Jason, hello!
Also I've found possible fix for that bug by lpacing this line in the 47
line of the script
if type(selName)!=(types.StringType) and type(selName)!=(types.NoneType):
By the way I've found another bug when I've tried to find the same motifs
in the several homolugues structures.
E.
Found it.
cmd.fragment
under modules/pymol/creating.py
Troels Emtekær Linnet
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2012/1/13 Troels Emtekær Linnet
> Hi you all.
>
> I need to build a cys residue for a script, to align it to a residue.
> I am looking at the command: frag cys
> cmd.do("f
Hi you all.
I need to build a cys residue for a script, to align it to a residue.
I am looking at the command: frag cys
cmd.do("frag cys")
but by script does not wait for frag to complete, and speed on.
Is there a cmd.frag ?
Or how can i find more information on frag?
Cheers
---
Jonathan,
"Clean" is integrated into the Incentive version for our paying
customers. But, you can build it in yourself by adding freemol
(http://freemol.org/) to your copy of PyMOL.
Cheers,
-- Jason
On Fri, Jan 13, 2012 at 2:28 PM, Jonathan Saboury wrote:
> I thought I would use ubuntu (throug
I thought I would use ubuntu (through virtualbox) and I installed pymol through
the app center. Still it was not allowing me to use clean maybe this is a
function for the paid version? If so that would suck for me bc im poor, I
really need that function :(
--
James,
First, there's a bug in the script. It's not dealing with selName
correctly. To get around this just provide something to selName:
findSeq S.G, 1a3h, selName=found_seq
If findSeq finds the sequence, it'll return the selected atoms in found_seq.
Next, SYG is not in that protein. If you s
Dear PyMol Users,
I need to search defined sequence motifs in my structures.
For that purpose I've used
http://www.pymolwiki.org/index.php/FindSeq script
but when I've try to use it I've got error
PyMOL>findSeq SYG, 1a3h
Error: selName was not a string.
There was an error with a parameter. Pl
Hi,
Cealign's the way to go here. If you have a massively powerful
computer you can continue turning off the "guide" which selects
special carbons to "guide" the alignment. We need to improve/extend
for nucleic acids. Would someone mind filing a feature request on the
open-source bug tracker? We a
> Have you checked the right path?
yes.
> Write in pymol cmd.
> pwd
>
> And check if the file is there.
> Could it be that easy?
Yes, it is easy, but there is no png image nowhere, just in case, if I
exec the command pnf from the pymol console. If I use python script,
there is no any output,
I decided to dig in and answer my own question about what the seq argument does.
seq:
positive means use sequence and structure
0 means use only structure
negative means only use sequence
For super, I assume you only want to use structure, so messing with
that argument is silly advice.
The probl
On 01/13/2012 02:37 PM, David Hall wrote:
> I think super does not handle nucleic acid sequences well.
>
> super ec-5s, hm-5s, seq=-1
>
> works.
>
> I'll leave it to someone else to say what that does. I just noted
> that align works, super doesn't, guessed it had to do with sequence
> and noted t
Hi Quyen,
unfortunately, the super command does a selection on CA atoms
internally. Maybe this should be considered a bug. If you have the
latest svn version of PyMOL, I recommend cealign for this task (older
versions of cealign do select CA atoms as well).
Cheers,
Thomas
On 01/13/2012 01:
Have you checked the right path?
Write in pymol cmd.
pwd
And check if the file is there.
Could it be that easy?
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2012/1/13 tusi
> I have got the same result: no png image has been generated.
>
> > Can you try doing
> >
> > fro
On Fri, Jan 13, 2012 at 4:34 AM, tusi wrote:
> Dear All,
>
> After updating to Ubuntu natty (11.04), cmd.do('png filename') does not
> work. When I execute the following commands in pymol I get the wanted
> png picture:
>
> load tmp.pdb tmp
> png tmp.png
>
>
> but, if I execute the following scrip
I think super does not handle nucleic acid sequences well.
super ec-5s, hm-5s, seq=-1
works.
I'll leave it to someone else to say what that does. I just noted
that align works, super doesn't, guessed it had to do with sequence
and noted that for align, the default value of seq was -1 and for
su
I have got the same result: no png image has been generated.
> Can you try doing
>
> from pymol import cmd
> cmd.load('tmp.pdb', 'tmp')
> cmd.png('tmp.png')
>
>
> -David
--
RSA(R) Conference 2012
Mar 27 - Feb 2
Save
Hi QT.
Some of the align functions need to have the same chain name of the
residues.
I don't know if that is the issue with super.
Have a look at Thomas Holders new pymol plugin
http://pymolwiki.org/index.php/TMalign
And also look at these messages at the pymol-users:
http://www.mail-archive.com
Dear all,
I'm having a tough time using the super command correctly. I want to
superimpose two 5S structures.
In pymol, I'll do the following
load 2awb.pdb
load 3cc2.pdb
create ec-5s, 2awb and chain a
create hm-5s, 3cc2 and chain 9
If I issue *super ec-5s, hm-5s* then the cryptic error "Execu
Hi Thomas.
Thanks!
And right now I am looking at my "big install script".
It is a mess, and I am cleaning it up.
The problem with gcc is not an issue anymore with Mint 12 and gcc 4.6.1
And now understand the "short version" of yours. :-)
Best
Troels
2012/1/13 Thomas Holder
> Hi Troels,
>
>
Hi Troels,
you need to reinstall. After "svn up", run this again (not your big
installation script, it does too much...):
http://pymolwiki.org/index.php/Linux_Install#Compile_and_install
Cheers,
Thomas
On 01/13/2012 12:34 PM, Troels Emtekær Linnet wrote:
> Hi.
>
> I use the open-source PyMO
Hi.
I use the open-source PyMOL with the svn repository.
But I have a question.
When I make a "svn up", do I then need to rebuild and install pymol again?
Or is it fine just with the "svn up".
Thanks.
Best Troels
--
RSA(
Venkatramanan Krishnamani.
How about posting it on http://www.pymolwiki.org/index.php/Category:Plugins
Then it will newer get "lost". :-)
Best
Troels
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Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
2012/1/13 Venkatramanan Krishnamani
> hi everyone,
>
> I wrote this plugin f
Dear All,
After updating to Ubuntu natty (11.04), cmd.do('png filename') does not
work. When I execute the following commands in pymol I get the wanted
png picture:
load tmp.pdb tmp
png tmp.png
but, if I execute the following script, the png file does not arise:
from pymol import cmd
cmd.do('l
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