Re: [ccp4bb] Save image in Postscript format from PYMOL
Pymol version 0.99 has the option to set the label position, similar to eg. molscript. Go to Select - Edit all - scroll down to label-offset - edit the x,y,z parameters. Pymol version 0.98 does not have this option. Julie. shi jiahai wrote: Hi, all I am drawing some stereo images with label by PYMOL. But the label interfere with protein. I try to output to Postscript format so that I can change the position of label. However, I can't output the image to Postscript format in Pymol. Is there anyboy know how to save image in Postscript format from PYMOL? Your help would be appreciated. Thank you very much! Shi Jiahai Dept of Biological Sciences National University of Singapore -- Julie Bouckaert, PhD[EMAIL PROTECTED] VIB Project leader VIB Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel Tel. 32-2-629-1988 Fax 32-2-6291963 ULTR, Building E 4.18 Vrije Universiteit Brussel Pleinlaan 2 1050 Brussel Belgium
Re: [ccp4bb] crystal shipping at room temperature
I know this is not what you ask for, but I have had good experience with mounting in capillaries (borosilicate, a bit stronger than quartz, but quartz should work also if you are very careful), leaving the crystals in the mother liquid, to fly them over by FEDex from USA to Europe. Leave the capillaries at the longest length possible, so that someone at the synchrotron can open the capillary and push the crystal out of the liquid and close again the capillary, or even push the crystal out and remount the crystal in a different way. For the flights, I left the cappilaries pending a little loosely in the air, with their ends stuck into cotton balls, into a smaller box, that on its turn was fixed shock-damping stuff into a strong, uncrushable box. Cheap, quick and easy! Julie Dear all, Sorry for the non CCP4 questions. We would like to ship some virus crystals to a synchrotron at room temperature (for room temperature diffraction). I am wondering if anybody has ever had any good experience for this kind of shipping. Especially, it would be great if anybody has any good ideas other than pre-mounting the crystals in quartz capillaries (I won't be driving from Houston to Chicago though :D). I would also like to know more about the things that I need to pay extra attention to, if I have to deal with capillaries. Any suggestions would be greatly appreciated. I'm now testing the more convenient MiTeGen MicroMounts. However, I am not sure whether the crystals can remain resting on the MicroMounts aperture during the course of a typical Fedex shipping (according to the MicroMounts instruction sheet, crystals should not be trapped in the aperture). It would be great if anybody would share your previous experience with regard to the MiTeGen stuff. Another question about the MiTeGen mounting tools is that I always observe a stong diffraction ring at about 5 A. Well, it is not exactly a ring; it's actually two thick arches (pretty thick, roughly from 5.5 A to 4.8 A), one at the top and the other at the bottom of the diffraction patterns (nothing on the left-hand or right-hand side). Does anybody have any idea what this might be (fiber?)? thanks a lot for your help! Junhua --- Junhua Pan Department of Biochemistry Cell Biology 327 Keck Hall, Rice University 6100 Main Street MS-140 Houston, TX 77005 Phone: (713)348-3346 Email: [EMAIL PROTECTED]
Re: [ccp4bb] Differentiating bound Mn Ca.
Hey David, You can do Mn2+ identification by its anomalous diffraction using the Cu Kalpha radiation. Mn is an anomalous scatterer at Cu Kalpha (1.5418 A), despite being distant from its absorption edge (somewhere around 1.96 A if I remember well). I did this for a double-manganese bound ConA, have a look into THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 275, No. 26, Issue of June 30, pp. 19778–19787, 2000 (you may need to use different programs for making your anomalous difference Patterson and Fourier maps these days). Julie. Kay Diederichs wrote: David Briggs wrote: Dear all. I have recently solved a structure in-house, 2.8A, CuKa. I have a metal ion bound very obvious hepta-valent co-ordination, which would suggest either Ca or Mn. Neither was present in the crystallisation setup, but there was some Mg around, which has contaminants of both Ca Mn. At 2.8A, I don't really think I can reliably discriminate between 2.15A 2.36A distances to coordinating atoms (http://tanna.bch.ed.ac.uk/newtargs_06.html http://tanna.bch.ed.ac.uk/newtargs_06.html). The B factors for refined Ca are 18, and Mn 30. The B-factors of coordinating atoms vary from... 18 30 - so no help there. I have a nice clear 6sigma anomalous difference peak, but then, according to http://skuld.bmsc.washington.edu/scatter/ both Ca (f ~1.3) and Mn (f ~2.8) scatter anomalously at that wavelength. The obvious solution is go to a synchrotron and scan around the Mn edge and see what happens, however, whilst waiting for beam time, is there any way I could... oh I don't know, use the peak in my anomalous difference Fourier to figure out what anomalous signal would be required to generate a peak of that size - a sort of back-transform??? Is this do-able, and if so, how would one go about it? Cheers, Dave Dave, f = 1.3 versus 2.8 sounds like quite a difference ... what is the anom peak height of the sulfurs in your structure? The f of sulfur at Cu Ka wavelength is 0.55 . So I'd expect the ratio of peakheights of your unknown metal divided by the average peakheight of sulfurs (of roughly 18-30 A**2 B-factor) to give you an idea of what you have. Of course this is no proof ... Are there any other anom scatterers in your structure? best, Kay -- Julie Bouckaert, PhD[EMAIL PROTECTED] VIB Project leader VIB Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel Tel. 32-2-629-1988 Fax 32-2-6291963 ULTR, Building E 4.18 Vrije Universiteit Brussel Pleinlaan 2 1050 Brussel Belgium
