Re: [ccp4bb] program to create cartoon image from a PDB file which have only C-alpha coordinates

Hi, I suppose any program that makes cartoons can handle a C_alpha-only-file. I just tried rasmol and molscript without problems. pymol probably also works, or ccp4mg. Have you had any problems, or are you just not familiar with programs that make cartoons? Cheers, Tim -Original Message-

Re: [ccp4bb] shelx HKLF4 to mtz conversion?

stitute of Technology > Division of Biology > 1200 E. California Blvd. MC 114-96 > Pasadena, CA 91125 > 626-395-2453 > [EMAIL PROTECTED] > http://www.br.caltech.edu/cmclab -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpuMHpGIBBuY.pgp Description: PGP signature

Re: [ccp4bb] Help with reducing crystal mosaicity

e doing anything else. It sounds like a very good candidate. -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpEJuDKsMqme.pgp Description: PGP signature

Re: [ccp4bb] The CCP4 license is ambiguous

t; I believe this is false. To take an obvious example, consider GPL > > software running on Windows and calling into the system libraries. > > Do you think that Cygwin has been in violation of the GPL all these > > years? > > > > Or perhaps I misunderstand. Are you sa

Re: [ccp4bb] compiling problems ccp4-6.0.2 and gcc-4.1.2

omon_/cmap_io.c:356: > warning: passing arg 3 of 'mat4_to_symop' from incompatible pointer > /usr/bin/ld: solomon: hidden symbol `__stack_chk_fail_local' in > /usr/lib/libc_nonshared.a(stack_chk_fail_local.oS) is referenced by DSO > /usr/bin/ld: final link failed: Nonrep

Re: [ccp4bb] Molscript and symbolic label

Before providing the label with the 'label' command, you must set the 'labelmask' to contain a '%g' at the Position of your greek letter, e.g. set labelmask '.%g' label "Ca" should produce an 'alpha' for the second letter. As far as I remember, this does not work with Raster3d-Output, though, y

Re: [ccp4bb] mac pro configuration for crystallographic computing

lly trying to do, and as soon as they see what they want to see the make a screen shot (not excluding me here). cheers, Tim -Original Message- From: Tim Grune <[EMAIL PROTECTED]> To: CCP4BB@JISCMAIL.AC.UK Date: Thu, 21 Jun 2007 13:26:54 +1000 Subject: Re: [ccp4bb] mac pro conf

Re: [ccp4bb] mac pro configuration for crystallographic computing

#x27;s only my very personal opinion). Tim -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpFhY3yeObxL.pgp Description: PGP signature

Re: [ccp4bb] problems with phaser for MR

Hi, this looks very familiar to me. I am pretty certain you have phenix installed, too, and ccp4i does use the phenix version of phaser, which shows this behaviour. You can test this by typing 'which phaser' from the command line. You should make sure that $CBIN comes before the phenix path, e.g

Re: [ccp4bb] COOT (version 0.2, Jan 2007) and .FCF file

> Finally chances are that coot uses an environment variable to call coot. nya, I meant a variable to call awk..., sorry for the typo.

Re: [ccp4bb] COOT (version 0.2, Jan 2007) and .FCF file

you its name then set it from /usr/bin/awk to /bin/awk and things should work. Tim -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpTdKrEILway.pgp Description: PGP signature

Re: [ccp4bb] Delphi question

afa, Ph.D. > Biochemistry and Molecular Biology Dept. > 201 Althouse Lab., Uinversity Park > Pennsylvania State University, PA16802 > > Tel. (814)863-8703 > Fax. (814)865-7927 > --- >--

Re: [ccp4bb] Simultaneous PHENIX and CCP4 burp

3.3 and v2.0 > > > > for ccp4 and > > > > > phaser respectively.) v2 has an older release date... > > > b) How can one fix the path to make both executables > > > > available to the > > > > > shell? > > > c) The same problem affects mmtbx and cctbx etc. > > > > > > > > > Shouldn't the ccp4 versions maybe get different names? > > > > > > phx. -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpltSPAECCxE.pgp Description: PGP signature

Re: [ccp4bb] MolRep with Phaser using a partial existing solution

aser manual and it seems that I cannot input a pdb with this > > partial solution and tell the program to fix this molecule. It seems > > that fixed solutions can be only input by putting in its Euler angles and > > fractional coordinate > > translations. Is this correct that

Re: [ccp4bb] MolRep with Phaser using a partial existing solution

ick way to identify the euler angles and > coordinate translations for Phaser. > > Thanks a lot!! > > Jay -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpm9nCMhOS3O.pgp Description: PGP signature

Re: [ccp4bb] Refmac5 restrained refinement could not keep the changes made in Turbo

___ >_Boardwalk for $500? In 2007? Ha! Play Monopoly Here and Now (it's > updated for today's economy) at Yahoo! Games. > http://get.games.yahoo.com/proddesc?gamekey=monopolyherenow -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpBK9wvWHvLH.pgp Description: PGP signature

Re: [ccp4bb] ccp4mg can't start

idea and may have a negative influence on ccp4mg's performance? Tim -Original Message- From: Yanming Zhang <[EMAIL PROTECTED]> To: Tim Grune <[EMAIL PROTECTED]> Date: Wed, 16 May 2007 01:47:08 -0400 (EDT) Subject: Re: [ccp4bb] ccp4mg can't start Dear Tim

Re: [ccp4bb] crystallographic magic

Z-file, or a CNS-map). ;-) On Tuesday 15 May 2007 15:36, you wrote: > uhhh????? > > 2007/5/14, Tim Grune <[EMAIL PROTECTED]>: > > Hi, > > > > I just found out that my magic file contains a large section with respect > > to crystallographic file formats

[ccp4bb] crystallographic magic

Hi, I just found out that my magic file contains a large section with respect to crystallographic file formats. I was pretty impressed. According to the header it is attributed to Joe Krahn. Full ACK to him! Tim -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168

Re: [ccp4bb] CCP4 GUI

As long as I have been using the ccp4i (which has been a couple of years now), this magic button has been there, and it has even been in the 'lower left corner': When you hold your mouse button on the "Run" button, a submenu appears, the second item of which is saying "Run&View com file". This o

Re: [ccp4bb] Program to find the center of mass

ted a rotation and translation matrix by > program lsqkab. Resolve also requires a center of mass input. Do you > know any program can estimate it either by map or pdb file? > Thanks. > > Nian Huang > Department of Biochemistry > Univ of Texas Southwestern Medical Center

Re: [ccp4bb] can truncate import Rfree?

to the man page, sorry about that. Cheers -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Tim Grune > Sent: 03 May 2007 00:16 > To: CCP4BB@jiscmail.ac.uk > Subject: can truncate import Rfree? > >

[ccp4bb] can truncate import Rfree?

from another MTZ" if I select the "Ensure unique data & add FreeR column" in the truncate GUI. Is this the correct way to go by selecting the file itself for the reference mtz file? This seems extremely error prone to me. Cheers, Tim -- Tim Grune Australian Synchrotron 800 Bla

Re: [ccp4bb] further inconsistencies (was: tcltkblt and python distributions)

Hello Oliver, if by 'conventional' you mean - download the source code - ./configure OS && make && make install I did not share your experience a couple of days ago when I did that. I used both the ftp and the download interface and nothing was missing. However from from your mentioning of 'BINA