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Thank you Matthew and every one for the answer on the second question.
On the first (remote ccp4):
I can't help you with the network question. Maybe you don't have write
permissions to the scratch directory on the remote machine? What error
messages do you get?
I have the write permission on /tmp/julien/. The error message is (I
translate it): /tmp/julien/ccp4_42_check.def.com no such file or directory.
Actually, this file exists in my /tmp on my localhost, but I think it is not
transfered to my remote host. I think remote ccp4 just works if data is on
an NFS-mouted filesystem shared over a network.
Julien
From: [EMAIL PROTECTED]
To: "Julien Lafrance-Vanasse" <[EMAIL PROTECTED]>m
CC: [email protected],[EMAIL PROTECTED]
Subject: Re: [ccp4bb]: 2 questions:
Date: Thu, 18 May 2006 13:31:33 -0400
Hi Julien -
I can't help you with the network question. Maybe you don't have write
permissions to the scratch directory on the remote machine? What error
messages do you get?
As for the R-factor question, it's not unusual to get different values with
different programs - sfcheck is probably not using the same solvent model,
B-factor correction, and TLS correction that Refmac is using. In
particular, the TLS correction usually gives a substantial drop in R factor
(compare your CNS output with your Refmac output) but it's not recorded in
your PDB coordinates unless you write out anisotropic temperature factors.
The difference in R factors is pretty low, and the prettier numbers are
what you'll put in the paper anyway. I wouldn't worry about it.
A question for the group: is there any push to get TLS parameters
incorporated into the standard PDB data format? Right now, the data gets
thrown into a comment record where no program really uses it. Even CCP4
programs don't read that information, and refmac has to be given the data
in a separate file.
- Matt
[EMAIL PROTECTED] wrote on 05/18/2006 01:04:47 PM:
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
>
> Hi
>
> Sorry for these real-ccp4 questions:
>
> 1. Remote jobs
> I tried to run a remote job on a distant computer. It didn't work. I
guess
> it has to run on a local network with the /home and /tmp shared by
NFS?!?
> Does anyone has a script integrated in ccp4 that transfers file to
another
> machine, runs the job and re-transfers the ouput?
>
> 2. R and r_free under REFMAC
> I decided to run refmac with TLS at the end of my refinement process.
I'm
> quite new to ccp4, because I usually use cns. The conversion between the
two
> went well.
>
> I ran SFcheck on the initial model, to mesure r and free_r which gives
> 0.186/0.208. There's a small difference with cns (0.1854/0.2060), but
that
> doesn't bother. What really bothers is those values at the end of the
> refinement with REFMAC. The values go down during the refinement process
(if
> I look at the log graph) and the pdb output gives:
> REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
> REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
> REMARK 3 R VALUE (WORKING + TEST SET) : 0.16981
> REMARK 3 R VALUE (WORKING SET) : 0.16822
> REMARK 3 FREE R VALUE : 0.20006
> REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0
> REMARK 3 FREE R VALUE TEST SET COUNT : 8921
>
> But if I run SFcheck on the output pdb, it gives me 0.187/0.217, which
is
> approx 0.02 difference with REFMAC! I really don't understand what
happens.
> I'm asking myself if the refinement went well and from two programs, I
have
> different values!
>
> Thank you,
>
> Julien
>
>
--
Matthew Franklin phone:(917)606-4116
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