Re: [ccp4bb] Dose anyone see this ligand before?

Wei I heartily second Dale's comment. Since you do know what has been in contact with your protein, you should be able to make a list of ALL POSSIBLE compounds your protein has been exposed to. However, don't go off the deep end. You say that "We guess that the molecular formula should be C8H

Re: [ccp4bb] Dose anyone see this ligand before?

Do you have any reason to expect either of these molecules would be in your crystal? The model you build has to fit the density, be consistent with the surrounding environment (which you haven't shared with us) and you have to have some story for how that molecule got in your crystal. Person

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Re: [ccp4bb] TLS refinement refmac

EEK, it seems to me that anything called simply "FP" should be unadulterated FP. If the software modifies a column in some way, it should give it a new label, shouldn't it? ++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Ch

Re: [ccp4bb] frosted crystals during storage in pucks

We put a supply line of compressed air (not sure how dry this is) in the dewar to wam it up and dry it out. We leave this running overnight, and this seems to result in the dewars being dry enough for later use. We haver never bothered to weight the dewars before and after use etc, so can't comment

Re: [ccp4bb] Dose anyone see this ligand before?

Try here: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=8031&loc=ec_rcs download the sdf and use the sdf to pdb converter Or I think phenix can read in sdf and convert them Jürgen On Jul 17, 2013, at 9:35 AM, Wei Feng wrote: Dear all, Thank you for your advices. I had tried to use MPD

Re: [ccp4bb] frosted crystals during storage in pucks

I heard or read (don't remember where) that repeated warming/cooling cycles are what can make the dewars less efficient and can "break" them. So we keep them always with liquid nitrogen, filling them every week if we can. But we are lucky that Madrid has low humidity most of the year. And perhaps

Re: [ccp4bb] Dose anyone see this ligand before?

Dear all, Thank you for your advices. I had tried to use MPD and pyrophosphate etc to fix the density map but all of them were too small. We guess that the molecular formula should be C8H18O2. So we search this formula in google and find two candidate molecules 1: http://flyingexport.en.ecplaza.n

Re: [ccp4bb] frosted crystals during storage in pucks

In response I felt I had to post the low-tech version (not mine)PhilOn 16 Jul 2013, at 11:57, Edward Lowe wrote:At Elspeth's request, here's a link to a picture of the rack we use fordrying out shipping dewars.https://www.dropbox.com/s/8ber2iikra9x73y/2013-02-21%2013.39

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Re: [ccp4bb] TLS refinement refmac

Oh dear - you should always start refinement against the original processed data - but others have told you that already.. The TLS files will not be appropriate for the rescaled FPs - it is surprising that the Rfactor actually goes down though! Or are you doing several cycles of refinement in thes

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Re: [ccp4bb] TLS refinement refmac

Am 17.07.2013 11:59, schrieb Guenter Fritz: Hi Stefan and Gottfried, thanks a lot for the answers. This is the point. Wouldn't it make more sense to add an extra column that contains the changed Fs? Best, Guenter Hi, it is strongly advised to use the original mtz e.g. scala.mtz as the refma

[ccp4bb] TLS refinement refmac

Dear all, one gets different R values, if you re-read in the mtz written out by refmac after TLS refinement. I think this issue had been a while ago in ccp4bb, but I can't find the right track. Here are the details. 1st run: If we do TLS + restr. refinement in refmac we get: InitialFina