Search found 62 matches

by sachrysts
2016.06.22 20:20
Forum: Model evaluation and manipulation
Topic: em2dam: meaning of output
Replies: 5
Views: 8557

Re: em2dam: meaning of output

But if that's true then the density of each dummy atom should change depending on the set threshold, right? not really, it will place a dummy atoms in the place where density is more than threshold, if less - no dummy atom is placed. The density of dummy atoms is uniform. it is an approximation, wh...
by sachrysts
2016.06.21 22:30
Forum: Model evaluation and manipulation
Topic: em2dam: meaning of output
Replies: 5
Views: 8557

Re: em2dam: meaning of output

Thanks for your quick response! If you do simple counting, you get expected number: em2dam alexander.shkumatov$ cat emd_6584_dam.pdb | grep ASP | WC 510589 6622161 38294175 Oh yes. forgot about that. Thanks! 1) What am I missing? How to interpret the numbers in the output? (I could not find this in ...
by sachrysts
2016.06.21 19:15
Forum: Model evaluation and manipulation
Topic: em2dam: meaning of output
Replies: 5
Views: 8557

em2dam: meaning of output

Hi! I am using EM2DAM to convert an electron density map to a coarse-grained dummy-atom model. However the meaning of the output is not entirely clear to me. For example, I get > em2dam emd_6584.map -t 0.095 -o emd_6584_dam.pdb [...] > head -30 emd_6584_dam.pdb REMARK REMARK Created by E M 2 D A M V...
by sachrysts
2015.05.25 00:10
Forum: ATSAS package in general
Topic: Ubuntu 14.04
Replies: 5
Views: 8266

Re: Ubuntu 14.04

I have the same issue here. The library libtiff4 is missing in Ubuntu 14. But there actually is a package libtiff5 and it works ok with ATSAS. But installing this does not remove the dependency problem, of course. I think the confusion is that Ubuntu14 has libtiff4-dev but not libtiff4.
by sachrysts
2014.05.23 22:04
Forum: Literature
Topic: Otto Glatter Homepage?
Replies: 8
Views: 16518

Re: Otto Glatter Homepage?

not working here either.
by sachrysts
2014.03.04 22:13
Forum: Ab initio shape determination
Topic: DAMMIF and UCSF Chimera
Replies: 6
Views: 7862

Re: DAMMIF and UCSF Chimera

I'm having trouble opening a dammif model in UCSF Chimera. When I try to open the dammif model I only see it as ribbon/lines, which does not make much sense for a dummy atom model. I cannot change this to spheres or surface representation. I can see in the thread that this bug should have been fixe...
by sachrysts
2013.10.07 09:00
Forum: Ab initio shape determination
Topic: [MONSA]"Error Openning Resolution File"
Replies: 6
Views: 3494

Re: [MONSA]"Error Openning Resolution File"

It seemed unable to upload the ".res" file. Anyway, here's what I put in "Au.res": [...] If your resolution file is called Au.res, why don't you write Au.res in your Au.con then? Currently, there is only Au written... Does this help? Thanks, but how exactly shall I integrate the resolution paramete...
by sachrysts
2013.10.02 10:02
Forum: Ab initio shape determination
Topic: [MONSA]"Error Openning Resolution File"
Replies: 6
Views: 3494

Re: [MONSA]"Error Openning Resolution File"

templarares wrote:It seemed unable to upload the ".res" file.

Anyway, here's what I put in "Au.res":

0.8
0.35
1100
180
6.0
0.10
0.1
0.000
If your resolution file is called Au.res, why don't you write Au.res in your Au.con then? Currently, there is only Au written...
Does this help?
by sachrysts
2013.09.30 15:49
Forum: Ab initio shape determination
Topic: [MONSA]"Error Openning Resolution File"
Replies: 6
Views: 3494

Re: [MONSA]"Error Openning Resolution File"

templarares wrote:Here is the resolution file.
Where exactly??
by sachrysts
2013.09.20 17:26
Forum: Ab initio shape determination
Topic: MONSA compilation error
Replies: 21
Views: 12486

Re: MONSA compilation error

cat monsa.mst MONSA file for KorA_Oa 20e3.0 20e3.0 0.0 0.0 0.0 0.0 0.0 0.0 0 0 0 0 'merge02_ed.con' -1 'koraoa_0_ed.con' -1 'koraoa_65_ed.con' -1 'koraoa_100_ed.con' -1 Well, line two is where the error occurs, as I said. So please change it to 20.0e3 20.0e3 0.0 0.0 (note the position of the points...
by sachrysts
2013.09.20 15:50
Forum: Ab initio shape determination
Topic: MONSA compilation error
Replies: 21
Views: 12486

Re: MONSA compilation error

In your working directory, could you post the output of the following six commands, please?
ls -l
cat monsa.mst
cat merge02_ed.con
cat koraoa_0_ed.con
cat koraoa_65_ed.con
cat koraoa_100_ed.con

Thanks!
by sachrysts
2013.09.20 15:04
Forum: Ab initio shape determination
Topic: MONSA compilation error
Replies: 21
Views: 12486

Re: MONSA compilation error

Looking at your mst-file again I realised that you have
20e3 20e3 0.0 0.0
in line two. What happens when you change this to
20.0e3 20.0e3 0.0 0.0
?
by sachrysts
2013.09.20 12:21
Forum: Ab initio shape determination
Topic: MONSA compilation error
Replies: 21
Views: 12486

Re: MONSA compilation error

I tried using zero's at line 3. Now there is no error message for compilation but the program won't run any further. See the image attached. Ok, unfortunately, Monsa isn't very good in telling what's wrong. The behaviour you see may be due to several reasons: 1) make sure the file monsa.mst is in y...
by sachrysts
2013.09.20 11:19
Forum: Ab initio shape determination
Topic: MONSA compilation error
Replies: 21
Views: 12486

Re: MONSA compilation error

Hello there, I am having similar problem with MONSA mst file. I am running 2.5.1 on Mac 10.8. I fail to work with the test.mst file that comes with atsas package in /Applications/ATSAS/share/doc/atsas-2.5.1/monsa/example. Any suggestions? Hi snowman! next time please open a new thread for your quer...
by sachrysts
2013.07.16 10:57
Forum: Rigid body modelling
Topic: CORAL fail to read config file
Replies: 6
Views: 5008

Re: CORAL fail to read config file

Your con file seems to have a lot of white space characters at the end. What happens if you remove those?