Re: [ccp4bb] CCP4 GUI

2007-05-11 Thread Clemens Vonrhein
Hi Martyn & Dirk, On Thu, May 10, 2007 at 02:18:14PM +0200, Dirk Kostrewa wrote: > I want to second Miguel: a switch between a "basic" GUI (could be with > even less options) and an "advanced" and "expert" GUI that allows > access to most and all options that can be used in scripts would be >

Re: [ccp4bb] CCP4 GUI

2007-05-11 Thread Clemens Vonrhein
On Thu, May 10, 2007 at 02:46:44PM +0100, Kolstoe S.E. wrote: > The most useful aspect of the ccp4i GUI is its automatic generation of > com files. However, I would prefer the GUI to output a .com file into my > working directory (rather than the obscure location they are saved to > now) every time

Re: [ccp4bb] Molecular Replacement issues with a WD-40 7-bladed beta propeller

2007-05-11 Thread Dirk Kostrewa
Hello Scott, hmmm - it is quite difficult to do a good analysis of your problem, remotely. You've tried the enantiomorphic space group I4(3), just to be sure? In principle, the molecular replacement solution given by Phaser sounds good, but this is no proof of whether it's correct. What sounds

[ccp4bb] xsect.dat=cossec.lib?

2007-05-11 Thread Bernhard Rupp
Dear Coders, Do I see this correctly that crossec.lib is the XSECT.DAT file from Don Cromer's FPRIME program? If so, has there ever been an update? Mine is from some reel tape I got from him long ago when I ported the code...seems to be the same. Thx, br -

Re: [ccp4bb] CCP4 GUI

2007-05-11 Thread Harry Powell
Hi > Maybe any parameter setting unchanged from the values in the > $CCP4/ccp4i/tasks/*.def file should be internally flagged as being at > the 'default value' - resulting in them _not_ being written to the > com-file? This way any potential change in defaults inside the actual > program would hav

Re: [ccp4bb] CCP4 GUI

2007-05-11 Thread Kevin Cowtan
Clemens Vonrhein wrote: One thing I found very confusing though, is that the com-files created by the CCP4i will often have (nearly) all possible keywords set, even if I haven't changed any of the defaults in the gui. Often, a CCP4 program has defaults itself and only requires keywords if one wan

Re: [ccp4bb] rmsd calculation

2007-05-11 Thread Eleanor Dodson
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 match all pairs with the

Re: [ccp4bb] CCP4 GUI

2007-05-11 Thread Liz Potterton
Dear CCP4bb, The intention with CCP4i GUIs is that those folders which are open by default (after you have chosen the mode of action from the top protocol folder) are for everyone and those that are closed by default are for experts OR difficult cases. Unfortunately that is an OR not an AND; t

Re: [ccp4bb] CCP4 GUI

2007-05-11 Thread Phil Evans
I would agree with Clemens that the Scala GUI task generates far too many keyworded commands, for things which have sensible defaults in the program. One problem conundrum for the GUI (because it works by generating a script without actually running the program) is that the GUI has no wa

Re: [ccp4bb] xsect.dat=cossec.lib?

2007-05-11 Thread Eleanor Dodson
Bernhard Rupp wrote: Dear Coders, Do I see this correctly that crossec.lib is the XSECT.DAT file from Don Cromer's FPRIME program? If so, has there ever been an update? Mine is from some reel tape I got from him long ago when I ported the code...seems to be the same. Thx, br -

Re: [ccp4bb] rmsd calculation. .

2007-05-11 Thread Miguel Ortiz Lombardia
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Excellent! Thank you Gerard, Miguel Gerard DVD Kleywegt escribió: >> But my understanding is that Iain's procedure gives the rmsds of the >> _aligned_ C-alphas, whereas Jenny actually seems to be more interested >> in those that she excludes from th

[ccp4bb] CNS problem: anneal.inp segmentation fault

2007-05-11 Thread jean
Hi all Apologies for the non-ccp4 question - hopefully some of you who use CNS can help me - I have a problem with anneal.inp in CNS: When I run the anneal script for my structure containing novel ligand, the program fails before the start of the torsion dynamics with no error message - exc

Re: [ccp4bb] Molecular Replacement issues with a WD-40 7-bladed beta propeller

2007-05-11 Thread Matthew . Franklin
CCP4 bulletin board wrote on 05/10/2007 09:31:59 PM: > Hello, > I'm an undergraduate and recently crystallized and obtained 2.9A > diffraction data for a protein which is predicted to fold into a WD40 > 7-bladed beta-propeller structure (which has been crudely verified by > cryo-EM by another lab

Re: [ccp4bb] . .

2007-05-11 Thread Kerr, Iain
Hi Emmanuel, Perhaps a little more information ? What was the Z-score and LLG in PHASER ? I take it the translation function solution is fairly well separated from the rest ? Are you sure the spacegroup is correct ? How complete is the model before refinement ? Not to be paranoid, but Hexagona

[ccp4bb] Filament Lifetime

2007-05-11 Thread Mark Agacan
I think the filament from one of our x-ray generators must be a record breaker. Yesterday it clocked up its 6000th hour or 250th day on the job, not counting down / holiday time. The intensity had only dropped by around 25 % of the value it was when I put it in, eight-and-a-half months ago... R

Re: [ccp4bb] Program to evaluate RNA torsion angles?

2007-05-11 Thread Robert Immormino
Forwarded from Jane Richardson: Yuan Lin, The sources you've been given (esp. the reduced-variable ones) are excellent for identifying RNA structural motifs but not very good for crystallographic validation, and the PDB tools are still primitive for nucleic acids. Fortunately, a suitable system

[ccp4bb]

2007-05-11 Thread Emmanuel Prata
Dear all, I have a structure (with 6 dissulphide bridges) at fairly low resolution (3A) that I am trying to refine with Refmac. I've used phaser with a template with 72% sequence identity. RFZ was 3.4 and TFZ 6.6, without clashes, with 80.7% of completeness. Space group was p3121 (pointless) and

Re: [ccp4bb] xsect.dat=cossec.lib?

2007-05-11 Thread Ethan Merritt
On Friday 11 May 2007 00:57, Bernhard Rupp wrote: > Dear Coders, > > Do I see this correctly that crossec.lib > is the XSECT.DAT file from Don Cromer's FPRIME > program? If so, has there ever been an update? I do not know the history of crossec.lib, but the X-ray scattering server http://sku

Re: [ccp4bb] quick question.... .

2007-05-11 Thread Kerr, Iain
Hi Jim, MAPMAN from the Uppsala software factory will do this. > re m1 ccp4.map (FORMAT) CCP4 > wr m1 xplor.map (FORMAT) X-PLOR Check the new map is written out on the same scale, just talking to a colleague I can't recall if any additional commands are required... Best, Iain -Original

[ccp4bb] quick question...

2007-05-11 Thread James Pauff
Good day all, First off, thank you all so much for your help a couple days ago! I just have a quick question regarding the use of CCP4 to generate density maps. Is there a way to generate a map(s) that can be read into PyMol? I understand that PyMol can only read CNS or XPLOR maps, is this corr

Re: [ccp4bb] quick question...

2007-05-11 Thread Nicholas Noinaj
Jim, i actually think you can read in CCP4 maps, at least i have been doing it for some time now. load *.map, format=ccp4 hope this helps. best of luck. cheers, nick -Original Message- From: James Pauff <[EMAIL PROTECTED]> To: CCP4BB@JISCMAIL.AC.UK Date: Fri, 11 May 2007 09:06:21

[ccp4bb] quick question... thanks

2007-05-11 Thread James Pauff
Thank you all, that was much easier than I expected. Best, Jim Boardwalk for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! Games. http://get.games.yahoo.com/

Re: [ccp4bb] Molecular Replacement issues with a WD-40 7-bladed beta propeller

2007-05-11 Thread Eleanor Dodson
You dont say how close your sequence ID is for your new protein and the model. It is often very hard to kick start refinement with low homology And what about internal symmetry Is there a Non crystallographic translation? Does the self rotation function show a relationship between the two mole

Re: [ccp4bb] rmsd calculation

2007-05-11 Thread Donnie Berkholz
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 w

Re: [ccp4bb] rmsd calculation

2007-05-11 Thread Olve Peersen
I would highly recommend Doug Theobald's program Theseus for this - the pictures at www.theseus3d.org say it all. Theseus does maximum likely hood superimpositions of multiple structures (i.e. NOT pairwise against a "master" copy), and the real beauty of it is that you don't have to pick w

Re: [ccp4bb] rmsd calculation

2007-05-11 Thread Douglas L. Theobald
Jenny, I of course would suggest that you follow Olve's advice, and use theseus to do a maximum likelihood, simultaneous superposition of all your structures ( http://www.theseus3d.org ). The variable bits, like your loop, will be naturally down-weighted in a rigorous statistical manner.

[ccp4bb] Laue for heavy atoms, etc.

2007-05-11 Thread Bryan W. Lepore
does anyone know of any reports where heavy atom positions were identified by any method (or mol. rep.) in a Laue data set (or sets)? also - i thought there was some Laue work out there on watching virus nucleic acids move around in a crystal, so again, if anyone knows any references (or names

Re: [ccp4bb] Program to find the center of mass

2007-05-11 Thread Nian Huang
WOW. There are so many ways to do it. Thank you all for replying. Nian Huang Department of Biochemistry Univ of Texas Southwestern Medical Center On 5/10/07, Charlie Bond <[EMAIL PROTECTED]> wrote: Just to complete the set, in pdb-mode for emacs, if you do pdb-increment-centroid 0 0 0 (e.g. to