Re: [ccp4bb] Alignment question

hat I did before. thanks in advance for your help. Ibrahim ---------- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park Pennsylvani

[ccp4bb] Alignment question

r help. Ibrahim ---------- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park Pennsylvania State University, PA16802 Tel. (814)863-8703 Fax. (814)865-7927 --

[ccp4bb] Re-Pymol - win

Hi all, Thanks for all your reply; I got it. I could not reach the link http://delsci.com/rel/099/ from Pymol Home page in the begining. thanks, Ibrahim -- Ibrahim M. Moustafa

[ccp4bb] Pymol - windows

m the pymol-src. thanks in advance, Ibrahim ---------- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park Pennsylvania State University, PA16802

Re: [ccp4bb] B-factor & Space gr questions!

nd re-run refinement for your own satisfaction. If R ==Rfree for the complex then I suspect they did not transfer the FreeR flags from the apo-protein data to the complex. Again if the data is available you may be able to check this. Eleanor Ibrahim M. Moustafa wrote: Hi all, While readin

[ccp4bb] B-factor & Space gr questions!

at an indication for improper refinement in these published structure? I'd love to hear your comments on that too. thanks, Ibrahim ------ Ibrahim M. Moustafa, Ph.D. Biochemistry and

[ccp4bb] Delphi question

ugh the installation. P.S. Hope this non-ccp4 question does not bother you guys! thanks, Ibrahim ---------- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse L

Re: [ccp4bb] Movie for Powerpoint in windows -Summary

want to spend time making the figures again. I already have the figures done in Pymol. thanks for your help in advance. thanks, Ibrhaim ------ Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular

[ccp4bb] Re-Movie for Power point presentation

th his/her ideas and experiences. Ibrahim ------ Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., Uinversity Park Pennsylvania State University, PA16802

[ccp4bb] Movie for Powerpoint in windows

figures again. I already have the figures done in Pymol. thanks for your help in advance. thanks, Ibrhaim ---------- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Altho

[ccp4bb] Re-calculating polar/apolar ASA at the interface

Hi all, Another solution to calculate the polar vs. non-polar portions of the ASA at the interface is, as suggested by Susan Crennel, to use the server: http://www.biochem.ucl.ac.uk/bsm/PP/server/ (actually before posting my question I tried that server which I used before, but I received

Re: [ccp4bb] Calculating apolar/polar surface area

Thanks to those who replied (Heidi and Paul). I tried Popscomp but it did not give what I want. I need to get Naccess ( as Heidi mentioned) it should do the job. thanks, Ibrahim At 12:28 PM 4/12/2007, Ibrahim M. Moustafa wrote: Hi All, I'm using Areamol to calculate the ASA

[ccp4bb] Calculating apolar/polar surface area

Hi All, I'm using Areamol to calculate the ASA. I'm interested to know the polar and apolar fractions of the calculated buried ASA between two proteins. I wonder if there is an available program/server able to do so. I googled to find anything to give me that particular information but wi

Re: [ccp4bb] Validate tool pdb structure

Actually, the structure is not mine. I just wanted to check the structure before using it for my work! The unit of the structure is: a = 141.59, b = 141.59, c = 43.68 alpha = 90.00, beta = 90.00, gamma = 120.00 So, it is H3 not R3! Checking the structure after editing the space

[ccp4bb] Validate tool pdb structure

Dear All, I wanted to check some structure using the validate server http://deposit.pdb.org/validate/ In the validation summary file I got a list of close contacts based on crystal symmetry:

Re: [ccp4bb] Solubility of ligands - Summary

Hi everybody, Two days ago I posted the question given below regarding the solubility of ligands for crystallization and activity assays. Thanks to everybody who replied to my question. I'm giving the summary of the answers below: I like the Anthony's approach, I think I'll follow i

Re: [ccp4bb] Solubility of ligands

Hi all, Thanks for those who replied so far. I can see that the solubility issue is not that problematic for the crystallization work (as Kendall mentioned). I recall that some people on the board reported in a different thread that they tried the solid powder in the crystallization dro

[ccp4bb] Solubility of ligands

Dear all, I have a small library of In-silico screened compounds to test for activity and for crystallization trials with our protein of interest. We only have about 10 mg/ml of each compound. As there is no available experimental information about solubility of these compounds, I have n

[ccp4bb] Summary: [ccp4bb] Toyopearl GF column vs. Superdex

Hi all, Thanks to those who replied to my question. I thought others might be interested, so I'm giving the summary below. I think, we'll go for the Superdex, as we have more experience with it. 1) If the prices are similar then toyopearl may be a better choice as it has slightly bette

[ccp4bb] Toyopearl GF column vs. Superdex

Dear folks, I have a question related to protein purification: We are thinking to buy a new GF column. We already have the HiLoad-superdex-75; we want to get the superdex-200 pg. However, some colleague mentioned the Toyopearl-HW as another alternative for Gel filteration. I wonde

[ccp4bb] RNA structure program

hi all, Thanks for Debanu Das for pointing me to the NAB package and helping for the installation. I also found another package NAMOT (from Bill's website, thanks Bill); I managed to install the package on MacOs PPC using fink. However, I have a problem to run the program: issuing "n

[ccp4bb] RNA structure software

Hi users, I'm looking for a software that can be used to make a crude 3D model from an RNA sequence and create a pdb file or other 3D-formats. It would be nice if the program would allow interactive editing for the built structure. Ultimately, I want to make a model of the RNA interacting

Re: [ccp4bb] relation between wavelength and inter-atomic distances

Hi Carlos, In his book "Crystals, X-rays and Proteins", Dennis Sherwood explained in the first chapter: why do use x-rays? Using his analogy: for a small boat (5 m length) in the ocean, waves come in from the ocean with a wavelength (say 20 - 30 m) are merely pass underneath the boat. On t