Hi Charlie -
I'm not able to reproduce your issue. I tried this with a random PDB and,
although the symmetry operation wasn't appropriate for that particular
structure, I got normal-looking cartoon representations.
One thing to consider might be that, if there are abnormalities in the
numberi
Do you need to rename the symmetry shifted chsain?
Eleanor
On 26 June 2015 at 16:33, Carter, Charlie wrote:
> I'm trying to generate an oligomer using pdbset with the script attached
> below. The rotated molecules appear to be oriented properly, but they
> cannot be viewed correctly in PYMOL bec
I'm trying to generate an oligomer using pdbset with the script attached below.
The rotated molecules appear to be oriented properly, but they cannot be viewed
correctly in PYMOL because the cartoon option fails to connect many of the
residues. What am I doing wrong?
Thanks,
Charlie
pdbset XY
ll 'grep', a command common on
> unixoid operating systems).
>
> By the way: how did you get negative B-values into your PDB-file?
>
> Best, Tim
>
> On 06/11/2013 10:22 AM, Swastik Phulera wrote:
>>>> -- Forwarded messag
>>
>> By the way: how did you get negative B-values into your PDB-file?
>>
>> Best,
>> Tim
>>
>> On 06/11/2013 10:22 AM, Swastik Phulera wrote:
>> > -- Forwarded message -- From: Swastik Phulera
>> > Date: Tue, Jun 11, 2013 at
M, Swastik Phulera wrote:
> > -- Forwarded message ------ From: Swastik Phulera
> > Date: Tue, Jun 11, 2013 at 1:51 PM
> > Subject: Re: [ccp4bb] pdbset To: Tim Gruene
> >
> >
> >
> > Dear Tim, Miguel Thanks for your suggestions, the program does
>
> On 06/11/2013 10:22 AM, Swastik Phulera wrote:
> > ------ Forwarded message -- From: Swastik Phulera
> > Date: Tue, Jun 11, 2013 at 1:51 PM
> > Subject: Re: [ccp4bb] pdbset To: Tim Gruene
> >
> >
> > Dear Tim, Miguel Thanks for your suggestio
Date: Tue, Jun 11, 2013 at 1:51 PM
> Subject: Re: [ccp4bb] pdbset To: Tim Gruene
>
>
>
> Dear Tim, Miguel Thanks for your suggestions, the program does work
> now, but it seems that it cant handle AnsioU s . It gives an
> error:
>
> PDBSET: *** AnisoU present: canno
13 10:22, Swastik Phulera wrote:
-- Forwarded message --
From: *Swastik Phulera* <mailto:swastik.phul...@gmail.com>>
Date: Tue, Jun 11, 2013 at 1:51 PM
Subject: Re: [ccp4bb] pdbset
To: Tim Gruene mailto:t...@shelx.uni-ac.gwdg.de>>
Dear Tim, Miguel
Thanks for your s
-- Forwarded message --
From: Swastik Phulera
Date: Tue, Jun 11, 2013 at 1:51 PM
Subject: Re: [ccp4bb] pdbset
To: Tim Gruene
Dear Tim, Miguel
Thanks for your suggestions, the program does work now, but it seems that
it cant handle AnsioU s . It gives an error:
PDBSET
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Swastik Phulera,
after the word 'output.pdb' you must first hit the Enter-key which
takes you into the program pdbset.
Then you type
B_reset Minimum 0
END
and the program runs.
If you wish to do it without interaction, e.g. in a script, you can
Dear All,
I am trying to use pdbset from the terminal and am constantly getting an
error:
[XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb B_reset
MINIMUM 0
>> CCP4 library signal ccp4_general:Use:
(Error)
raised in ccp4fyp <<
pdbset: Use:
pdbset: Use:
Times: Us
Hello,
Would it be possible to have pdbset take care of only the ATOM
lines in a given PDB?
I managed to make it do what I want but in case there are
ANISOU lines, I want to ignore them.
Currently, I'm using grep before pdbset, but I would prefer
to avoid it as I am doing some computational expe
even though I also don't fully understand the code, your interpretation
seems to make sense. I don't know a fix for the code. Yet, when I used
pdbset from ccp4-6.0.99e, this error did not occur (but did with pdbset
from ccp4-6.0.2). So if it's an option you might simply update to the
latest bet
I believe I found the bug, but I don't understand enough to know how to
fix the code correctly.
In $CCP4/lib/src/mmdb/mmdb_rwbrook.cpp, lines 1546-1561:
if (FTN_STR(ID)[0]==' ') {
atomName[0] = char(0);
if ((FTN_STR(AtNam)[1]=='H') ||
((FTN_STR(AtNam)[1]=='D') && (FTN_S
I used PDBSET (ccp4-6.0.2; linux; script at end of email) to generate
symmetry-related chains (with chain renaming).
Certain atom names get mangled. Specifically, the NAP residue, which as
many of us are painfully aware is named unusually, comes out wrong:
Example input:
ATOM 12107 AOP1 NAP G100
> It seems to me that posting in ccp4bb is one of the correct ways to
> report a problem. Am I wrong? The other option is to send it to
> [EMAIL PROTECTED], but I assume that this address is subscribed to ccp4bb
> anyway.
>
> Ed.
Herewith the official line:
The correct way of reporting problem
bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ed Pozharski
> Sent: Thursday, July 10, 2008 2:31 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] pdbset bug - seqres record
>
> There is a bug in pdbset: when you output a sequence (using "SEQU PDB"), the
> res
, 2008 2:31 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] pdbset bug - seqres record
There is a bug in pdbset: when you output a sequence (using "SEQU PDB"), the
residue names are shifted to the left by one position. Here is how it looks
like:
In PDB-file downloaded from the PDB:
SEQRES
There is a bug in pdbset: when you output a sequence (using "SEQU PDB"),
the residue names are shifted to the left by one position. Here is how
it looks like:
In PDB-file downloaded from the PDB:
SEQRES 5 A 171 ALA THR CYS ...
PDBSET output:
SEQRES 5 A 171 ALA THR CYS ...
I lo
dear colleagues,
i just noticed a to me somewhat unexpected behaviour of pdbset.
as it turns out, it seems to make a difference whether i do run pdbset
all in one go, changing the cell and applying transformations at once:
pdbset XYZIN ... << eof-pdbset
cell
spacegroup ...
rotate euler
shif
Upon translation using pdbset, the secondary
structure records are removed and need to be pasted
back for a number of graphics programs to display
sec str properly.
Removal of sec str info does not seem to be neccessary for
operations that do not change any atom/residue/chain/numbering.
Best,br
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