[ccp4bb] Off topic question. NACCESS

2011-06-17 Thread Armando Albert
Does anyone has got some information about how to get a mac version (intel), of the old unix program naccess?. It was meant to calculate the solvent accessibility per residue from a pdb file. Armando

Re: [ccp4bb] Off topic question. NACCESS

2011-06-17 Thread Francois Berenger
On 06/17/2011 05:25 PM, Armando Albert wrote: Does anyone has got some information about how to get a mac version (intel), of the old unix program naccess?. It was meant to calculate the solvent accessibility per residue from a pdb file. Armando Maybe this server can do the job: http://cgal.

[ccp4bb] Fortran runtime error, Refmac

2011-06-17 Thread Abhik Mukhopadhyay
Hello everyone, I got this error, attached below, while running a restrained refinement in Refmac-5.5.0109. I tried to run the refinement by removing the SCALE entries in pdb file but got the same error. * Information from CCP4Interface script **

Re: [ccp4bb] Follow-up: non-waters among structured solvent atoms

2011-06-17 Thread Thomas Womack
On 16 Jun 2011, at 17:19, Pavel Afonine wrote: > Hi, > > On Thu, Jun 16, 2011 at 7:49 AM, Jan Dohnalek wrote: > > Modeling more UNKNOWN atoms might be the future for these cases? > > one needs to specify chemical element type in 77-78 position, otherwise these > records are useless. But if

Re: [ccp4bb] Help! low resolution protein-DNA complex

2011-06-17 Thread Xun Lu
Thank you!! It's really encouraging & refreshing to begin a day with so many advices! ccp4bb is always helpful~ Thanks to one of my committee member who suggested me to get out a paper from the structure, and thanks to all the people at the mid-Atlantic crystallography meeting who told me my struct

Re: [ccp4bb] Help! low resolution protein-DNA complex

2011-06-17 Thread Robbie Joosten
Dear Xun, > > I have a 3.2A dataset for a protein-DNA complex. The protein is > > a homodimer, and the DNA is almost palindromic (except one base pair > > in the middle and two or three base pairs at both two ends). It is my > > first time solving structures, and unfortunately the resolutio

Re: [ccp4bb] Follow-up: non-waters among structured solvent atoms

2011-06-17 Thread Robbie Joosten
For the record:-UNK is for unknown residues only. That means that you know that you are looking at an amino acid you just don't know which. You should assign element types. It used to be defined to CB (just like ALA), it now goes to CG. I don't see the point of this update.-UNL is for unknown h

Re: [ccp4bb] Help! low resolution protein-DNA complex

2011-06-17 Thread Jürgen Bosch
Another thing you should bookmark and check out is the Molprobity page (google for it), upload your pdb file and let it evaluate what you have done. The chart it generates will guide you through your structure and you will be able to do a good job. Jürgen .. Jürgen Bosch Jo

Re: [ccp4bb] Nanodrop versus Nanophotomter Pearl versus good old Bradford.

2011-06-17 Thread Arnon Lavie
To add to this discussion: Many of the comments to my question that started this thread do not sufficiently differentiate between accuracy and precision. While we all want an assay that is internally consistent (i.e., high precision), we do care a lot about accuracy ("the degree of closeness of

[ccp4bb] Ghostview in CCP4 configure interface

2011-06-17 Thread Tatyana Sysoeva
Hi! I am having a problem of visualizing the PLT files in CCP4 6.1.13 CCP1 interface 2.0.7 running on Windows 7/64. I installed the GSscript and GSview but I am not sure how to change parameters in the System administration. Any help and advice will be highly appreciated!

Re: [ccp4bb] Ghostview in CCP4 configure interface

2011-06-17 Thread Ian Tickle
Hi, the '.plt' files are in an internal CCP4 format & cannot be visualised directly. You have to convert them first to PostScript (.ps) format using the 'pltdev' program; then you can visualise them with ghostscript (or any other PS viewer). Cheers -- Ian On Fri, Jun 17, 2011 at 5:53 PM, Tatyan

Re: [ccp4bb] Ghostview in CCP4 configure interface

2011-06-17 Thread Tatyana Sysoeva
Thanks! How do I get the pltdev? I checked the program list in CCP4 and it is not there, so I need to download it, I presume, and install. cheers, Tanya On Fri, Jun 17, 2011 at 1:25 PM, Ian Tickle wrote: > > Hi, the '.plt' files are in an internal CCP4 format & cannot be visualised > directly.

Re: [ccp4bb] Ghostview in CCP4 configure interface

2011-06-17 Thread Clemens Vonrhein
On Fri, Jun 17, 2011 at 06:25:14PM +0100, Ian Tickle wrote: > Hi, the '.plt' files are in an internal CCP4 format & cannot be visualised > directly. You have to convert them first to PostScript (.ps) format using > the 'pltdev' program; then you can visualise them with ghostscript (or any > other

Re: [ccp4bb] Ghostview in CCP4 configure interface

2011-06-17 Thread Zhijie Li
Hi Tatyana, It is funny that I just had that same problem a few days ago. Here is the solution: First of all, install Ghostgum and Ghostscript to your computer- which you have done. I installed them to my C:\Program Files\ directory. Then in CCP4i->system configuration->Config CCP4interface->

Re: [ccp4bb] Ghostview in CCP4 configure interface

2011-06-17 Thread Zhijie Li
Forgot to mention: the trick is, CCP4i uses the Linux/UNIX '/' to specify the subdirectories, not the Windows '\'. That is why if you copy the path from windows explorer and paste it it won't work. From: Tatyana Sysoeva Sent: Friday, June 17, 2011 12:53 PM To: CCP4BB@JISCMAIL.AC.UK Subject

Re: [ccp4bb] Ghostview in CCP4 configure interface

2011-06-17 Thread Tatyana Sysoeva
Thank you! this works perfectly fine! (I was not smart enough to put the path into both boxes) Yes, had to change forward to backward slash (or how one calls them) and it is saved now. Thank you very much!!! Cheers, Tanya On Fri, Jun 17, 2011 at 4:30 PM, Zhijie Li wrote: > ** > Hi Tatyana,