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
Venkatramanan Krishnamani.
How about posting it on http://www.pymolwiki.org/index.php/Category:Plugins
Then it will newer get lost. :-)
Best
Troels
Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
2012/1/13 Venkatramanan Krishnamani ve...@andrew.cmu.edu
hi everyone,
I
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 PyMOL
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
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
On Fri, Jan 13, 2012 at 4:34 AM, tusi t...@enzim.hu 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
Have you checked the right path?
Write in pymol cmd.
pwd
And check if the file is there.
Could it be that easy?
Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
2012/1/13 tusi t...@enzim.hu
I have got the same result: no png image has been generated.
Can you try doing
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
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 that for
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
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, as I
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 also
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
PyMOLfindSeq SYG, 1a3h
Error: selName was not a string.
There was an error with a parameter.
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
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 :(
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 jsab...@yahoo.com wrote:
I thought I would use
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
Found it.
cmd.fragment
under modules/pymol/creating.py
Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
2012/1/13 Troels Emtekær Linnet tlin...@gmail.com
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
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.
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