Re: [ccp4bb] how to model this density?

Thank you all. I have build a (NAG)2MAN core sugar chain into the density. It seems more MAN can be fit into the density. On Jan 9, 2008 5:07 AM, Li Zhijie <[EMAIL PROTECTED]> wrote: > Hi Jiamu, > > I think you can safely say that it is an N-linked glycan. > > To model the sugar, check COOT's "

Re: [ccp4bb] DNA contamination post-Talon?

Hi, Typically one does not expect massive contamination with DNA unless the protein you work with is either very basic, or is a DNA/nucleotide binding protein. Having said this, I must add that in almost every IMAC preparation that I have *ever* run, regardless of the resin used, there was alwa

Re: [ccp4bb] Any programs other than GRASP have a surface scribing function?

> As far as I am aware, the plugin is not > compatible with the non-X-windows PyMOL on OS X. Actually, it is -- the trick is to rename the "MacPyMOL.app" executable "PyMOLX11Hybrid.app". However, people should note that current MacPyMOL builds are commercial products (not FREE) avialable from

[ccp4bb] Drug target crystallography and virtual discovery course, PSP Jan 21-22 2008

Dear All, we still have a few places open for a 2-day pre-conference training course ahead of the Advances in Protein Crystallography 2008 conference. Palm Springs is nice in winter and the APC is right before the Lab Automation 2008 meeting. I teach the crystallography part and Katherine Kantar

Re: [ccp4bb] Any programs other than GRASP have a surface scribing function?

Just to add to that, on OS X, if you install the apbs and pymol packages via fink, everything will be set up for you. I think this is also true of at least Ubuntu and other debian linux varieties. As far as I am aware, the plugin is not compatible with the non-X-windows PyMOL on OS X. On Tue,

[ccp4bb] nCNS - neutron diffraction patch for CNSsolve 1.1 has been released.

=== *nCNS* 1.0.0 software Release === Software *nCNS* version 1.0.0 has just been released. *nCNS* is a patch for CNSsolve V1.1 , combining for th

Re: [ccp4bb] DNA contamination post-Talon?

DNA carry-through in protein purification is quite common, especially if you are working with basic proteins. A Talon step certainly doesn't guarantee the removal of nucleic acid, and large fragments will certainly run in the void volume of your gel-filtration column. You can try washing the Ta

Re: [ccp4bb] Any programs other than GRASP have a surface scribing function?

I have used CCP4MG to produce a molecular surface of the model that i have been working on. There is an example in the online documentation to produce a molecular surface for the entire molecule or for a subset of atoms, and color it by solvent accessibility or other properties. It produces beautif

Re: [ccp4bb] Any programs other than GRASP have a surface scribing function?

You can use APBS plugin in PyMol. See installation instruction at http://www-personal.umich.edu/~mlerner/PyMOL/ or http://www.pymolwiki.org/index.php/APBS Holly > Date: Tue, 8 Jan 2008 14:01:02 -0600 > From: [EMAIL PROTECTED] > Subject: [ccp4bb] Any programs othe

[ccp4bb] Any programs other than GRASP have a surface scribing function?

Dear CCP4'ers, Any Windows/Linux/OS X programs have a surface scribing function similar to that found in GRASP, to quickly draw the border of a surface selection (or subset) and calculate or display local features of the molecular surface? I have no access to SGIs now. I have a memory o

Re: [ccp4bb] How to refine large moleculars?

How does the Molprobity report look like ? How many Rama outlieres, bad Cbeta, rotamers ? What's your percentile ? Look at the multicriterion chart to fix your problems :-) http://molprobity.biochem.duke.edu/ Juergen Yongchao Li wrote: Dear all, Thanks for all replies. After water addition,

Re: [ccp4bb] How to refine large moleculars?

Dear all, Thanks for all replies. After water addition, R work is 0.27 and R free 0.33. TLS and NCS results no significant approve. Space group seem right, other space group like P21212 is worse. >From truncate result, it is not twinning. More detail is below: space group P212121 a=150.099 b=148.

[ccp4bb] REFMAC 5.4.0034

I keep finding that the Refmac version from 5.4.0034 is more "stable" at least with full anisotropic refinement at 1.35 Å resolution. The R- factor stays relatively similar and there is a slow decrease of R- free with R-work. It doesn't jump around compared with an identical refinement in cu

Re: [ccp4bb] How to refine large moleculars?

Have you tried TLS and NCS? Maybe these can lower the R free a little. But ,the quality of your model depends on the quality of your data and completeness of your model etc. Yongchao Li wrote: I have a large molecule to refine.There are about three thousand residues in one asymmetric unit. Ex

Re: [ccp4bb] how to model glycosylated residues?

Hi Jiamu, You can use Sketcher to make the library for Coot. You'd better to get the PDB file from http://www.dkfz.de/spec/glycosciences.de/tools/pdbcare/ . Good luck! liu Jiamu Du wrote: Thanks for all the replies above. I have pasted the figure of the electrondensity map in the attachment.

Re: [ccp4bb] How to refine large moleculars?

Yongchao Li wrote: I have a large molecule to refine.There are about three thousand residues in one asymmetric unit. Except for the lack of electron densities in several places, where the loops have been deleted, the rest parts fits well with density. But the R free and R work are all beyond 0.

Re: [ccp4bb] Refmac 5.4.0066 versus Refmac 5.4.0034

As you say - it is 17.006 in all versions of atomsf.lib I have access to! It is good that f' and f" will now reflect the wave length, although the wavelengh is so often wrongly recorded that this had better be an optional request rather than the default! Eleanor Ethan Merritt wrote: On Th

Re: [ccp4bb] resolution & R-free

I doubt if you should ever t hrow away data if the I/SigI is sensible in the outer shell. Have you tried TLS refinement or loosened the B restraints? Often higher Rfree at higher resolution are related to B refinement problems. Eleanor 杨柳青 wrote: > Hi,dear all: > I try to refine one protein

[ccp4bb] how to model glycosylated residues?

Dear Jiamu, The density is definitely carbohydrate. The N-links are highly conserved so build N-acetylglucosamine (NAG) beta 1-Asn. Both the C2 acetyl group and the C6 group lie outside the ring so look for the diagonal bulge in your density to assign the orientation. To sanity check your tors

[ccp4bb] how to model glycosylated residues?

Dear All: As mentioned before, I am working on a 2.6 A resolution structure. There might be a glycosylated Asn. I want to model some carbohydrate molecule into my structure. My question is how to model them? Should I treat them as small molecules? Best Regards. -- Jiamu Du State Key Laboratory o