Re: [ccp4bb] coot & other graphics programs draw too many bonds

Hi Fred, are you using the output from vina directly (I think it is called pdbrq)? If so, you could try converting it to mol2, before loading it into pymol. Cheers, Johannes Am Do., 1. Apr. 2021 um 15:59 Uhr schrieb Robbie Joosten < robbie_joos...@hotmail.com>: > Hi Fred, > > I think this is a

Re: [ccp4bb] Rigaku CrystalTrak Web not working

> in Dr. Frank Sicheri lab at Mount Sinai Hospital in Toronto, ON, Canada. Is > this the local installation you are talking about? I am just using my Czech > email account, since I have the CCP4BB already set up on this account... > > Thanks, > > Pavel > > -- Původ

Re: [ccp4bb] Rigaku CrystalTrak Web not working

Hey Pavel, afaik our local installation of the software still works. So if going there physically is an option for you, you can try that. Cheers, Johannes Am Do., 18. Feb. 2021 um 18:21 Uhr schrieb Pavel Mader < mader.pa...@seznam.cz>: > Hello everyone, > > is there anyone else, who is using

Re: [ccp4bb] wsl2 Ubuntu 20.04

his may not be an option for > everyone though. The universal solution is for SHELX executables that > don't require vsyscall to be made available, but we rely on the SHELX > maintainers for that. > > Regards, > > Peter. > > > > > This link might be related: > >

[ccp4bb] wsl2 Ubuntu 20.04

Dear board, has anyone gotten ccp4 (specifically shelx and arpwarp) installed and working under wsl2 (windows subsystem for linux)? arp warp refuses to install with the following error: Segmentation fault *** ERROR *** This machine cannot run ARP/wARP executables that are statically linked to

Re: [ccp4bb] cannot access ccp4 download webpage

ProtonMail mobile > > > > Original Message ---- > On 3 Dec 2020, 14:47, Johannes Cramer < johannes.cra...@gmail.com> wrote: > > > Dear all, > > I cannot access the ccp4 downloads webpage from my institute's pc or > mobile. > Is it just me? Is it a known problem?

[ccp4bb] cannot access ccp4 download webpage

Dear all, I cannot access the ccp4 downloads webpage from my institute's pc or mobile. Is it just me? Is it a known problem? I get a 502 Proxy Error. http://www.ccp4.ac.uk/download/ Cheers, Johannes To unsubscribe from

[ccp4bb] ftp://strucbio.biologie.uni-konstanz.de/pub down?

Dear collegues, I am trying to install xdsgui, however, I cannot access any files on the ftp server ftp://strucbio.biologie.uni-konstanz.de/pub. https://www.isitdownrightnow.com/ suggests, that it is not just me, but the server is really down. Does anyone have information about whether or when

[ccp4bb] unable to run Jligand

Dear ccp4bb, I am trying to start JLigand from a ccp4 installation on a Windows7 VirtualBox host running a kubuntu 18.04 client, but I get the following error: Exception in thread "main" java.lang.ExceptionInInitializerError > at JLigand.main(JLigand.java:35) > Caused by:

[ccp4bb] definition of "apo" and alternatives?

Dear collegues, a while ago, there was a discussion in the board on the term apo-structure as a way to descibe a native, free, or unbound protein (no ligands). I think the conclusion was that an apo-form is a halo enzyme lacking a cofactor and should not be used as a substitute for "unbound". We

Re: [ccp4bb] cavities in protein structures

Hi Claudia, another program that I used with success is Hollow ( https://www.ncbi.nlm.nih.gov/pubmed/19014592). It is really easy to use. You can get is here http://hollow.sourceforge.net/ It finds pockets in a defined area, fills them with water molecules and generates a pdb with those waters.

Re: [ccp4bb] proxy settings for ccp4 package manager

kanori Nakane > > On 2018/01/09 13:18, Johannes Cramer wrote: > >> Dear CCP4bb, >> >> does anyone know how I can make the ccp4 package manager use a proxy for >> downloading in Linux 64bit versions? >> This would make installing and updating a whole lot e

[ccp4bb] proxy settings for ccp4 package manager

Dear CCP4bb, does anyone know how I can make the ccp4 package manager use a proxy for downloading in Linux 64bit versions? This would make installing and updating a whole lot easier for me... I exported http_proxy, https_proxy, ftp_proxy (and all their capital letter equivalents) and setup the

Re: [ccp4bb] PyMol question

you can try the 'hide cell' command. This should hide the unit cell box, however, I don't know why it is not displayed in your 'unrendered' gui... Cheers, Johannes 2017-12-11 23:47 GMT+01:00 Cygler, Miroslaw : > Hi, > When I loaded the ed map into PyMol v1.8.4.1 and

Re: [ccp4bb] 3D stereo and pymol

Hi Christine, as far as I know, it does not work at all with Geforce cards. The Nvidia drivers do not support windowed quad buffered GL, which you need for coot/pymol. It does not matter whether you use Windows or Linux. But this is based on my personal experience from around Oct. 2016. Maybe

[ccp4bb] ccp4i2 crashes on start

Dear CCP4 bb, I would like to use ccp4i2, but every time I try to start it via command line, I get the following error message: Running CCP4i2 browser from: /home/cramejo/programs/ccp4-7.0/share/ccp4i2 > Python 2.7.10 (default, Aug 28 2015, 12:10:46) > [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] >

Re: [ccp4bb] Ligand building in real space

Hey Mohamed, I am not sure, if this is what you want, but you can import different PEG molecules from coot's "File-> Get monomer". A list of different length PEGs three letter codes can be found on page 1278 of this paper: Naschberger et al., (2016) http://doi.org/10.1107/S205979831601723X. I

Re: [ccp4bb] suggestion on protein crystallization optimization from phase separation

Dear Joseph, You have probably already done so, but have you tried in- or decreasing your protein+DNA concentration? I had a similar problem with proteins that were concentrated too low. I had to increase protein and decrease Ammonium sulfate (precipitant in my case) concentration. Cheers,

Re: [ccp4bb] ligand with out space group information

Hi, I had the same problem once. Some chemistry programs are not really good at exporting to pdb. Check the file format definition of pdb files, here: ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf Most interesting for you is probably pp. 174. Also make sure, there is an

Re: [ccp4bb] intermolecular dissulphides

Dear Eleanor, sorry for the late reply. I found a similar case (id: 2OEF, Cys 92). I mutated the Cys to Ser, but it did not change anything (xtal conditions and quality remained the same). In solution the protein is a monomer. However, adding 1 mM DTT resulted in a significant increase in crystal

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

Hi Xiao, did you try manually changing the Hz in the nvidia system control panel? It is somewhere under Resolution-> adapt (or something like that, sorry, I don't have an english version). There you can change the frequency. If it doesn't work and you only see a black screen, the system switches

Re: [ccp4bb] ccp4 package manager

Dear Edwin, I had a similar problem and it had to do with our institutions proxy settings. The proxy settings in ccp4i did not affect the updater settings. I could not resolve it and always had to manually download the full update package. Cheers, Johannes 2016-11-29 21:02 GMT+01:00 Edwin

Re: [ccp4bb] Good 3D Monitor for Molecular Modelling

Hi Matt, I guess you are talking about hardware. For a year or so, this should have become quite cheap. A recent Nvidia Geforce card, a 120 Hz 3D Monitor and a 3D vision kit should do the trick. However, personally I only have experiences with the "professional" NVidia quadro grafics card series.