The file(MBA2.tar.gz) attached in "File" section is the code and a (minimal) documentation. Note that the program requires large computational resources. We...
Hello all. I have been unable to get sparky to accept an RNA sequence. Using atomnames.py as a guide I input the one-letter residues codes. When I click OK...
Sorry for my less experience, I didn't use the atomnames.py extension before. But as I know, sparky don't check the protein/DNA/RNA name. While you do the...
Has anyone complied sparky from the source? I recently install a new computer with Fedora Core 4, and the prebuild package cann't be installed. I try to...
I got sparky working with fedora core 4. I first had problems with it (just install as normal, extract to a directory) but i managed to get it to work. Firstly...
thank you James! Here's the thing: our lab buy a new computer with cpu is intel P630(p4 3.0GHz, 2M cache, 800MHz bus frequency, HT). When I install Red Hat 9 ...
Hi Tieying, I'm guessing that the trouble running the binary Sparky distribution on Fedora Core 4 Linux is that libstdc++.so.5 is not part of that new OS...
Hi Tieying, I think the reason Sparky works when you upgrade from Redhat 9 to Linux kernel 2.6.10, but not when you simply install FC4 (kernel 2.6.11) is that...
Hi Claudia, I suspect that adding http://www.cgl.ucsf.edu/home/goddard/temp/libstdc++.so.5 to your Sparky distribution in directory sparky/lib will allow...
Hi Kyle, I think the problem getting Sparky and Chimera to agree on atom names is that the PDB file format is wrong. The PDB format specifies exactly which...
Thanks you! I think you are right. The sparky complains this older library cann't be found. Thanks, all you guys! Tieying Zhang at SIBS ... distribution on ......
Actually regarding the java thing I was wrong. The files you've been told you need libstdc++.so.5 were needed for my gfx card and hence I put them on there...
... on my system it is this, def is_standard_name(group_symbol, atom_name): return atomnames.standard_group_atom_table.has_key((group_symbol, atom_name)) two...
In the BRMB software application description i have to fill the blank ID. If I don't find i will let it blank, but it should be better if i find what does it...
... could be your sparky version number, but it's better to ask the bmrb people Eiso ... -- _________ _________________/ Eiso AB \___________________________...
If the BMRB id field turns out to be the software version number you can find the version of Sparky at the top of the main Sparky window above the menus. Tom...
Thanks, Goddard! Thanks, Eiso! I have install the linux platform 3.110 version. The Python Shell(report error) will not showup. I have a misunderstanding...
... yes, but be carefull if you mix two naming systems. sparky will decide on the basis of the first characteristic nam that it finds. so if you have HA1 as...
Hi Tieying, With your linux Sparky 3.110 does the Extensions menu have any entries? If it is empty, this means Sparky is running without Python because it...
Hi Tieying, You are correct that the "atom name translation" tool does not change resonance names -- it just uses rules for matching PDB atom names and...
Sorry for my improper expression. What I mean is everything is ok, so the Python Shell doesn't prompt any error report. Thanks for your patience!:-) Tieying...
Dear all, I want to report fancy problem that I've experienced with sparky 3.110 under Fedora Core linux 4 and mac OSX Tiger 10.4.3. It is all about peak...
Hi Kamil, You can adjust the size of peak markers using the ornament sizes dialog (oz, menu entry Peak / More / Ornament sizes). The peak size is expressed in...
Hello, I wonder if somebody could share their way of working with Sparky-MARS tandem on the backbone assignment. I do not like how I do it. Making the input...
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