Sorry I should have copied this to the BB as it may be of general
interest:
-----Original Message-----
From: Ian Tickle
Sent: 17 September 2008 11:05
To: 'Jan Dohnalek'
Subject: RE: [ccp4bb] Topp fails: TOP: Open failed: File:
/people/...../myfile.pdb
OK try this one: looking at the program I see that it searches for the
string 'pdb' in the pathname and uses the name up to that point:
IF (INP(1:4).EQ.'MOL1') THEN
ISP = INDEX(INP,' ')
indpdb=INDEX(INP,'pdb')
i=isp
do i=isp,indpdb
if(inp(i:i).ne.' ') goto 2255
enddo
2255 continue
FILE1=INP(i:indpdb+2)
So if your file is called say 'junk.pdb' it's fine, if it's called
junkpdb.pdb it will try to open 'junkpdb'!!
Your pathname doesn't have the string 'pdb' somewhere in it (except at
the end) by any chance?
-- Ian
> -----Original Message-----
> From: Jan Dohnalek [mailto:[EMAIL PROTECTED]
> Sent: 17 September 2008 10:33
> To: Ian Tickle
> Subject: Re: [ccp4bb] Topp fails: TOP: Open failed: File:
> /people/...../myfile.pdb
>
> Dear Ian,
> I have done this exercise even before I sent my original e-mail (as
you
> may notice in my original e-mail).
> The shortest path length was 33 characters. I know this normally
fixes
> many of these problems.
> This time it does not ...
> Jan
>
>
> Ian Tickle wrote:
> > Hi Jan
> >
> > We had this problem, I think it's because the character strings used
to
> > store pathnames are only 80 chars long, so if you have a long
pathname
> > (you didn't show your full pathname!) then it has a problem. You
can
> > either fix the program, or do as we did make a soft link in the
current
> > directory.
> >
> > Cheers
> >
> > -- Ian
> >
> >
> >> -----Original Message-----
> >> From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]
> >>
> > On
> >
> >> Behalf Of Jan Dohnalek
> >> Sent: 17 September 2008 10:02
> >> To: ccp4bb
> >> Subject: Topp fails: TOP: Open failed: File:
/people/...../myfile.pdb
> >>
> >> Hi all,
> >> Using the 6.0.2 distribution of CCP4, the top program keeps failing
> >> because it just can't see the pdb files. The files can be accessed
by
> >> the text viewer of CCP4. (the button VIEW)
> >> I have tried to put them in other directories to make the path
string
> >> shorter, etc. None of those helped.
> >> I have tried moving to various Linux versions (64bit,32bit, var.
> >>
> > levels
> >
> >> of Fedora or RHEL)....
> >>
> >> Any ideas?
> >> Jan Dohnalek
> >>
> >> --
> >> ==============================================
> >> Mr. Jan Dohnalek, Ph.D
> >> Institute of Macromolecular Chemistry
> >> Academy of Sciences of the Czech Republic
> >> Laboratory of Structural Analysis of Molecules
> >> Heyrovskeho nam. 2
> >> 16206 Prague 6
> >> Tel: +420 296809205
> >> Fax: +420 296809410
> >>
> >> http://protein.awardspace.com/
> >> ==============================================
> >>
> >
> >
> >
> > Disclaimer
> > This communication is confidential and may contain privileged
> information intended solely for the named addressee(s). It may not be
used
> or disclosed except for the purpose for which it has been sent. If you
are
> not the intended recipient you must not review, use, disclose, copy,
> distribute or take any action in reliance upon it. If you have
received
> this communication in error, please notify Astex Therapeutics Ltd by
> emailing [EMAIL PROTECTED] and destroy all copies of the
> message and any attached documents.
> > Astex Therapeutics Ltd monitors, controls and protects all its
messaging
> traffic in compliance with its corporate email policy. The Company
accepts
> no liability or responsibility for any onward transmission or use of
> emails and attachments having left the Astex Therapeutics domain.
Unless
> expressly stated, opinions in this message are those of the individual
> sender and not of Astex Therapeutics Ltd. The recipient should check
this
> email and any attachments for the presence of computer viruses. Astex
> Therapeutics Ltd accepts no liability for damage caused by any virus
> transmitted by this email. E-mail is susceptible to data corruption,
> interception, unauthorized amendment, and tampering, Astex
Therapeutics
> Ltd only send and receive e-mails on the basis that the Company is not
> liable for any such alteration or any consequences thereof.
> > Astex Therapeutics Ltd., Registered in England at 436 Cambridge
Science
> Park, Cambridge CB4 0QA under number 3751674
> >
> >
>
>
> --
> ==============================================
> Mr. Jan Dohnalek, Ph.D
> Institute of Macromolecular Chemistry
> Academy of Sciences of the Czech Republic
> Laboratory of Structural Analysis of Molecules
> Heyrovskeho nam. 2
> 16206 Prague 6
> Tel: +420 296809205
> Fax: +420 296809410
>
> http://protein.awardspace.com/
> ==============================================
>
Disclaimer
This communication is confidential and may contain privileged information
intended solely for the named addressee(s). It may not be used or disclosed
except for the purpose for which it has been sent. If you are not the intended
recipient you must not review, use, disclose, copy, distribute or take any
action in reliance upon it. If you have received this communication in error,
please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy
all copies of the message and any attached documents.
Astex Therapeutics Ltd monitors, controls and protects all its messaging
traffic in compliance with its corporate email policy. The Company accepts no
liability or responsibility for any onward transmission or use of emails and
attachments having left the Astex Therapeutics domain. Unless expressly
stated, opinions in this message are those of the individual sender and not of
Astex Therapeutics Ltd. The recipient should check this email and any
attachments for the presence of computer viruses. Astex Therapeutics Ltd
accepts no liability for damage caused by any virus transmitted by this email.
E-mail is susceptible to data corruption, interception, unauthorized amendment,
and tampering, Astex Therapeutics Ltd only send and receive e-mails on the
basis that the Company is not liable for any such alteration or any
consequences thereof.
Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park,
Cambridge CB4 0QA under number 3751674
