[ccp4bb] Fwd: [ccp4bb] suggestions on a microscope for Crystallography

-- Forwarded message -- From: Daniel M. Himmel, Ph. D. Date: Wed, Mar 7, 2018 at 12:23 AM Subject: Re: [ccp4bb] suggestions on a microscope for Crystallography To: Chandramohan Kattamuri My best experience was with Leica

[ccp4bb] suggestions on a microscope for Crystallography

Hi I'm looking for suggestions on a good microscope for looking at crystals, which includes polarization, light source (fiber optics), crosshairs and camera mount. What Models and make? Thanks in advance Chandra

Re: [ccp4bb] Unknown density

Hi Rajesh, It might be water molecules present at the symmetry axis, one more water molecule at the centre (exactly at the axis, with occupancy of 0.5). If you put three water molecule you probably may find the other three symmetry-mates water molecules in opposite sides. OR One water molecule

Re: [ccp4bb] Unknown density

Hi Rajesh, You may find this database is also useful while refining your model http://mespeus.bch.ed.ac.uk/MESPEUS_10/ and for calcium http://mespeus.bch.ed.ac.uk/MESPEUS_10/_5.jsp Abhik On Tue, Mar 6, 2018 at 10:59 PM, Patrick Loll wrote: > Calcium likes to form

Re: [ccp4bb] Unknown density

Calcium likes to form octahedral complexes with water (or other oxygen-containing) ligands. This looks like a classic example. After you model and refine this, you’ll want to check water-metal distances, to make sure they are appropriate for calcium. There is a nice literature on such things,

Re: [ccp4bb] Unknown density

You could try to put CA (as you have CA in your crystallisation condition) and waters for coordinating atoms. If after refinement distances are around 2.3-2.4 (if I remember correctly) and B values of atoms (CA and waters) are consistent, i.e. similar to each other then CA is good

Re: [ccp4bb] Unknown density

Hi Rajesh, Can you please let everyone know the buffer/reagents involved throughout the process. Also, how strong is the density? In other words, until what contour level you see it in the Fo-Fc map? Anyways, looking at the shape, it looks well coordinated - could be cacodylate? Or water, am

Re: [ccp4bb] Unknown density

Hi Hussain, Crystallization condition is 200 mM CaCl2 and 20% PEG 3350. I some what realized that it could be Ca++ with coordinated waters. But I really wanted to have second opinion from our group. Thank you every one. -Rajesh On Tue, Mar 6, 2018 at 5:37 PM, Hussain Gps

Re: [ccp4bb] Unknown density

Mg2+(H20)6 ? > On 6 Mar 2018, at 22:19, Rajesh Kumar wrote: > > Dear All, > > Have you had experience with this kind of density? I am wandering what this > could be? > > Thank you very much for the help. > > -Rajesh > > > >

Re: [ccp4bb] Unknown density

It looks like 6 coordinated metal atom with coordinated (possibly) with waters. The simplest case could be NA. You could use anomalous difference map to see if there is any anomalous signal there. Regards Garib On 6 Mar 2018, at 22:19, Rajesh Kumar wrote: > Dear All,

Re: [ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

Last update... Everything works well with the same files and the same Coot version on an other computer. The problem may come from the os of my computer which is too old and has to be upgraded. Thank you for your help. 2018-03-06 9:20 GMT+01:00 M T : > Dear all, > > I did

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[ccp4bb] Structural neurobiology postdoc opportunity at UCL

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Re: [ccp4bb] AW: [ccp4bb] Small molecule not refined in coot.

Dear all, I did something very simple... Starting from the pdb I obtained from PRODRG server (manual drawing, then transfer to PRODRG and download of the pdb from server), in CCP4 I used ProDrg to generate a new .cif and a new .pdb. After I used "View Job Results (ew style)" to open my new pdb