[ccp4bb] How to show density map in pymol?

Hi All, If I want to show the density map in pymol--like coot open mtz file--, what format should I use? It seems pymol doesnot recognise the mtz format . Thanks!

Re: [ccp4bb] Crystal Screens

Dear Ray: The Crystal Screen I is based on a screen that was developed over a period of years in Sung-Hou Kim's lab, and is heavily weighted with conditions that were successful for obtaining the protein crystals that were particular to his lab at that time (which was when I was a graduate stud

[ccp4bb] Sliding window net charge program?

Hello all, does anybody know of a program which calculates net charge within a sliding window of user-defined size? Hydropathy programs are almost this, but not quite--they use absolute values rather than the signed ones (what is the opposite of an absolute value called? the relative value?).

Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement

Yes, as the twinning fraction increases from 0 to 0.5, the cumulative intensity distribution curve changes in a continuous way from untwinned to perfectly twinned. The exact way in which it does this was calculated by Rees (Acta A 36, 578 (1980)). Note that the variation is markedly non-linear - if

Re: [ccp4bb] How to show density map in pymol?

Dear Yang Li, to quote from Stefan Schmelz's post on this topic: "Date: Mon, 29 Oct 2007 08:40:42 + From: Stefan Schmelz <[EMAIL PROTECTED]> To: Subject: Re: [ccp4bb] pymol help Dear Yanming, To show "pretty" density of a model you have to import a ccp4 density map and display it around y

Re: [ccp4bb] Crystal Screens

There are some screens for sale based on experiences of large Structural Genomics consortia, the JCSG (+) screen is an example. Screens like these are often biased towards the type of organism targeted by the consortium (e.g. eukaryotic/prokaryotic) Flip -Original Message- From: CCP4 bul

[ccp4bb] Protein Charge in a Moving Window

Does anyone have or know of a program to calculate net charge of a protein sequence in a user-defined sliding window? Somewhat like a hydropathy plot, but with positive and negative values instead of absolutes. It should be out there, I would think. Jacob *

[ccp4bb] your favorite crystallization screens

Hello, I usually try out Hampton crystal screen I & II, and PEG/ion screens on my proteins, sometimes varying protein concentrations and incubation temperature. If no hints are obtained, I will go back to test alternative constructs and purification protocols. With more and more companies s

Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement

The cumulative intensity depends on correctly estimating weak reflections, so it is a bit vulnerable to the integration procedures. I prefer the 4th moment of E - 2nd moment of I. Providing there is no pseudo-translation they are pretty reliable indicators of twinning Eleanor Bryan W. Lepore

[ccp4bb] Programs for analysing the "drugability" of a small-molecule binding pocket

Dear colleagues, I am looking for a computational method to assess reliably the "drugability" of a small- molecule binding pocket (volume, surface, interaction potential etc.) on a protein surface. Any recommandations and experiences are welcome! Many thanks in advance! Karsten Niefind

Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement

On Mon, 29 Oct 2007, Iain Kerr wrote: The cumulative intensity distribution plot from crystal A did suggest partial twinning (attached, doesn't look too bad though..) notwithstanding other plots/statistics, does the cum. intens. dist. plot (e.g. from truncate) really show a continuum from untw

Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement

I am a big fan of the RvR statistic (http://journals.iucr.org/d/issues/2006/01/00/ba5089/index.html) This statistic is very usefull when a model is available. When no model is present, the L test is nice as well and is relatively robust in the presence of pseudo centring. P 2007/10/31, Elean

[ccp4bb] converting structure factor files to mtz files

Hi, Could anyone give a quick hint for the Fortran format for the following structure factor mmCIF file? or Is there any easy program or better way to convert it? I think I need to skip first 3 columns. Thanks in advance. Joe loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code

Re: [ccp4bb] converting structure factor files to mtz files

If you want to "roll your own"... If you add the data_xxx line to make this a legal CIF, you should be able to read it with ciftbx if you are working in a Fortran application or CBFlib if you are working in a C application. You will find a variety of CIF tools pointed to from the IUCr web site

Re: [ccp4bb] converting structure factor files to mtz files

Someone knowing fortan showed me that in many cases you can simply omit the FORMAT keyword in f2mtz, provided the columns never use up the full column width (i.e., in your case: there is no reflection with amplitude > 999.99). Simply use SKIP, LABOUT and CTYPOUT to read in your data (and t