Re: [ccp4bb] ARP/wARP 7.0 error

Hi there - That error is indeed something totally misleading from python. Somehow, the error messages get hard-coded at compilation time and list the directories that compilation took place at (in this case Gerrit's laptop). We will try and suppress this message since its totally misleading.

[ccp4bb] 21st Rhine-Knee Regiomeeting 2007

Registration for the 21st Rhine-Knee Regiomeeting 2007 in Hölstein (CH) is open until August 31th, 2007 under http://www.bioc.uzh.ch/index.php?204&L=1 . Best regards, Peer Mittl

Re: [ccp4bb] CCP4 Wiki

Yes, that is our intention. CCP4 would probably be at the third level of a hierarchy including: Macromolecular crystallographic techniques Structure solution, analysis and visualisation software The CCP4 suite So there would be room for other software packages at the same level as CCP4,

Re: [ccp4bb] resolution and solvent accessible surface area

Hi Hyunchul Kim, the paper that Miguel quotes concludes that the ASA doesn't show any correlation with resolution, but i would like to respectfully disagree. In the paper, the authors limit themselves to structures determined at a resolution no lower than 2.3 A. Many complex structures though a

[ccp4bb] mosflm error

Date: Tue, 24 Jul 2007 11:49:35 +0100 From: Stephen Brian Carr <[EMAIL PROTECTED]> To: ccp4bb@jiscmail.ac.uk Subject: mosflm error Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear ccp4bb-ers, I have started encountering an error in mosflm (version 6.2.6 with ccp4 6

Re: [ccp4bb] mosflm error

Hi, >From the error message if seems that the programs is trying to read in a file that should be specified with the COORDS keywords. It is trying COORDS as a filename, which is usually a sign that the filename itself is missing. When writing out a file that should not be too much of a problem as

[ccp4bb] mosflm error follow up

Thanks for the replies so far. Here is some more information I should have included last time. The COORDS file is being written, but mosflm seems unable to read it. The simple things like the file permissions are all correct and there is plenty of free space on the disk. Thanks again Steve

Re: [ccp4bb] resolution and solvent accessible surface area

Hi Rob, Hyunchul Kim and Miguel, I was just about to write a comment on this, but Rob was quicker.. Rob is right, our dataset of hen egg-white lysozymes does not contain any structures with resolution lower than 2.3 Aone may say that these are all relatively high-resolution structures, the

[ccp4bb] low b factors

I am working with a small protein in a relatively high space group p6322 and have good data to a modest 2.5 A resolution. During the first rounds of restrained refinement however the B factors drop to an average of 15 and as low as 2 A^3. This has the effect of producing large amounts of negative

[ccp4bb] Help with coordinate file

Hello all, I have a coordinate file of an energy minimized molecule which was apparently done using Chem 3D Pro. Does anyone know how I can convert this to a pdb file? Thank you Mona Rahman -- Mona N. Rahman, Ph.D. Post-doctoral Fellow Botterell Hall, Room 634 Department of Biochemistry Queen

Re: [ccp4bb] Help with coordinate file

Hi Mona, No idea what format may be that file, but if you find it out, most often in these cases openbabel (http://openbabel.sourceforge.net/wiki/Main_Page) is your friend. M. 2007/7/24, Mona N. Rahman <[EMAIL PROTECTED]>: Hello all, I have a coordinate file of an energy minimized molecule

Re: [ccp4bb] ARP/wARP 7.0 error

Thank you for the help. It seems as if the new Refmac5 has done the trick. Thanks Craig Craig McElroy, Ph.D. Department of Molecular and Cellular Biochemistry Ohio State University 483 Hamilton Hall 1645 Neil Ave. Columbus, OH 43210 (614) 688-8630 Anastassis Perrakis wrote: Hi there - That e

Re: [ccp4bb] Help with coordinate file

Hello Mona, I am guessing you have the atom name,number and coordinates in your file. I did something like that and Openbabel will convert it to the pdb file you desire but as far as I know, you will have to assign a residue name to the atom yourself. I did this by superimposition on the original f

Re: [ccp4bb] Help with coordinate file

Thanks for the advice everyone. I downloaded the graphic interface for Open Babel but for some reason it's not converting my file. I'll play around more with this later but any hints would be greatly appreciated. On Tue, July 24, 2007 09:50, Seth Horne wrote: > Try Open Babel at http://openbabe

[ccp4bb] Low B factors Resolved

First, Thank you all for the help and suggestions, it truly resolved the issue. First I reset the B factors to something close to the Wilson B average (53). Then making sure the B-solvent contribution flag was set and refining isotropic b-factor I reran the job. The B-factors now are reasonable

Re: [ccp4bb] Help with coordinate file

[EMAIL PROTECTED] wrote: Hello Mona, I am guessing you have the atom name,number and coordinates in your file. I did something like that and Openbabel will convert it to the pdb file you desire but as far as I know, you will have to assign a residue name to the atom yourself. I did this by super

Re: [ccp4bb] FPLC vs Duo Flow

Thanks to all those who responded. Here is a summary of the responses. Overall, there are mixed feelings, but there is a clear bias towards Akta, with a better service and durability – individual experiences with service might be due to geographical distributions? Filip _

[ccp4bb] reagarding CNS domain definitons

Hello to all, I'm a bit new to CNS. I am using CNS for rigid body refinement but i don't know how to define domains in the input file and also for annealated simulations which one I have to chose. I mean either "cartesian " or "torsion" molecular dynamics. Thanx in advance for

[ccp4bb] phenix mtz to ccp4 mtz conversion

Hi, I have an mtz file from Phenix I am trying to convert for use in Refmac. The labels are currently: H K L I-obs SIGI-obs R-free-flags I can't seem to get it to work. I am using Import, it runs, spits out a new mtz, and then Refmac complains about the labels. What is the easiest way (ie

Re: [ccp4bb] phenix mtz to ccp4 mtz conversion

Use truncate to convert I-obs to F-obs. No format change is needed. Peter John Bruning wrote: Hi, I have an mtz file from Phenix I am trying to convert for use in Refmac. The labels are currently: H K L I-obs SIGI-obs R-free-flags I can't seem to get it to work. I am using Import, it

Re: [ccp4bb] reagarding CNS domain definitons

Since I was reading it this afternoon again, I cant help but suggest to all refinement newbies and more experienced 'refiners' my favorite read: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2156-68. Epub 2004 Nov 26. Introduction to macromolecular refinement. Tronrud DE.

Re: [ccp4bb] Help with coordinate file

You might need to make sure that the input format you are entering is the correct one for the program that created the file. > Thanks for the advice everyone. I downloaded the graphic interface for > Open Babel but for some reason it's not converting my file. I'll play > around more with this l