Search found 27 matches

by tankozavr
2011.08.12 20:50
Forum: Primary Data Processing
Topic: GNOM Batch mode
Replies: 23
Views: 15508

oops, true. I would never guess how to deal with such simple thing if I would not have done my home work with the commands "for i in" and "while read i".


Many thanks!
by tankozavr
2011.08.12 19:59
Forum: Primary Data Processing
Topic: GNOM Batch mode
Replies: 23
Views: 15508

Yo-hoo! It is working!
(at least it worked for a test set of three files and use of a for loop)

Thank you so much for the magic!

Best,
Tanya
by tankozavr
2011.08.11 21:18
Forum: Primary Data Processing
Topic: GNOM Batch mode
Replies: 23
Views: 15508

Thanks Daniel! will try later today when switch to my linux tasks for the day and report the results) so far I could run DATGNOM on lists of files in dos command line and results are quite consistent with other methods. True about Dmax, it is written in the manual to DATGNOM, but sometimes manuals d...
by tankozavr
2011.08.11 15:06
Forum: Primary Data Processing
Topic: GNOM Batch mode
Replies: 23
Views: 15508

run gnom on a set of data files?

Hi! (1) I was trying to use gnom.cfg to run one cfg on a series of files. I tried to do it by running a few jobs at a time : after first run with all input parameters - add lines to continue NEXTJOB C [ y ] INPUT1 C [ bsa_001.dat ] Input file name (first file) OUTPUT C [ bsa_001.out ] Output file Wh...
by tankozavr
2011.02.22 19:41
Forum: ATSAS Package in General
Topic: comments in an input file
Replies: 7
Views: 5048

thanks! I was silly enough to not try putting gaps in front of the !comments. That works for me just fine and simplifies input files preparations. It is much easier with the comment instead of just empty lines. Especially if you are shuffling among several versions of the software. with comment line...
by tankozavr
2011.02.13 22:50
Forum: ATSAS Package in General
Topic: comments in an input file
Replies: 7
Views: 5048

I am uploading two input templates for Gasbor, which I believe would be helpful.

Cheers,
Tanya
by tankozavr
2011.02.10 01:14
Forum: ATSAS Package in General
Topic: comments in an input file
Replies: 7
Views: 5048

due to some reasons commenting does not work totally in input files for linux cluster runs -

it works fine when there is an explicit value given and does not work if there is CR only, followed by the !comment phrase


hope it may help someone!

Tanya
by tankozavr
2011.02.04 18:03
Forum: Rigid Body Modelling
Topic: CORAL
Replies: 5
Views: 4215

thank you! I am planning with trying first advices from Haydyn, will see what I can achieve)
by tankozavr
2011.02.04 18:02
Forum: Rigid Body Modelling
Topic: Bunch keeping oligomer organisation
Replies: 8
Views: 5384

thanks Haydyn! will try this!

Cheers,
Tanya
by tankozavr
2011.02.02 01:53
Forum: Rigid Body Modelling
Topic: Bunch keeping oligomer organisation
Replies: 8
Views: 5384

belated Thanks to you Haydyn!


you mentioned Coral in one of your posts and I have it in the last downloaded ATSAS package but I could not find a manual so far. Could you advise where to look at?

Cheers,
Tanya
by tankozavr
2011.02.02 01:50
Forum: Rigid Body Modelling
Topic: Need an advice on how to model loops in assym.complex
Replies: 7
Views: 3731

thank you! I used Masha to shift the oligomer to the center and cut a subunit.
still trying to get "compact" loops though.


cheers,
Tanya
by tankozavr
2011.02.02 01:44
Forum: Rigid Body Modelling
Topic: CORAL
Replies: 5
Views: 4215

is there any manual available? I have checked Doc folder and the download site ...and probably I am missing something

Thank you!


Tanya
by tankozavr
2011.01.20 00:49
Forum: Rigid Body Modelling
Topic: Bunch keeping oligomer organisation
Replies: 8
Views: 5384

Hi!

I apologize up front for a silly question, but I cannot figure out a way to save only one subunit out of a pdb, containing 6 subunits in it.

Would you help me with a link or advice?


Cheers
Tanya
by tankozavr
2011.01.19 21:40
Forum: Rigid Body Modelling
Topic: Need an advice on how to model loops in assym.complex
Replies: 7
Views: 3731

Thanks Alex! (1) I tried it this morning and got a new silly problem on how keep the monomer in the correct position before the moment when Bunch applies symmetry? If I use PreBunch I can either keep the position or bring it to the center. - I keep the monomer in the initial position which is too fa...
by tankozavr
2011.01.19 21:15
Forum: Rigid Body Modelling
Topic: Need an advice on how to model loops in assym.complex
Replies: 7
Views: 3731

I mean that in each monomer I have one or two loops which I want to model according to a SAXS profile. In case of no symmetry, the number will be anywhere from 6 to 14.