastle
On Thu, 20 Sep 2007 17:23:05 +0100 "R. J. Lewis" <[EMAIL PROTECTED]> wrote: a large signalling complex called the 'stressosome' from B. subtilis. - If you decide to go for the human form of this signalling complex, I am an over-producing strain.
[ccp4bb] post-doc possibility in newcastle
Dear all There is a vacancy in my lab for a biochemist. It's a 3-year position funded by the UK BBSRC. The post is to provide a functional interpretation of our structure determination (unpublished) of a large signalling complex called the 'stressosome' from B. subtilis. Ideally, I'm looking for someone who has solid experience of fluorescence/ITC/SPR and has good molecular biology skills. There will be scope to learn some crystallography and cryo-EM, but the focus of the post will be on the biochemistry of the system. You can find further details: http://www.ncl.ac.uk/vacancies/vacancy.phtml?ref=A1003R Although the deadline is, in theory, Monday 24th, applications up to 1st October will be considered. Rick -- R. J. Lewis Professor of Structural Biology Institute for Cell and Molecular Biosciences Faculty of Medical Sciences Tel: +44 (0)191 222 5482 University of Newcastle Fax: +44 (0)191 222 7424 Newcastle upon Tyne, NE2 4HH, UKEmail: [EMAIL PROTECTED]
Re: [ccp4bb] unsubscibe
Go to the jiscmail page and follow the directions. On Thu, 20 Sep 2007 16:31:07 +0200 Anat Bashan <[EMAIL PROTECTED]> wrote: unsubscibe
[ccp4bb] unsubscibe
unsubscibe
Re: [ccp4bb] anisotropic scaling in refmac versions
Dear Eleanor, no I was not talking about a cubic SG (in my case, as an example, it's actually orthorhombic). I think that the most likely explanation is that there was indeed a bug, at least on Refmac's version 5.3.0032 Here go some selected fragments of a 0032 log (no confusion with aniso atomic displacement factors): >... > > ### > ### > ### > ### CCP4 6.0: Refmac_5.3.0032version 5.3.0032 : 02/16/06## > ### > User: alebus Run date: 8/ 5/2007 Run time: 10:57:27 >... >Data line--- refi type REST resi MLKF meth CGMAT bref ISOT > REFI > Data line--- ncyc 10 > NCYC > Data line--- scal type BULK reso 2.100 39.621 LSSC ANISO > EXPE > SCAL > Data line--- solvent YES VDWProb 1.2 IONProb 0.8 RSHRink 0.8 > SOLV >... >Cell from mtz :34.743 124.050 138.30390.00090.00090.000 >Space group from mtz: number - 19; name - P 21 21 21 >... >--- > Restraint type N restraints Rms Delta Av(Sigma) >Bond distances: refined atoms 3149 0.018 0.022 >Bond distances: others 2177 0.002 0.020 >--- > >- >Overall : scale =1.143, B = -0.029 >Babinet"s bulk solvent: scale =0.133, B = 229.342 >Partial structure1: scale =0.404, B = 35.602 >Overall anisotropic scale factors > B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00 >- > >- >Overall R factor = 0.2092 >Free R factor= 0.2497 >Overall figure of merit = 0.8314 >- > Trying gamma equal 0.000E+00 > Gamma decreased to 0.000E+00 >... Indeed, now I've updated to Refmac_5.3.0040, and the problem is solved (Rfactors, as expected, are a bit better now; same input, last cycle's figures : >--- > Restraint type N restraints Rms Delta Av(Sigma) >Bond distances: refined atoms 3149 0.017 0.022 >Bond distances: others 2177 0.002 0.020 >--- > >- >Overall : scale =1.154, B = -0.003 >Babinet"s bulk solvent: scale =0.169, B = 300.000 >Partial structure1: scale =0.403, B = 43.715 >Overall anisotropic scale factors > B11 = 0.13 B22 = 1.51 B33 = -1.64 B12 = 0.00 B13 = 0.00 B23 = 0.00 >- > >- >Overall R factor = 0.2046 >Free R factor= 0.2424 >Overall figure of merit = 0.8444 >- ). I believe version 5.3.0032 was the first announced release when going from 5.2 to 5.3, at the time the very useful keyword 'anom formfactor' was added among other changes (but maybe I'm wrong here...). Anyway, of course we should be ourselves aware of keeping updated with the latest versions of the software that we use. A lesson for me as well, is to look carefully at the whole output of the programs, not overlooking parameters/figures that we tend to leave as 'unimportant' when they certainly are (even if it's not the Rfac, which tends to become _the_ figure to look at in refinement...). It might be useful for others though, to check on the Refmac version they're now running and see if these messages are pertinent to them. cheers, Ale On 20/09/2007, Eleanor Dodson <[EMAIL PROTECTED]> wrote: > I cant answer - but this version certainly generates anisotropic scales.. > > We have ccp4.6.0.2 installed) > > > ### > ### > ### > ### CCP4 6.0: Refmac_5.3.0037version 5.3.0037 : 03/29/06## > ### > User: eleanor Run date: 18/ 9/2007 Run time: 09:3
Re: [ccp4bb] anisotropic scaling in refmac versions
Hi I think there you're confusing overall aniso scaling of the Fcalc's to the Fobs's (normally the default) which is controlled by SCALE LSSC ANISO, and refinement of individual atomic displacement parameters controlled by REFI BREF ISOT/ANISO. In the script aniso scaling is turned on (even though it's the default) and there were no Bij's output. -- Ian > -Original Message- > From: Benini, Stefano [mailto:[EMAIL PROTECTED] > Sent: 20 September 2007 09:56 > To: Ian Tickle > Subject: RE: [ccp4bb] anisotropic scaling in refmac versions > > I think it has nothing to do with versions of refmac (which > has been always very reliable!) > > I thought it could be because in one of the scripts the guy > had the B factor refinement as ISOT > > > > > refi - > > > > type REST - > > > > resi MLKF - > > > > meth CGMAT - > > > > bref ISOT > > as you can see in the original posting > > and I guess that scaling aniso would not refine B factor > anisotropically > > best regards > > Stefano > > *** > Stefano Benini PhD > Structural Biology - DECS > Mereside 50S38 > Alderley Park > Phone:+44-1625-518293 (ext.: 28293) > http://structuralbiology-ap.rd.astrazeneca.net/people/Stefano- > Benini/Stefano-Benini.html > ** > > > -Original Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] > Behalf Of Ian > Tickle > Sent: 20 September 2007 08:32 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] anisotropic scaling in refmac versions > > > I can't say because I didn't install 0037 (I went straight > from 5.2.0019 to 5.3.0040 so I was blissfully unaware of the > problem!). However according to the original posting it's > easy to tell because if the alleged bug is present you don't > see the overall Bij terms in the output PDB file. > > HTH > > -- Ian > > > -Original Message- > > From: [EMAIL PROTECTED] > > [mailto:[EMAIL PROTECTED] On Behalf Of Nalam, Madhavi > > Sent: 19 September 2007 14:57 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: RE: [ccp4bb] anisotropic scaling in refmac versions > > > > I used Refmac 5.3.0037 to refine a structure. Is there a > > problem with this version too? > > Thank you in advance, > > Madhavi > > > > > > -Original Message- > > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On > > Behalf Of Ian Tickle > > Sent: Wednesday, September 19, 2007 8:21 AM > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] anisotropic scaling in refmac versions > > > > I think this isn't a problem in the latest version of Refmac > > (0040 I think), so try downloading it from the York site. > > > > -- Ian > > > > > -Original Message- > > > From: [EMAIL PROTECTED] > > > [mailto:[EMAIL PROTECTED] On Behalf Of Alejandro > > Buschiazzo > > > Sent: 19 September 2007 13:20 > > > To: Lari Lehtio > > > Cc: CCP4BB@JISCMAIL.AC.UK > > > Subject: Re: [ccp4bb] anisotropic scaling in refmac versions > > > > > > Hello, > > > I wonder if there was any direct answer to the question that > > > Lari made a > > > couple of days ago. > > > Sorry if I missed it, but I believe there wasn't any > > response to the > > > ccp4bb... > > > > > > thanks > > > > > > Alejandro > > > > > > > > > Lari Lehtio wrote: > > > > Dear All, > > > > > > > > I just came back from the beam line and started to continue > > > my work on a structure that I solved > > > > while collecting other data. I noticed that my R-factors > > > were a lot higher at home lab although > > > > I was using the exact same input files. > > > > > > > > I then noticed that the version was different: > > > > > > > > The one giving lower R-factors was > > > > Refmac_5.2.0019version 5.2.0019 : 06/09/05 > > > > > > > > And the one giving higher: > > > > Refmac_5.3.0032version 5.3.0032 : 02/16/06 > > > > > > > > I happened to have the older version also in my home pc, so > > > I tried again and indeed, 5.2.0019 > > > > gives lower R-factors. > > > > > > > > The input command is identical, but when I "diffed" the > > > pdb-files, I noticed that anisotropic > > > > scale is missing in the newer files. Did I make a mistake? > > > How can I turn it back on. > > > > > > > > Below is the diff output and the command used for refmac. > > > > > > > > Thank you in advance, > > > > > > > > ~L~ > > > > > > > > < REMARK 3 PROGRAM : REFMAC 5.2.0019 > > > > > > > >> REMARK 3 PROGRAM : REFMAC 5.3.0032 > > > >> > > > > < REMARK 3 R VALUE (WORKING + TEST SET) : 0.21101 > > > > < REMARK 3 R VALUE(WORKING SET) : 0.20867 > > > > < REMARK 3 FREE R VALUE : 0.25559 > > > > > > > >> REMARK 3 R VALUE (WORKING + TEST SET) : 0.23077 > > > >> REMARK 3 R VALUE(WORKING SET) : 0.22807 > > > >> REMARK 3 FREE R VALUE : 0.
Re: [ccp4bb] phaser and percent composition result [ part 2]
On Sep 18 2007, Bryan W. Lepore wrote: i wrote "(ensemble) / (sequence)" to get a percent composition i forgot to emphasize that i do not mean the Vm or the "Z" composition, but the composition as one would enter e.g. COMPosition ENSEmble mol1 FRACtional 0.22 or COMPosition SCAttering -bryan In the current version of phaser, if you give the command "VERBOSE ON", then you get information about molecular weights and the fraction of the asymmetric unit that each ensemble represents. But it's a good point -- I've frequently wanted to know myself what Phaser thought the fractional composition was. So I've just changed the imminent release so that it will print out a brief summary of the fractional composition to the normal (non-verbose) logfile. Regards, Randy Read
Re: [ccp4bb] anisotropic scaling in refmac versions
I cant answer - but this version certainly generates anisotropic scales.. We have ccp4.6.0.2 installed) ### ### ### ### CCP4 6.0: Refmac_5.3.0037version 5.3.0037 : 03/29/06## ### User: eleanor Run date: 18/ 9/2007 Run time: 09:34:20 . - Overall : scale =0.480, B = -7.297 Partial structure1: scale =0.383, B = 84.682 Overall anisotropic scale factors B11 = -1.37 B22 = -1.37 B33 = 2.06 B12 = -0.69 B13 = 0.00 B23 = 0.00 - You havent got a cubic spacegroup have you? Eleanor Alejandro Buschiazzo wrote: Hello, I wonder if there was any direct answer to the question that Lari made a couple of days ago. Sorry if I missed it, but I believe there wasn't any response to the ccp4bb... thanks Alejandro Lari Lehtio wrote: Dear All, I just came back from the beam line and started to continue my work on a structure that I solved while collecting other data. I noticed that my R-factors were a lot higher at home lab although I was using the exact same input files. I then noticed that the version was different: The one giving lower R-factors was Refmac_5.2.0019version 5.2.0019 : 06/09/05And the one giving higher: Refmac_5.3.0032version 5.3.0032 : 02/16/06I happened to have the older version also in my home pc, so I tried again and indeed, 5.2.0019 gives lower R-factors. The input command is identical, but when I "diffed" the pdb-files, I noticed that anisotropic scale is missing in the newer files. Did I make a mistake? How can I turn it back on. Below is the diff output and the command used for refmac. Thank you in advance, ~L~ < REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 PROGRAM : REFMAC 5.3.0032 < REMARK 3 R VALUE (WORKING + TEST SET) : 0.21101 < REMARK 3 R VALUE(WORKING SET) : 0.20867 < REMARK 3 FREE R VALUE : 0.25559 REMARK 3 R VALUE (WORKING + TEST SET) : 0.23077 REMARK 3 R VALUE(WORKING SET) : 0.22807 REMARK 3 FREE R VALUE : 0.28228 < REMARK 3 BIN R VALUE (WORKING SET) :0.240 REMARK 3 BIN R VALUE (WORKING SET) :0.262 < REMARK 3 BIN FREE R VALUE:0.288 REMARK 3 BIN FREE R VALUE:0.343 < REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.271 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.941 < REMARK 3B11 (A**2) : 2.35 < REMARK 3B22 (A**2) : -1.99 < REMARK 3B33 (A**2) : 0.32 REMARK 3B11 (A**2) : 0.00 REMARK 3B22 (A**2) : 0.00 REMARK 3B33 (A**2) : 0.00 < REMARK 3B13 (A**2) : 0.90 REMARK 3B13 (A**2) : 0.00 _ make check NONE make - hydrogen YES - hout NO - peptide NO - cispeptide YES - ssbridge YES - symmetry YES - sugar YES - connectivity NO - link NO refi - type REST - resi MLKF - meth CGMAT - bref ISOT ncyc 10 scal - type SIMP - reso 2.100 19.976 - LSSC - ANISO - EXPE solvent YES - VDWProb 1.4 - IONProb 0.8 - RSHRink 0.8 weight - MATRIX 0.1 monitor MEDIUM - torsion 10.0 - distance 10.0 - angle 10.0 - plane 10.0 - chiral 10.0 - bfactor 10.0 - bsphere 10.0 - rbond 10.0 - ncsr 10.0 labin FP=FP SIGFP=SIGFP -FREE=FreeRflag labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM PNAME unknown DNAME unknown130907 RSIZE 80 END ___ Lari Lehtiö Structural Genomics Consortium Medical Biochemistry & Biophysics Dept. Karolinska Institute Stockholm, Sweden ___
Re: [ccp4bb] anisotropic scaling in refmac versions
I can't say because I didn't install 0037 (I went straight from 5.2.0019 to 5.3.0040 so I was blissfully unaware of the problem!). However according to the original posting it's easy to tell because if the alleged bug is present you don't see the overall Bij terms in the output PDB file. HTH -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Nalam, Madhavi > Sent: 19 September 2007 14:57 > To: CCP4BB@JISCMAIL.AC.UK > Subject: RE: [ccp4bb] anisotropic scaling in refmac versions > > I used Refmac 5.3.0037 to refine a structure. Is there a > problem with this version too? > Thank you in advance, > Madhavi > > > -Original Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On > Behalf Of Ian Tickle > Sent: Wednesday, September 19, 2007 8:21 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] anisotropic scaling in refmac versions > > I think this isn't a problem in the latest version of Refmac > (0040 I think), so try downloading it from the York site. > > -- Ian > > > -Original Message- > > From: [EMAIL PROTECTED] > > [mailto:[EMAIL PROTECTED] On Behalf Of Alejandro > Buschiazzo > > Sent: 19 September 2007 13:20 > > To: Lari Lehtio > > Cc: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] anisotropic scaling in refmac versions > > > > Hello, > > I wonder if there was any direct answer to the question that > > Lari made a > > couple of days ago. > > Sorry if I missed it, but I believe there wasn't any > response to the > > ccp4bb... > > > > thanks > > > > Alejandro > > > > > > Lari Lehtio wrote: > > > Dear All, > > > > > > I just came back from the beam line and started to continue > > my work on a structure that I solved > > > while collecting other data. I noticed that my R-factors > > were a lot higher at home lab although > > > I was using the exact same input files. > > > > > > I then noticed that the version was different: > > > > > > The one giving lower R-factors was > > > Refmac_5.2.0019version 5.2.0019 : 06/09/05 > > > > > > And the one giving higher: > > > Refmac_5.3.0032version 5.3.0032 : 02/16/06 > > > > > > I happened to have the older version also in my home pc, so > > I tried again and indeed, 5.2.0019 > > > gives lower R-factors. > > > > > > The input command is identical, but when I "diffed" the > > pdb-files, I noticed that anisotropic > > > scale is missing in the newer files. Did I make a mistake? > > How can I turn it back on. > > > > > > Below is the diff output and the command used for refmac. > > > > > > Thank you in advance, > > > > > > ~L~ > > > > > > < REMARK 3 PROGRAM : REFMAC 5.2.0019 > > > > > >> REMARK 3 PROGRAM : REFMAC 5.3.0032 > > >> > > > < REMARK 3 R VALUE (WORKING + TEST SET) : 0.21101 > > > < REMARK 3 R VALUE(WORKING SET) : 0.20867 > > > < REMARK 3 FREE R VALUE : 0.25559 > > > > > >> REMARK 3 R VALUE (WORKING + TEST SET) : 0.23077 > > >> REMARK 3 R VALUE(WORKING SET) : 0.22807 > > >> REMARK 3 FREE R VALUE : 0.28228 > > >> > > > < REMARK 3 BIN R VALUE (WORKING SET) :0.240 > > > > > >> REMARK 3 BIN R VALUE (WORKING SET) :0.262 > > >> > > > < REMARK 3 BIN FREE R VALUE:0.288 > > > > > >> REMARK 3 BIN FREE R VALUE:0.343 > > >> > > > < REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.271 > > > > > >> REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.941 > > >> > > > < REMARK 3B11 (A**2) : 2.35 > > > < REMARK 3B22 (A**2) :-1.99 > > > < REMARK 3B33 (A**2) : 0.32 > > > > > >> REMARK 3B11 (A**2) : 0.00 > > >> REMARK 3B22 (A**2) : 0.00 > > >> REMARK 3B33 (A**2) : 0.00 > > >> > > > < REMARK 3B13 (A**2) : 0.90 > > > > > >> REMARK 3B13 (A**2) : 0.00 > > >> > > > > > > > > __ > > ___ > > > make check NONE > > > make - > > > hydrogen YES - > > > hout NO - > > > peptide NO - > > > cispeptide YES - > > > ssbridge YES - > > > symmetry YES - > > > sugar YES - > > > connectivity NO - > > > link NO > > > refi - > > > type REST - > > > resi MLKF - > > > meth CGMAT - > > > bref ISOT > > > ncyc 10 > > > scal - > > > type SIMP - > > > reso 2.100 19.976 - > > > LSSC - > > > ANISO - > > > EXPE > > > solvent YES - > > > VDWProb 1.4 - > > > IONProb 0.8 - > > > RSHRink 0.8 > > > weight - > > > MATRIX 0.1 > > > monitor MEDIUM - > > > torsion 10.0 - > > > distance 10.0 - > > > angle 10.0 - > > > plane 10.0 - > > > chiral 10.0 - > > >
