Re: [ccp4bb] Question regards to binding affinity of the protein complex?

By the way, I would like to mention that I was sloppy with the language in the original reply - I was referring to complex half-life (T1/2) which is expressed in direct units of time, not the kon or koff, which are expressed in inverse units of time. Thank you Raji Edayathumangalam for pointing thi

Re: [ccp4bb] Why wwPDB and members are doing a poor job.

Dear Colleagues, Warren makes a good point, but let me recast it slightly. We are all part of the structural biology community, and we, as a community, need to get together and explore our options for interchange of information. Some of us already have a proposal pending with the NSF for a co

Re: [ccp4bb] Why wwPDB and members are doing a poor job.

Nevertheless, there is a huge problem with interoperability between software packages, and this core issue greatly frustrates everyone, not only Joe. Frankly, it is a disgrace that even in 2007, software users in structural biology and computational chemistry still cannot reliably exchange basic m

Re: [ccp4bb] Why wwPDB and members are doing a poor job.

Joe, I think this is neither a constructive or accurate statement. I have collaborated with the PDB (both the RCSB and the EBI) for many years and I believe that they are doing a very good job under very difficult circumstances. They have been tasked with curating an ever increasing vol

Re: [ccp4bb] arp/warp in p22121

So I vote for a default of preserving the input convention whatever it is, and I definitely vote against all axis permutations unless a) it's absolutely necessary (e.g. for consistency with other datasets), and b) the user specifically requests it (and really really means it!). Phew! It makes

Re: [ccp4bb] Has anyone seen such density?

Hello, This density is the 'evil sausage-like blobule' that tends to crop up whenever something ill-defined (but sausage-like) binds weakly to the surface of the protein. It could be almost anything - something from the polyacrylic acid, something from Triton (it has lots of sausage-like shapes),

Re: [ccp4bb] Question regards to binding affinity of the protein complex?

Dear TriNgo, The Kd is only 1/2 of the picture. You also should contemplate the consequences of the on and off rate for the complex formation. If the off rate is in the range of minutes then you can have successful purification over size exclusion even though the Kd may be high micromolar. Other

Re: [ccp4bb] Question regards to binding affinity of the protein complex?

I do not know about the affinity required for gel filtration, but I have had success crystallizing a number of protease-inhibitor complexes just by incubating and setting up drops with equimolar amounts of the two components. It is probably to our advantage that we have functional inhibition ass

Re: [ccp4bb] arp/warp in p22121

On second reading maybe I misunderstood what you were saying. If Phaser reads an MTZ file which doesn't conform to the convention (e.g. a<=b<=c NOT true in primitive orthorhombic) then it certainly should not by default permute the axes on output, I agree that that certainly would cause confusion.

Re: [ccp4bb] arp/warp in p22121

Hi Sue It's certainly true that the convention in the 1935 and 1952 editions of IT Volume 1 *appeared* to be the 'standard setting' convention that you describe because only the 'standard' settings were listed, and this was the way that many crystallographers interpreted it (actually only macromol

[ccp4bb] Torsion restraints in refmac

Dear all, just checking my cofactor dictionary produced with prodrg in refmac I realized that the torsion restraints are not taken into account with my default settings. I noticed the old posting from 2001, that "var_" is not used, but if I input an additional line by hand with restr tors inc

Re: [ccp4bb] arp/warp in p22121

I'm confused now, sticking to the IUCr convention should not require any axis permutation. My beef is specifically against unnecessary axis permutations! Surely it's when the program doesn't support the convention that you are forced to permute the axes? Besides I did solve a structure in P22121

Re: [ccp4bb] arp/warp in p22121

The problem is specifically that ARP/wARP *doesn't* support the IUCr convention as given in IT (Vol. A, >= 1983 edition, Table 9.3.4.1, p.758 in 5th ed.) regarding choice of cell in primitive orthorhombic space groups, and I suspect in centred monoclinic ones also. AFAIK ARP/wARP and pointless ar

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 Subje

Re: [ccp4bb] Archiving onto DVD with RH linux

Acording to the product specs from NEC that drive model is only designed to write up to 8X speed, it was never intended to write any faster. Nothing wrong with the drive, it just is not designed to burn any faster. For burning 16X discs at 8X speed, maybe a firmware update, or maybe it is a s

[ccp4bb] Jobs at the Macromolecular Structure Database at the EBI.

Hello, The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) is currently looking for suitable candidates to fill in three job vacancies (Scientific Database Curator, Scientific Programmer and Software Engineer) at the EBI, Hinxton (near Cambridge, UK). Interested candi

[ccp4bb] sealed tube estimations

Dear all, we are in the progress of 'collecting data' on a sealed tube machine which we want to buy. I know that this issue was handled several times here and I also looked through older mails. However, my impression is that the generators that are offered change quite quickly according to recent

Re: [ccp4bb] Seeking Linux experts' adivice

Sounds like an OpenGL graphics driver misconfiguration to me. What is the graphics card and driver, and like Kay asked, how was the driver configured? A friend's computer at one of the lab's here had similar issues, turns out the NVidia driver was severly misconfigured. Fixed following the re

Re: [ccp4bb] arp/warp in p22121

> -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Victor Lamzin > Sent: 18 September 2007 12:48 > To: [EMAIL PROTECTED]; CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] arp/warp in p22121 > > Dear Florian, > > ARP/wARP supports 65 space groups where pr

Re: [ccp4bb] anisotropic scaling in refmac versions

Hi, Indeed, I just tested version 5.3.0040, and there the ANISO seems to work. ~L~ ___ Lari Lehtiö Structural Genomics Consortium Medical Biochemistry & Biophysics Dept. Karolinska Institute Stockholm, Sweden __

Re: [ccp4bb] Archiving onto DVD with RH linux

Hi Dave, I have found in the past that some DVD writers need a bios / firmware upgrade to be able to cope with the faster DVD's. Usually this is a windows program you run which overwrites something inside the DVD hardware itself, which will then work fine for writing. This is unlikely to be helpfu

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 >

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

[ccp4bb] Archiving onto DVD with RH linux

Dear ccp4BB, Sorry for the non-ccp4 post. I have been using a NEC DVD_RW ND-2500A drive to archive onto DVD-Rs (using 'mkisofs' and 'dvdrecord' commands) from our RH linux system. This has worked very well with 8x compatible DVD-R disks, but doesn't recognise the newer 16x disks that only seem t

[ccp4bb] Question regards to binding affinity of the protein complex?

Dear CCP4 Users, I'd like to solve the structure of the protein-protein complex. I intend to purify and incubate the complex then run gel-filtration before setting crystal. I'd like to know your experience about the Kd value of the interaction in order to get the complex after running the gel-filt

[ccp4bb] Summary: pymol movies scripts

Hi there! here's my original post: Hi all, I'm starting using pymol to generate movies to show my structure. While its seems fairly easy to generate simple movies with rocking or rotating molecules, I have been finding some difficulties understanding how to generate more complex movies. For i

Re: [ccp4bb] REFMAC and Hetroatoms

You need the atom name CA and CL moved one space to the left relative to C O N etc.. And correct the atom type in cols 76?? from C to CL and CA ( again moved one space to left) Eleanor Vineet Gaur wrote: Hi all i am having Ca2+ and Cl- as hetroatoms in my protein structure. while doing refin

[ccp4bb] PhD and postdoc positions at Tromsø

Dear ccp4bb readers, Two research positions funded by the Norwegian Research Council will be available starting in January 2008 at the University of Tromsø, Norway. A PhD student and a postdoctoral scientist will study structural selectivity determinants of protein kinase ligands and ramificati

Re: [ccp4bb] Seeking Linux experts' adivice

Yanming Zhang schrieb: Hi, All, After lunching pymol, if I drag the Xterm window produced by PYMOL using mouse, my computer will suddenly freeze, the keyboard seems no longer functioning. The only thing I can do is to re-boot my Linux system. This problem makes it almost impossible for me to