Re: [ccp4bb] LSQKAB, version 6.0 vs version 6.1

I think the LSQKAB change at Line 291(old)/Line 300(new) DOES introduce new and possibly incorrect logic. I haven't looked at all the code, but this one change does seem to substitute a check that chain, residue number, and atom name (only 3 characters; incorrect) match [OLD] for a check that chai

Re: [ccp4bb] ccp4i 6.1.0 and file paths

I think a behavior much like this IS seen in earlier versions. One especially nasty example is when you are re-running a job (say, to correct a parameter or two), make a few wrong clicks as Miguel mentions, and the interface asks "Overwrite file X", and you say Yes, thinking "It's file X from my

Re: [ccp4bb] ccp4-6.1.0: iMosflm

Hi Tim: I know, I've been through it with them too, but neither debian nor ccp4 want to change, so it was easier just to roll my own bltwish package, being the natural born diplomat that I am. As for the debian maintainer, it seems kind of arbitrary to remove an executable that builds by

[ccp4bb] Off topic question

Hi CCP4ers Apologies for the off topic... I have been trying to get hold of L-ribulose-5-phosphate (D- is readily available). Does anyone know where I can get such a compound? Thanks in advance for any suggestions and Merry Xmas! Gina

[ccp4bb] A primer on linux shared libs [was: ccp4-6.1.0: iMosflm libtermcap.so.2 error - SOLVED]

On Monday 22 December 2008, Winter, G (Graeme) wrote: > Dear Victor and BB, > > For reasons which are opaque at best some linux distributions > name this file libtermcap.so, and some libtermcap.so.2. This much I can explain, and since it is useful knowledge for tracking down linux library prob

Re: [ccp4bb] ccp4-6.1.0: iMosflm

I had a quick look at the wiki. It claims one requires the executable bltwish for ccp4i to work correctly. However, the maintainer is correct (I asked him the same thing some time ago) - the blt-library works perfectly if only you replace the few occurrences of 'bltwish' in the scripts in $CCP4

Re: [ccp4bb] LSQKAB, version 6.0 vs version 6.1

In case it helps, you can see the diffs between the 6.0.2 version and the 6.1 version here: http://www.ccp4.ac.uk/ccp4bin/viewcvs/ccp4/src/lsqkab.f.diff?r1=text&tr1=1.51&r2=text&tr2=1.42.2.2&diff_format=h The obvious changes seem to be some code from Clemens to make sure that insertion codes m

Re: [ccp4bb] ccp4-6.1.0: iMosflm

Hi Harry et al: Well, it it makes you feel any better, imosflm works great for me on ubuntu ibex: http://diablo.ucsc.edu/~wgscott/debian/imosflm_xubuntu_ibex.png I just lost my imosflm virginity at the synchrotron a few nights ago (they have it working or rh at SSRL). If it helps anyone,

Re: [ccp4bb] LSQKAB, version 6.0 vs version 6.1

Hi Tim, Not a stupid question at all. This is how I came to think that version 6.0 uses atoms with alternative conformations: If I do the same superposition (with a pdb file that contains alternative conformations) with LSQKAB version 6.0 and 6.1: 1) Version 6.0 reports 110 atoms "to be refi

[ccp4bb] mitegen loops with Rigaku Actor robot

Does anybody have any tips on getting the automatic centering option of the Rigaku Actor Robot (Cameraman software) to work with Mitegen loops? Thanks Roger Williams Laboratory of Molecular Biology Medical Research Council Hills Road Cambridge CB22QH UK Phone: +44-1223-402171 FAX: +44-122

Re: [ccp4bb] LSQKAB, version 6.0 vs version 6.1

Not using lsqkab very often, this might be a stupid question: How do you know that version 6.0 _DOES_ include multiple conformations? Maybe it only does not report their omission? Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On M

Re: [ccp4bb] Refmac and MSE?

Sorry - Garib points out form factors are there - labelled atom type scat cromer ... You shoulfd find SE if there is a SE atom in the pdb file Eleanor loop_ _atom_type_symbol _atom_type_scat_Cromer_Mann_a1 _atom_type_scat_Cromer_Mann_b1 _atom_type_scat_Cromer_Mann_a2 _atom_

[ccp4bb] LSQKAB, version 6.0 vs version 6.1

Dear colleagues, While using LSQKAB I have encountered what it seems a different behavior between version 6.1 and 6.0. If I superpose two structures with LSQKAB version 6.1 (included in CCP4-6.1.0), residues with alternative conformations are not included for the calculations. This is an exa

[ccp4bb] ccp4i 6.1.0 and file paths

Dear all, I have a request to the developers of CCP4I. I find very bizarre and potentially quite confusing that the default value for file paths is not _strictly_ the project directory but, instead, any directory that you happen to choose a moment before using 'Full-path', for instance (s

Re: [ccp4bb] Refmac and MSE?

I also see such peaks. I have assumed it is because the default in REFMAC is to use the CuKa SE formfactor, which should be modified at shorter wave lengths. (Solution - copy $C:IBD/atomsf.lib and modify Se c to c(CuKa) - f' for your wavelength.. then assign ATOMSF myversion/atomsf.lib in the

Re: [ccp4bb] Transferring a Free R set.

Alun R. Coker wrote: Hi All, I have been in the habit of transferring my initial free R assignments to any new data sets or to isomorphous data sets such as substrate complexes. Although theoretically this is necessary to obtain a valid free R many of my colleagues maintain that this is comp

Re: [ccp4bb] ccp4-6.1.0: iMosflm libtermcap.so.2 error - SOLVED

Hi Just to let you all know - (1) tkImageLoad.so is also obsolete - we stopped using it a couple of versions ago (so I should have removed it from the distro...) (2) The files starting with .# are relics from edits, and shouldn't be necessary - again, I should have removed those So it lo

Re: [ccp4bb] Bug in Sketcher?

Dear James, I have just tried this on a linux binary installation and it appeared to work fine. Please could you tell me what platform you are running on? Many thanks, Graeme CCP4 Support Team -Original Message- From: CCP4 bulletin board on behalf of James M. Vergis Sent: Sun 12/21/2

Re: [ccp4bb] refmac 5.5.063 vs. 5.5.066

Just to add to that, Windows users can download a Refmac 5.5.0070 binary from the CCP4 prerelease page. www.ccp4.ac.uk/prerelease Norman Norman Stein CCP4 Daresbury Laboratory -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Pavol Skubak Sent: 19

Re: [ccp4bb] ccp4-6.1.0: iMosflm libtermcap.so.2 error - SOLVED

Dear Victor and BB, For reasons which are opaque at best some linux distributions name this file libtermcap.so, and some libtermcap.so.2. Evidently the binary worked fine on the collection we tested. Fortunately there is a relatively simple if inelegant fix: cd $CLIB ln -s /usr/lib/libtermcap.