Re: [ccp4bb] PyMOL v. Coot map 'level'

One cannot understand what is going on without knowing how this map was calculated. Maps calculated by the Electron Density Server have density in units of electron/A^3 if I recall, or at least its best effort to do so. This is what I was looking for! (i.e. what the units are) Thanks.

Re: [ccp4bb] PyMOL v. Coot map 'level'

Hi Emilia et al., I tried to figure out the PyMOL vs. Coot normalization discrepancy a while ago. As far as I remember, PyMOL normalizes on the raw data array, while Coot normalizes across the unit cell. So if the data doesn't exactly cover the cell, the results might be different. Cheers,

[ccp4bb] crystal habit/morphology and the relationship to unit cell contents

I'm interested in knowing how to figure out the relationship between the unit cell contents and the crystal habit in these crystals (small attachment, two roughly orthogonal views). Space group is P64 (enantiomeric) , and you can clearly see the six-fold. The question becomes how to determine

Re: [ccp4bb] PyMOL v. Coot map 'level'

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 You are correct about this. The magnitude of this effect depends on the amount of solvent in your crystal (which tends to be flatter) but it rarely reaches a factor of two. This does point out a serious flaw with contouring a map relative to

Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents

Maybe I confused the question by asking about the direction of the screw axis. I'm referring to the top and base of the actual crystal. If all the molecules in the unit cell are oriented in the same direction (with respect to the c cell), I want to know if there is a way to find out which

Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents

Hi Sorry about this, it's been a hard day and it's the first thing I thought of when I saw the pics of crystals... Brits of a certain age may be reminded of Gerry Anderson's UFOs... On 1 Jun 2015, at 17:20, Paul Paukstelis wrote: I'm interested in knowing how to figure out the relationship

[ccp4bb] Allignment of multiple structures

I apologize if this question this question has been asked before but I still need help finding an answer to the following. I am looking for a program/web-server that will calculate the superposition of multiple structures (non-protein!) Thanks --

Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents

Can't you break the ambiguity if there is significant anomalous signal? So, you'd need to have collected data from a protein crystal with SeMet, or a heavy atom, or near the S edge, and know the orientation of the crystal w.r.t. the direction of the unique crystal axis (for instance from face

Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents

Yes, but where is the screw axis in that UFO? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Harry Powell Sent: Monday, June 01, 2015 12:36 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents Hi

Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents

Hi Paul, If you have access to diffractometer equipped with a 4-circle goniometer, you should be able to index the faces of the crystals. All you need to do is collect some images to index the lattice and determine the orientation matrix. Most instruments have software that allows one to

Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents

I would have thought that what the indexing routine defined as [001] vs [00-1] would be essentially random as one would obtain the equivalent indexing in 622 in both up and down alignment of the crystallographic a/b/c axes with respect to crystal morphology. Phil Jeffrey Princeton On

Re: [ccp4bb] [phenixbb] Allignment of multiple structures

Dear Jens J. Birktoft, lsqman from the Uppsala Software Factory (USF) is very flexible in terms of atom selection etc. and it is scriptable. You may need to choose one reference structure amongst your coordinates, though. Best wishes, Tim On Mon, Jun 01, 2015 at 03:53:54PM -0400, jens j

Re: [ccp4bb] [phenixbb] Allignment of multiple structures

THESEUS should be able to do it rather easily. You can email me offlist if you need some guidance. On Jun 1, 2015, at 3:53 PM, jens j birktoft birkt...@nyu.edu wrote: I apologize if this question this question has been asked before but I still need help finding an answer to the

Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents

Is it possible to distinguish P64 from P62 without having basically solved the structure? Given that it is P64, is the +ive direction of the c axis arbitrary? A left-hand helix is left hand either way you point it, and the molecules in the asymmetric units could be pointing the opposite way.

Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents

All the crystals are unipyramidal, regardless of how they are grown. The crystal habit seems to be dictated by the arrangement of the molecules in the unit cell. The structure is solved, so this is really an exercise in trying to figure out if what we see in the crystal packing can explain the

Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents

Dear Paul, could you check if the crystals are optically active and find out which way they rotate the polarisation of light? I am not sure how to deduce the screw direction from this, I would first try to determine an angle... Best, Tim On Mon, Jun 01, 2015 at 04:41:41PM -0400, Paul

Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents

You need: a) to have an image of your crystal mounted on the goniometer in orientation, in which the axis of interest (6-fold) is perpendicular to the beam. You should know the system well enough to relate the coordinate system of the crystal on this image to the beam-gravity coordinate system.

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