[ccp4bb] SHELX as model building

Hello I have been using ARP/WRAP to trace the initial model. Now, I am interested to use SHELX for this purpose. Does somebody know that which package of SHELX can be used as the auto tracing of main chain? Regards, Rojan

[ccp4bb] Pymol import error

Hello: I am trying to use Pymol in the python script but I am facing very simple error: "No module named pymol". I guess this is very simple error. I have installed binary file of Pymol. When I tried to import the pymol, the error message was displayed. >From where I could get Pymo

[ccp4bb] origin_shift in polar space group

Hello: In polar space group when the two or more copies molecules are superimposed, the origin is shifted. Does anybody have the solution to tackle this problem? Regards, Rojan

Re: [ccp4bb] origin_shift in polar space group

roup symmetry can be used to transform subsequent pairs. For this I find it easiest just to view the structure on the graphics, work out which is appropriate space-group operator and apply it just to the 2nd molecule using PDBSET. Hope this is all clear - there are many traps here for the unwary

[ccp4bb] Saxs reviews or books

Hello: I am very novice about Small Angle X-ray Scattering. I am looking for introductory books or review papers. Could you recommend this type of document? Regards, Rojan

Re: [ccp4bb] Saxs reviews or books

Hello: Thank you to all for nice information about SAXS. Regards, Rojan From: Catarina Rodrigues [mailto:catarina.rodrig...@afmb.univ-mrs.fr] Sent: Tuesday, January 11, 2011 3:26 PM To: ro...@riken.jp Subject: Re: [ccp4bb] Saxs reviews or books Hi, I recommend you the revie

[ccp4bb] SAXS collection

Hello: I am searching for SAXS data depositor like protein data bank for protein structure and EDS from electron density map. I have no idea how can I get SAXS data. Is there a depository for SAXS collection? If not so, what is the usual way to get it? Regards, Rojan

[ccp4bb] Electron density server

Hello, Is EDS (electron density server) dead? In the absence of EDS, how can be mtz file directly downloaded? Regards, Rojan

[ccp4bb] Tool to compute F/FP from F(+) / F(-)

Hello, What is the tool in CCP4 to calculate F from F(+) and F(-) with their standard deviations? Regards, Rojan

[ccp4bb] How degenerate keyword in Phaser can be used?

Hello, Can somebody tell me how the Phaser degenerate function can be used with MR_BTF? My script is as follows: #my_phaser_run.com phaser << eof TITLe BTF_RUN MODE MR_BTF HKLIn a.mtz LABIn F=Fobs SIGF=Sigma ENSEmble mol1 PDB a.pdb IDENtity 100 # this is model structure not

[ccp4bb] SC example

Hello, I like to use surface complementary(sc) program of CCP4. Since I am a new user, I would like to see the example. The example link of website is dead. Can somebody provide simple example of running SC from CCP4? Regards, Rojan

Re: [ccp4bb] SC example

Dear Tim, Thank you very much. I have checked on the location for example. I found the example script (sc.exam). Regards, Rojan -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Wednesday, June 15, 2011 10:27 AM To: Rojan Shrestha Cc: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] SC example

e 15, 2011 10:27 AM To: Rojan Shrestha Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] SC example Dear Rojan, Since you have CCP4 installed, you should have the example file in $CCP4/examples/unix/non-runnable/sc.exam. I attach the file for convenience. Tim On Wed, Jun 15, 2011 at 09:44:28AM +0

[ccp4bb] Surface complementary output

Hello, Does somebody know the meaning of output of SC? What is the meaning of From and To in "Distance between surfaces"? >From To Area Cumulative_Area % Cumu. % Similarly, what is the meaning of surface complementarity? >From To Number

[ccp4bb] Arp/Wrap problem while model building

Hello, I am facing a problem in running "auto_tracing" in arp/wrap. At first I have tried using command line mode however I missed R-free value. I have added the "freelabin " FREE=FREE "" and have got an error "Refmac_5.5.0102: Error in label assignments in LABIN" In another way, I use

[ccp4bb] Error in overlapmap

Dear all, I am trying to calculate the correlation between two 2Fo-fc maps but I was getting error. The error is: CCP4 library signal library_file:Cannot open file (Error) This error was appeared after reading the given map files and trying to calculate correlation betwe

[ccp4bb] Error while compiling ccp4 source in mac os

Dear all, I would like to compile the CCP4 in mac book pro with intel cpu. The purpose of installing ccp4 using source code is to compile the clipper library. Although I have already installed ccp4 dmg package provided for mac os, I could not compile the clipper using ccp4. The problem occurr

[ccp4bb] High number of clashes with high TFZ score

Hello, I am trying phasing using homology models with Phaser. We obtained very high TFZ scores with many clashes. The number of clashes are around more than 100. The space group is P321. We tried two other space groups P3121 and P3221 but both gave same problem. Can you help on this problem?