... 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...
I am not exactly sure what you find so weird in the MARS formats, but here is the general strategy that I use when running assignments with MARS. I first...
Thank you Josh. I think what I was asking is how people do the input files for the second, third, etc. run of Mars. After the first run we get these files:...
Ah, alright. I understand now. :) I think it is easiest to avoid that problem by not renaming the pseudoresidues until you are completely finished with MARS....
Dear Vitaliy Gorbatyuk, I encountered the situation you mention. I didn't read the "sparky_CO-1.out" into sparky HNCO spectrum. While I notice the MARS program...
Thank you guys for your suggestions and time. I thought that MARS developers meant a way which I could not figure out from their paper. Anyway, what about...
Dear Vitaliy Gorbatyuk, I have tryed the "rp" command in Sparky to read in the "sparky_CO- 1.out" file. It works well, it can creat peak according the chemical...
HI, I am a long time Sparky user and I always seem to have a hard time with peak integration in 3D-spectra. I often get the "Bounding contour too large"...
In the integration settings dialog [Peak -> Integrate... (it)], you will find the boxes to adjust the min and max linewidth parameters. If you go through your...
Hi Bradley, One way to avoid the "bounding contour too large" problem is to turn on "Use data within rectangle" in the Integration Settings dialog (it). Then...
Is anyone familiar in calculating Hbonds using WHATIF. My lab has the software and I need to calculate the hbonds from our starting pdb. Or can you tell me...
hi all, after a couple of hours of work with sparky 3.11 and python 2.3 on a linux box, i noticed that python seems to hang: top shows a process python2.3 w/...
Hi Markus, Does the 99% CPU usage only start after you quit Sparky? If Sparky is not drawing contours or integrating peaks then its CPU usage should drop to...
hi tom, ... no, i don't think so. but see below ... [snip] ... that sounds precisely like the problem i have. i mean, it's not a real problem, i can still...
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