[ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed

Dear All, I tried to convert my x-ray diffraction sca data from HKL200 (.sca file) to mtz in CCP4 using Scalepack2mtz and it failed, I do not know what should I supposed to do next to correct the problem, any suggestions are appreciated. I pasted the message from part of log file below: ANISOTRO

[ccp4bb] a question related to WinCoot 0.8.1

Dear All,  When I use WinCoot 0.8.1 to open a PDB file, it comes, Fix Nomenclature Errors. Correct them? Asp [spec: 1 "A" 128 ""]PHE[spec: 1 "A" 134""]PHE [spec: 1 "A" 371""] But when I check the 3 residues, I cannot find any error. Will you let me know the issue? Dialing

Re: [ccp4bb] Active site Volume

Hi Ayan, Try 3V: http://3vee.molmovdb.org It has worked nicely for me. You'll need to delete the substrate/inhibitor from your coordinate file for one of the runs. Cheers, Chris On Saturday, January 10, 2015, Bio Physics wrote: > > Hello CCP4bb: > > Help me to advice any program/server to cal

[ccp4bb] Active site Volume

Hello CCP4bb: Help me to advice any program/server to calculate active site volume without substrate/inhibitor and volume of the substrate/inhibitor itself. Q-site-finder website is not working. Thank you, Ayan

Re: [ccp4bb] Postdoctoral Fellow Position – Structural Biology at Rutgers University School of Dental Medicine

Hello CCP4bb: Help me to advice any program/server to calculate active site volume without substrate/inhibitor and volume of the substrate/inhibitor itself. Q-site-finder website is not working. Thank you, Ayan On Fri, Dec 19, 2014 at 7:51 AM, Vijay Parashar wrote: > A postdoctoral position

Re: [ccp4bb] Off-topic - PyMol map sampling at unit cell boundary

On 09/01/15 21:08, Shane Caldwell wrote: Hi ccp4bb, Apologies for a cross-post. I previously asked this question on the pymol-users mailing list, but I thought I'd ask here as well, in case someone who doesn't follow that bb might have run into my problem rendering maps in PyMol. I'm starting

[ccp4bb] Off-topic - PyMol map sampling at unit cell boundary

Hi ccp4bb, Apologies for a cross-post. I previously asked this question on the pymol-users mailing list, but I thought I'd ask here as well, in case someone who doesn't follow that bb might have run into my problem rendering maps in PyMol. I'm starting to think it's a non-trival problem to solve.

Re: [ccp4bb] Bulk solvent

I always try both methods - usually there is little difference. However, For CueO (multicopper oxidase) where there are about 25 disordered (unseen) residues in a loop, using Babinet scaling instead of the default refmac scaling reduced the R factors by about 2% (both R and Rfree) and improve

Re: [ccp4bb] Bulk solvent

Dear Armando, Is there any reason for using Babinet scaling for bulk solvent correction > instead of mask based scaling? > in addition to Dirk's excellent comment: Babinet bulk-solvent model is fine at resolutions lower than 15-20Å while not so much at higher resolutions as demonstrated by Podja

Re: [ccp4bb] active 3D monitors: successor of Asus VG278HR?

On 01/09/2015 12:11 AM, Jens Kaiser wrote: In addition to what others have -- correctly -- stated I want to add one more thing: Yes, you are right, if you do not get your hands on a monitor with built-in emitter, you'll need ad least a K4000 and in many cases the VESA din bracket (~$50). You do

Re: [ccp4bb] imosflm error

Hi, I suggest you upgrade to ccp4-6.5 in the first place. I used to have this problem (or a similar one) with the initial 6.4 release but it has been fixed with later updates. In 6.5 it's completely gone (I'm using Centos 6.6)            Cheers,                        Boaz     Boaz Shaan

[ccp4bb] imosflm error

Dear All, Whenever I start imosflm there was an error message *iMosflm version 7.1.1, 24th March 2014"ipmosflm" is not compatible.Please configure iMosflm with the correct executable.on configure* the imosflm window is closed and there *Tcl platform is unix x86

[ccp4bb] IGBMC call for Group Leader positions in Integrated Structural Biology

Dear all, I would like to draw your attention to the opening of two Group leader positions in the Integrated Structural Biology (ISB) department of the Institute of Genetics and Molecular and Cellular Biology (IGBMC) in Illkirch, France (http://www.igbmc.fr/research/department/3/). Detailed in

Re: [ccp4bb] active 3D monitors: successor of Asus VG278HR?

Dear Tobias, BenQ (Model: XL2411Z - 24"W 3D monitor) ViewSonic (VX2268wm - 22" 3D monitor) NVIDIA 3D Vision 2 Kit 1. Both the abovementioned monitors work well on Linux/Ubuntu with the NVIDIA Quadro K4000 graphics card. You may have to edit the Xorg file for proper 3D access in BenQ or ViewSoni

Re: [ccp4bb] How far does rad dam travel?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Jacob, the top-hat profile is one of the reasons why inhouse machines produce better quality data than synchrotrons. However, the often much increased resolution you achieve at the synchrotron is generally worth more than the quality of the data at

Re: [ccp4bb] Bulk solvent

On 09.01.2015 08:56, Armando Albert wrote: Dear all, Is there any reason for using Babinet scaling for bulk solvent correction instead of mask based scaling? Armando Dear Armando, yes: the mask bulk solvent correction depends on the proper calculation of a protein mask. The bulk solvent dens

Re: [ccp4bb] Protein precipitating at higher concentration!!

Hi Ivan, according to my experience, if you remove at the same time GuHCl and Triton, you have huge risk of precipitation if the protein is not properly folded. In my opinion, you have to do something like re-folding. It seems that your protein could be solubilized from inclusion-body. In the sa

Re: [ccp4bb] active 3D monitors: successor of Asus VG278HR?

Dear Jens, Jim, Todd and all, Thanks for your replies and suggestions! >Yes, you are right, if you do not get your hands on a monitor with >built-in emitter, you'll need ad least a K4000 That is the reason I was looking for the monitor with built-in emitter, because then I could use the much che