SAXIER

Ab Initio Methods :: RE: Representing the envelope

AL — Mon, 01 Dec 2008 15:46:06 GMT

Author: AL
Subject: representation of Dammin results
Posted: 2008.12.01 16:46 (GMT 1)

Roessle's reply concerning representation of Dammin results might be helpful.

Ab Initio Methods :: Representing the envelope

auroranr — Mon, 01 Dec 2008 14:18:28 GMT

Author: auroranr
Subject: Representing the envelope
Posted: 2008.12.01 15:18 (GMT 1)

Does anyone know how to represent the output from dammin in the form of a continuous surface, in PYMOL for example?

Thank you

Rigid Body Modelling :: DAMAVER in batch mode

sasq — Mon, 01 Dec 2008 01:58:16 GMT

Author: sasq
Subject: DAMAVER in batch mode
Posted: 2008.12.01 02:58 (GMT 1)

Hi,

I have been able to run damaver in the batch mode on a Windows XP PC but am having problems doing the same on a linux cluster. I am copying all the executable files of damaver and supcomb in the folder that contains pdb files to be averaged. Yet, I get the error supcomb20.opt: command not found and the program eventually crashes.

How can I fix this problem.

Thanks a lot

PDB Oriented Tools :: SANS I(s) prediction for prot-duet protein complex

tmulhern — Sun, 30 Nov 2008 22:58:42 GMT

Author: tmulhern
Subject: SANS I(s) prediction for prot-duet protein complex
Posted: 2008.11.30 23:58 (GMT 1)

Hi,

I want to use CRYSON to predict the I(s) profiles for a protein complex where one component is deuterated.

Reading the paper it seeems CRYSON calculates scattering lengths based only on exchange of hydrophillic side chain NHn, OH and SH groups and backbone NH groups.

E.g How do I incorporate info on global 80% H>D replacement for CHn for protein from expression in deuterated media?

Thanks,

Terry

Rigid Body Modelling :: globsymm contacts

Hayds — Sun, 30 Nov 2008 19:29:54 GMT

Author: Hayds
Subject: globsymm contacts
Posted: 2008.11.30 20:29 (GMT 1)

Hi gang,

what exactly is the string I need to enter (from the input pdb file) to define a contact in Globsymm?

At the prompt for the first atom of the pair do I enter an actual string:

eg. CA THR A
(directly from the PDB file)

Or, if this is the first CA in the file maybe just:

eg. 1

I'm pretty sure I don't enter a sasref-like term.

Anybody able to sort me out on this one?

Cheers,

Hayds

Data Processing :: Question about I(0) values

jont — Fri, 28 Nov 2008 16:38:15 GMT

Author: jont
Subject: Question about I(0) values
Posted: 2008.11.28 17:38 (GMT 1)

Hi everyone,

I have a question about I(0) values. If I have a mixture of protein species, e.g. monomer + dimer, is the observed I(0) value equal to the population-weighted average I(0) value? Or do the I(0) values for the monomer and dimer add to each other to give the observed value?

I have a situation where my I(0) is 3xmonomer but I'm fairly sure that I don't have trimer. Is the following equation true?

I(0)obs = I(0)monomer + I(0)dimer

Hope that makes sense.

Thanks
Jon

Mixtures and Flexible Systems :: adding a structure to the pool

tmulhern — Thu, 27 Nov 2008 22:06:18 GMT

Author: tmulhern
Subject: adding a structure to the pool
Posted: 2008.11.27 23:06 (GMT 1)

Hi,

I am looking a protein that where the two domains that can become dislocated. I believe the SAXS profile represents folded protein plus a small fraction of dislocated protein. I generated a pool with the two domains in random orientations, and the gajaoe output agrees with my intial hypothesis, having a narrow highly populated Rg peak that corresponds well to the intact protein and then a broader higher Rg contribution from the dislocated species. However, none of the selected conformers really resembles the folded state with the two domains in conatct via the correct interface. Can I add the intact conformer to the pool and see if it gets selected?

Terry

Mixtures and Flexible Systems :: loop modeling in EOM

tmulhern — Thu, 27 Nov 2008 21:56:13 GMT

Author: tmulhern
Subject: loop modeling in EOM
Posted: 2008.11.27 22:56 (GMT 1)

Hi,

Want to model a long felxible loop in EOM. Is there a direct way of doing it, or do I need to define the two parts of the PDB as separate domains and then fix their positions? I couldn't see how to fix positions in EOM.

Terry

Ab Initio Methods :: RE: Dammin and gasbor results are different

Dhiraj Drivastava — Wed, 26 Nov 2008 18:37:14 GMT

Author: Dhiraj Drivastava
Posted: 2008.11.26 19:37 (GMT 1)

Yes. I was saying that the two results are different based on the output of supcomb. NSD value for dammin run is about 1.2 but for gasbor run it's 2.5. My protein is flexible and long.

Ab Initio Methods :: RE: random number generator in DAMMIN and *.fir file

SaxsMax — Wed, 26 Nov 2008 15:24:48 GMT

Author: SaxsMax
Posted: 2008.11.26 16:24 (GMT 1)

The answer regarding the random seed is here

http://www.saxier.org/forum/viewtopic.php?t=190

Rigid Body Modelling :: RE: A question MASSA

SaxsMax — Wed, 26 Nov 2008 15:20:27 GMT

Author: SaxsMax
Posted: 2008.11.26 16:20 (GMT 1)

Please check if you have fib14.ph in C:\Atsas
If not, you need to download Massha package and
extract it content to C:\Atsas

Ab Initio Methods :: RE: random number generator in DAMMIN and *.fir file

SaxsMax — Wed, 26 Nov 2008 15:17:09 GMT

Author: SaxsMax
Posted: 2008.11.26 16:17 (GMT 1)

The constant is added to the fit (instead of subtracting from the experimental intensity)

Ab Initio Methods :: RE: Reset core option in DAMMIN

SaxsMax — Wed, 26 Nov 2008 15:13:32 GMT

Author: SaxsMax
Posted: 2008.11.26 16:13 (GMT 1)

The phases of some core beads in the input structure may
be fixed. If the option is reset than no special rule is applied.

Ab Initio Methods :: RE: ab initio modeling of protein with channel

SaxsMax — Wed, 26 Nov 2008 15:12:03 GMT

Author: SaxsMax
Posted: 2008.11.26 16:12 (GMT 1)

First run Dammin without any assumptions.
If the resulting shape is consistent with what you expect,
you may try to use (hollow)cylindrical search volume

Ab Initio Methods :: RE: Dammin and gasbor results are different

SaxsMax — Wed, 26 Nov 2008 15:10:25 GMT

Author: SaxsMax
Posted: 2008.11.26 16:10 (GMT 1)

Actually for Dammin only the low angle part should be used,
while for Gasbor the entire data range is required.
Did you run Supcomb to superimpose Dammin and Gasbor
averaged results? What was the NSD value?

Data Processing :: RE: Kratky Plot

AL — Mon, 24 Nov 2008 11:15:48 GMT

Author: AL
Subject: Cutting the higher angles data
Posted: 2008.11.24 12:15 (GMT 1)

For Gasbor you should use the full range.
For Dammin/DammiF cut the higher angles at s*Rg ~ 7-8.

Rigid Body Modelling :: A question MASSA

Cytosis — Fri, 21 Nov 2008 17:34:32 GMT

Author: Cytosis
Subject: A question MASSA
Posted: 2008.11.21 18:34 (GMT 1)

I am pretty new with ATSAS. When I was trying to use MASSA to open a SLD file obtained by film2sld.exe. I got a error message:

can not open file C:\ATSAS\fib14.ph
Maybe bad data in C:\ATSAS\fib14.ph

could someone help with this? thanks.

Ab Initio Methods :: random number generator in DAMMIN and *.fir file

sasq — Fri, 21 Nov 2008 16:36:57 GMT

Author: sasq
Subject: random number generator in DAMMIN and *.fir file
Posted: 2008.11.21 17:36 (GMT 1)

Hello Everyone,

I am running 10 rounds of DAMMIN on a computer cluster simultaneously. Since the random number generator in DAMMIN is based on time, the random sequences for all of my DAMMIN runs are the same. Is there a way of changing this so that different runs can be started at the same time but have different random sequences ?

Also, at the end of my DAMMIN log file, I don't see a a final Chi against raw data from which constant has been subtracted. In the *.fir file, I don't have a column for the same. Is there something wrong with my dammin run ? Part of the fir file is dispalyed below and attached.

sExp | iExp | Err | iFit(+Const) | SQRT(Chi)= 1.163
0.01794 0.359200E+03 0.875100E+01 0.328803E+03
0.01855 0.348500E+03 0.782400E+01 0.321890E+03
0.01916 0.341400E+03 0.897600E+01 0.314912E+03
0.01976 0.332500E+03 0.727400E+01 0.307999E+03
0.02037 0.320700E+03 0.773800E+01 0.300930E+03

Thanks a lot !

Data Processing :: RE: Kratky Plot

sasq — Fri, 21 Nov 2008 15:19:56 GMT

Author: sasq
Posted: 2008.11.21 16:19 (GMT 1)

Thanks for the replies. Should I eliminate the higher S data from modeling with DAMMIN/GASBOR ?

Rigid Body Modelling :: RE: P1 symmetry in bunch8

AL — Fri, 21 Nov 2008 15:11:32 GMT

Author: AL
Subject: see 'contact conditions across symmetry mates in BUNCH'
Posted: 2008.11.21 16:11 (GMT 1)

Please find the answer in the foregoing discussion.

Data Processing :: RE: Kratky Plot

AL — Fri, 21 Nov 2008 15:04:47 GMT

Author: AL
Subject: Kratky plot
Posted: 2008.11.21 16:04 (GMT 1)

May be this figure (originally by Saxologos) will help.

Data Processing :: RE: Kratky Plot

Saxologos — Thu, 20 Nov 2008 14:53:31 GMT

Author: Saxologos
Posted: 2008.11.20 15:53 (GMT 1)

It is true that at higher angles it looks like it is increasing (in theory showing flexibility) but to me it looks more like the result of the subtraction.
The peak is also rather sharp and while I cannot exclude there is some flexibility involved I would rather say it is relatively compact.

Data Processing :: Kratky Plot

sasq — Wed, 19 Nov 2008 17:38:05 GMT

Author: sasq
Subject: Kratky Plot
Posted: 2008.11.19 18:38 (GMT 1)

Hello Everyone,

I have saxs data on a large protein complex composed of multiple polypeptide chains. The kratky plot for this complex shows a parabola followed by a linear region

How should I interpret this plot ? Do I have a mixture of folded and unfolded regions in the protein complex ?

Thanks

Rigid Body Modelling :: P1 symmetry in bunch8

AZ — Wed, 19 Nov 2008 12:11:30 GMT

Author: AZ
Subject: P1 symmetry in bunch8
Posted: 2008.11.19 13:11 (GMT 1)

It seems that bunch8 doesn't support default P1 symmetry in combination with contact condition (at least on my PC):

File name, contacts conditions, CR for none <cnd>: contacts
- E -- Wrong format of conditions file
1 77 77 2 86 86

For P2 symmetry it works fine.

Cheers,
Alexey

Ab Initio Methods :: Reset core option in DAMMIN

auroranr — Tue, 18 Nov 2008 14:44:32 GMT

Author: auroranr
Subject: Reset core option in DAMMIN
Posted: 2008.11.18 15:44 (GMT 1)

What does the reset core option mean in the expert mode of dammin? Does it have anything to do with the initial file?

Thanks