Re: [ccp4bb] How to handle b-factors at low resolution and very incomplete model?

On 11:15 Tue 23 Aug , Engin Özkan wrote: I distinctly remember reading a paper where B factors were predicted based on the location of the atoms (core vs exposed, main chain vs side chain) and the predicted values were not that far off. Here's one along those lines: Flexibility and

Re: [ccp4bb] generating separate pdb files

On 08:02 Tue 14 Dec , Charles W. Carter, Jr wrote: I've run aground trying to find a program to write out individual pdb files from a long file with multiple (100) models. My file does not contain separate chain IDs, so I cannot use moleman2 or splitpdb.p. I want to retain information

Re: [ccp4bb] - subtracting diffraction images?

On 10:51 Wed 17 Nov , Warren, Mark R wrote: I am trying to compare the difference between two diffraction images from a Mar detector before and after irradiation. At present I have used the marcombine program to subtract the diffraction images, but I don't have any statistical

Re: [ccp4bb] Molecular replacement question

On 09:50 Tue 14 Sep , Dirk Kostrewa wrote: I would spend some time in improving the search model, first. If there are more than one possible search molecules in the PDB, I usually do a structural alignment (ssm superposition) to get an idea about the flexibility of the search molecules.

Re: [ccp4bb] Hydrogen Bond Restraints

On 09:41 Wed 14 Apr , Bradley Hintze wrote: I am looking for published examples where hydrogen bond restraints were helpful in refinement. Can anyone point me to some papers? Try this one: An improved hydrogen bond potential: Impact on medium resolution protein structures. Felcy Fabiola,

Re: [ccp4bb] sulfur sad phasing

On 13:16 Wed 11 Nov , Matthias Zebisch wrote: What is the optimal wavelength for Sulfur SAD phasing? Is it 1.9A or should one go below that to reduce absorption/damage. Some additional advice about factors other than wavelength: For S-SAD on a home Cu source, my previous lab showed that

Re: [ccp4bb] gpp4 version 1.2 released

On 10:36 Mon 05 Oct , Kevin Cowtan wrote: Given that the current CCP4 build system is somewhat non-standard, I might be prepared to support an effort which provided an alternative build system to work with the CCP4 provided source code, however. I made about half of such an effort a few

Re: [ccp4bb] question of extra high B factor

with an average B of 80 A^2 (JMB 328:893 (2003)). One referee had some objections to this, so we performed analyses of the whole Protein Data Bank for proteins at 2.5-3.0 A (see Fig. 2D in the paper). You may find this figure useful if you need to convince anyone. -- Thanks, Donnie Donnie

Re: [ccp4bb] Official PDB Nomenclature?

, SIGUIJ, and LINK are converted, as are DNA residue names (e.g., A, C, T, G of v2.3 cf. DA, DC, DT, DG of v3.2). -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University pgpgYDJcko5Yh.pgp Description: PGP signature

Re: [ccp4bb] [offtopic?] putting b-factors from two pdbs on the same scale and interpretation

give you 10-30 != 30-100, and 45-30 != 150-100. -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University pgpFuOGMByPUC.pgp Description: PGP signature

Re: [ccp4bb] homology modeling

a multiple-template-based model using Modeller, all with very little knowledge or input required on the user end. Evaluating the likely correctness afterwards is a different story... -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University pgpWMs80Q7nEF.pgp Description: PGP

Re: [ccp4bb] Computer hardware and OS survey

references to the point of being unfixable. My current workflow involves switching to Endnote in OS X as a final step for adding references after writing the rest in Google Docs. -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University pgphkiwcC371X.pgp Description: PGP

Re: [ccp4bb] ccp4mg and OS X

: http://www.ysbl.york.ac.uk/~ccp4mg/download2/ I clicked the source code link and it didn't send me anywhere. Is the source code going to show up at some point, or will that wait until the rewrite is entirely complete? -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State

Re: [ccp4bb] Low-level disable ccp4i database...?

). -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University pgpq9dGnAUi5j.pgp Description: PGP signature

Re: [ccp4bb] Fix for MIFit8 compatibility issue with CCP4 6.1.1

(not just water peaks) -- Thanks, Donnie Donnie Berkholz P. Andrew Karplus lab Oregon State University pgpXoh69TK36J.pgp Description: PGP signature

Re: [ccp4bb] Off-topic: Open Source / Freeware Binding Curve Fitting Software

http://www.unipress.waw.pl/fityk/ or extrema http://exsitewebware.com/extrema/. -- Thanks, Donnie Donnie Berkholz Developer, Gentoo Linux Blog: http://dberkholz.wordpress.com pgpJ2XljtpW4n.pgp Description: PGP signature

Re: [ccp4bb] [PyMOL] Caution - 120 Hz LCDs: Not CRT killers yet...

will be supported with the NVIDIA GeForce 3D vision glasses in upcoming driver release by spring 2009. http://www.nvidia.com/object/quadro_stereo_technology.html -- Thanks, Donnie Donnie Berkholz Developer, Gentoo Linux Blog: http://dberkholz.wordpress.com pgpMPcd7crlIu.pgp Description: PGP signature

Re: [ccp4bb] Replacement for arp_waters?

a GUI for it, it effectively doesn't exist for them. I would enjoy understanding what the philosophy of the Coot developers is on this matter. -- Thanks, Donnie Donnie Berkholz Developer, Gentoo Linux Blog: http://dberkholz.wordpress.com pgpzevSbMp2N7.pgp Description: PGP signature

Re: [ccp4bb] RNA Torsion Angle Measurement Error

data set? -- Thanks, Donnie Donnie Berkholz Developer, Gentoo Linux Blog: http://dberkholz.wordpress.com pgpnbZGcQtis8.pgp Description: PGP signature

Re: [ccp4bb] general ccp4 building question

slightly older versions? Bill, I set up all the libraries to build separately from the applications using this patch. It would be much more convenient if ccp4 had an --onlyapps flag to accompany --onlylibs. -- Thanks, Donnie Donnie Berkholz Developer, Gentoo Linux Blog: http

Re: [ccp4bb] libxml2

../libxml2/include:-I/usr/include/gc -I/usr/include/libxml2:g' \ LOOP/Makefile.am eautoreconf popd -- Thanks, Donnie Donnie Berkholz Developer, Gentoo Linux Blog: http://dberkholz.wordpress.com pgpd7OG9u7ExQ.pgp Description: PGP signature

Re: [ccp4bb] off-topic: Enzymology textbook recommendations?

to hear how it goes. -- Thanks, Donnie Donnie Berkholz Developer, Gentoo Linux Blog: http://dberkholz.wordpress.com pgpao3SEoAdrY.pgp Description: PGP signature

Re: [ccp4bb] Hardware problem: nVidia NV41 [Quadro FX 3450/4000 SDI] on Redhat EL 5 (needed for stereo viewing)

On 16:05 Thu 10 Jul , Christian Rausch (Biol. Chemie) wrote: We have tried the following installation scripts from Nvidia: NVIDIA-Linux-x86-173.14.05-pkg1.run NVIDIA-Linux-x86-173.14.09-pkg1.run And tried it with the following kernels: vmlinuz-2.6.18-92.1.1.el5PAE

Re: [ccp4bb] Reminder - still no 3D stereo under OS X 10.5

On 17:41 Thu 26 Jun , Warren DeLano wrote: In point of fact, however, Linux-based stereo 3D remains dependent on proprietary graphics drivers tied to the underlying hardware. There is no 100% open-source option for stereo 3D visualization. Therefore, the scientific visualization

[ccp4bb] 2 postdoc positions at Cornell Oregon State

TWO POSTDOCTORAL POSITIONS Cornell University and Oregon State University As seen in the 09 May issue of Science Two Postdoctoral positions are available as part of a collaborative project between Cornell University and Oregon State University to undertake a structure/function analysis of

Re: [ccp4bb] rmsd calculation

Eleanor Dodson wrote: It is a bit clunky - you can use siperpose molecules - fit residues to fit a selected range (1-40; 60-100 say) and write out a complete fitted pdb file. Then you could use a VERY old program compar xyzin1 original.pdb xyzin2 fitted.pdb (xyzin3 another.pdb) and it will