From dchen at caltech.edu  Thu Aug  4 08:25:21 2005
From: dchen at caltech.edu (David Chenoweth)
Date: Thu, 4 Aug 2005 08:25:21 -0700
Subject: [Chimera-users] Making and Breaking bonds in Chimera
Message-ID: <15DA4BFD-CCE0-474F-948F-37F6E071DC30@caltech.edu>

Dear Chimera users,

Does anyone know how to make a new bond or delete a bond between two  
atoms within a PDB file using chimera?

-Thanks
DC


From meng at cgl.ucsf.edu  Thu Aug  4 10:03:13 2005
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 4 Aug 2005 10:03:13 -0700
Subject: [Chimera-users] Making and Breaking bonds in Chimera
In-Reply-To: <15DA4BFD-CCE0-474F-948F-37F6E071DC30@caltech.edu>
References: <15DA4BFD-CCE0-474F-948F-37F6E071DC30@caltech.edu>
Message-ID: <d654fac7d43e75d08e9e19e9ae273347@cgl.ucsf.edu>

Hi David,
See the command bond, plus the "see also" commands in its man page:

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html

If you didn't want to type the atom names, you can select the two atoms 
and then use

bond sel
(to create the bond)
~bond sel
(to delete the bond)

An approach with the menu is to select the bond (but not the flanking 
atoms) and then use Actions... Atoms/Bonds... delete

Another way to add bonds is to add CONECT lines to the PDB file, but 
then you have to put in CONECT lines for that whole residue, and it can 
get complicated.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Aug 4, 2005, at 8:25 AM, David Chenoweth wrote:

> Dear Chimera users,
>
> Does anyone know how to make a new bond or delete a bond between two 
> atoms within a PDB file using chimera?
>
> -Thanks
> DC


From sabuj.pattanayek at Vanderbilt.Edu  Tue Aug  9 10:04:45 2005
From: sabuj.pattanayek at Vanderbilt.Edu (Pattanayek, Sabuj)
Date: Tue,  9 Aug 2005 12:04:45 -0500
Subject: [Chimera-users] 
Message-ID: <1123607085.42f8e22d33abc@vuwebmail.vanderbilt.edu>

Hi all,

Is there a modification I can do to the multi-align viewer code so that "-"
(gaps) characters are not counted in the alignment numbering (but are still
displayed for alignment purposes) from a fasta file in the multi-align viewer?
The numbering should correspond to the first sequence found in the fasta file
(i.e. I don't care about the numbering due to gaps in the second, third, etc
sequences).

Thanks,
Sabuj Pattanayek


From pett at cgl.ucsf.edu  Tue Aug  9 11:42:24 2005
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 9 Aug 2005 11:42:24 -0700
Subject: [Chimera-users] 
In-Reply-To: <1123607085.42f8e22d33abc@vuwebmail.vanderbilt.edu>
References: <1123607085.42f8e22d33abc@vuwebmail.vanderbilt.edu>
Message-ID: <B906CE49-8E62-4FFF-BBB0-C721B27CDEE9@cgl.ucsf.edu>

Hi Sabuj,
     I've appended a context diff for MAV's SeqCanvas.py file.  It  
makes the ruler use the ungapped numbering of the first sequence.   
For positions where there is a gap in the first sequence it uses  
'?'.  I think this is what you wanted, but let me know if I got that  
wrong.
     On another note, the new AL2CO conservation measures in the  
1.2154 snapshot don't work on the Mac and possibly on Linux  
(depending on your execution path).  If you want to get them to work,  
I've also appended a context diff for Conservation.py below and have  
also made the entire replacement file available at http:// 
www.cgl.ucsf.edu/home/pett/chimera/Conservation.py (which, on a Mac,  
you put in Chimera.app/Contents/Resources/share/MultAlignViewer  
[which you may have to use Terminal.app to access] and on Linux in  
<your install dir>/share/MultAlignViewer).

--Eric

On Aug 9, 2005, at 10:04 AM, Pattanayek, Sabuj wrote:

> Hi all,
>
> Is there a modification I can do to the multi-align viewer code so  
> that "-"
> (gaps) characters are not counted in the alignment numbering (but  
> are still
> displayed for alignment purposes) from a fasta file in the multi- 
> align viewer?
> The numbering should correspond to the first sequence found in the  
> fasta file
> (i.e. I don't care about the numbering due to gaps in the second,  
> third, etc
> sequences).
>
> Thanks,
> Sabuj Pattanayek
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>

*** SeqCanvas.py        6 Aug 2005 00:08:50 -0000       1.59
--- SeqCanvas.py        9 Aug 2005 17:57:45 -0000
***************
*** 1056,1063 ****

                 end = min(self.seqOffset + self.lineWidth, len 
(self.seqs[0]))
                 for chunkStart in range(self.seqOffset, end, 10):
                         text = self.mainCanvas.create_text(x, y,  
anchor='s',
!                               font=self.font, text="%d" %  
(chunkStart+1))
                         self.rulerTexts.append(text)
                         x += self.chunkGap + 10 * (self.fontPixels[0]
                                                         +  
self.letterGaps[0])
--- 1056,1068 ----

                 end = min(self.seqOffset + self.lineWidth, len 
(self.seqs[0]))
                 for chunkStart in range(self.seqOffset, end, 10):
+                       seq1index = self.seqs[0].gapped2ungapped 
(chunkStart)
+                       if seq1index is None:
+                               dispText = "?"
+                       else:
+                               dispText = str(seq1index+1)
                         text = self.mainCanvas.create_text(x, y,  
anchor='s',
!                               font=self.font, text="%s" % (dispText))
                         self.rulerTexts.append(text)
                         x += self.chunkGap + 10 * (self.fontPixels[0]
                                                         +  
self.letterGaps[0])


*** Conservation.py     3 Aug 2005 20:19:15 -0000       1.16
--- Conservation.py     9 Aug 2005 18:28:45 -0000
***************
*** 56,62 ****
                 tf = open(tfName, "w")
                 save(tf, None, self.seqs, None)
                 tf.close()
!               command = "al2co -i %s -f %d -c %d -w %d -g %g" %  
(tfName,
                         prefs[AL2CO_FREQ], prefs[AL2CO_CONS],
                         prefs[AL2CO_WINDOW], prefs[AL2CO_GAP])
                 if prefs[AL2CO_CONS] == 2:
--- 56,65 ----
                 tf = open(tfName, "w")
                 save(tf, None, self.seqs, None)
                 tf.close()
!               import os, os.path
!               chimeraRoot = os.environ.get("CHIMERA")
!               command = os.path.join(chimeraRoot, 'bin', 'al2co') + \
!                       " -i %s -f %d -c %d -w %d -g %g" % (tfName,
                         prefs[AL2CO_FREQ], prefs[AL2CO_CONS],
                         prefs[AL2CO_WINDOW], prefs[AL2CO_GAP])
                 if prefs[AL2CO_CONS] == 2:


From sabuj.pattanayek at vanderbilt.edu  Tue Aug  9 12:55:36 2005
From: sabuj.pattanayek at vanderbilt.edu (Sabuj Pattanayek)
Date: Tue, 09 Aug 2005 14:55:36 -0500
Subject: [Chimera-users]
In-Reply-To: <B906CE49-8E62-4FFF-BBB0-C721B27CDEE9@cgl.ucsf.edu>
References: <1123607085.42f8e22d33abc@vuwebmail.vanderbilt.edu>
	<B906CE49-8E62-4FFF-BBB0-C721B27CDEE9@cgl.ucsf.edu>
Message-ID: <42F90A38.5080003@vanderbilt.edu>

Hi,

I'm getting the following error:

  File "/usr/local/sbin/chimera/share/MultAlignViewer/SeqCanvas.py", 
line 1057
     self.rulerTexts.append(text)
     ^
SyntaxError: invalid syntax

I had to modify the file manually since the line numbers didn't match. 
This is my diff (unified format):

--- SeqCanvas.py        2005-08-09 14:45:57.000000000 -0500
+++ SeqCanvas.py.bak    2005-08-09 14:34:01.000000000 -0500
@@ -1045,19 +1045,13 @@
          x = self.labelWidth + self.letterGaps[0] + self.fontPixels[0]/2
          y = self.topY + self.fontPixels[1] + self.letterGaps[1]

-         end = min(self.seqOffset + self.lineWidth, len (self.seqs[0]))
-             for chunkStart in range(self.seqOffset, end, 10):
-                 seq1index = self.seqs[0].gapped2ungapped (chunkStart)
-                       if seq1index is None:
-                               dispText = "?"
-                       else:
-                  dispText = str(seq1index+1)
-                  text = self.mainCanvas.create_text(x, y,  anchor='s',
-                         font=self.font, text="%s" % (dispText))
-                         self.rulerTexts.append(text)
-                         x += self.chunkGap + 10 * (self.fontPixels[0]
-                                                  + self.letterGaps[0])
-
+          end = min(self.seqOffset + self.lineWidth, len(self.seqs[0]))
+               for chunkStart in range(self.seqOffset, end, 10):
+                   text = self.mainCanvas.create_text(x, y, anchor='s',
+                          font=self.font, text="%d" % (chunkStart+1))
+                       self.rulerTexts.append(text)
+                       x += self.chunkGap + 10 * (self.fontPixels[0]
+                                                  +self.letterGaps[0])
               if not rerule:
                  self.bottomY += self.fontPixels[1] + self.letterGaps[1]
                  self.bottomRulerY = self.bottomY

Thanks,
Sabuj

Eric Pettersen wrote:
> Hi Sabuj,
>     I've appended a context diff for MAV's SeqCanvas.py file.  It  makes 
> the ruler use the ungapped numbering of the first sequence.   For 
> positions where there is a gap in the first sequence it uses  '?'.  I 
> think this is what you wanted, but let me know if I got that  wrong.
>     On another note, the new AL2CO conservation measures in the  1.2154 
> snapshot don't work on the Mac and possibly on Linux  (depending on your 
> execution path).  If you want to get them to work,  I've also appended a 
> context diff for Conservation.py below and have  also made the entire 
> replacement file available at http:// 
> www.cgl.ucsf.edu/home/pett/chimera/Conservation.py (which, on a Mac,  
> you put in Chimera.app/Contents/Resources/share/MultAlignViewer  [which 
> you may have to use Terminal.app to access] and on Linux in  <your 
> install dir>/share/MultAlignViewer).
> 
> --Eric
> 
> On Aug 9, 2005, at 10:04 AM, Pattanayek, Sabuj wrote:
> 
>> Hi all,
>>
>> Is there a modification I can do to the multi-align viewer code so  
>> that "-"
>> (gaps) characters are not counted in the alignment numbering (but  are 
>> still
>> displayed for alignment purposes) from a fasta file in the multi- 
>> align viewer?
>> The numbering should correspond to the first sequence found in the  
>> fasta file
>> (i.e. I don't care about the numbering due to gaps in the second,  
>> third, etc
>> sequences).
>>
>> Thanks,
>> Sabuj Pattanayek
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
> 
> *** SeqCanvas.py        6 Aug 2005 00:08:50 -0000       1.59
> --- SeqCanvas.py        9 Aug 2005 17:57:45 -0000
> ***************
> *** 1056,1063 ****
> 
>                 end = min(self.seqOffset + self.lineWidth, len 
> (self.seqs[0]))
>                 for chunkStart in range(self.seqOffset, end, 10):
>                         text = self.mainCanvas.create_text(x, y,  
> anchor='s',
> !                               font=self.font, text="%d" %  
> (chunkStart+1))
>                         self.rulerTexts.append(text)
>                         x += self.chunkGap + 10 * (self.fontPixels[0]
>                                                         +  
> self.letterGaps[0])
> --- 1056,1068 ----
> 
>                 end = min(self.seqOffset + self.lineWidth, len 
> (self.seqs[0]))
>                 for chunkStart in range(self.seqOffset, end, 10):
> +                       seq1index = self.seqs[0].gapped2ungapped 
> (chunkStart)
> +                       if seq1index is None:
> +                               dispText = "?"
> +                       else:
> +                               dispText = str(seq1index+1)
>                         text = self.mainCanvas.create_text(x, y,  
> anchor='s',
> !                               font=self.font, text="%s" % (dispText))
>                         self.rulerTexts.append(text)
>                         x += self.chunkGap + 10 * (self.fontPixels[0]
>                                                         +  
> self.letterGaps[0])
> 
> 
> *** Conservation.py     3 Aug 2005 20:19:15 -0000       1.16
> --- Conservation.py     9 Aug 2005 18:28:45 -0000
> ***************
> *** 56,62 ****
>                 tf = open(tfName, "w")
>                 save(tf, None, self.seqs, None)
>                 tf.close()
> !               command = "al2co -i %s -f %d -c %d -w %d -g %g" %  (tfName,
>                         prefs[AL2CO_FREQ], prefs[AL2CO_CONS],
>                         prefs[AL2CO_WINDOW], prefs[AL2CO_GAP])
>                 if prefs[AL2CO_CONS] == 2:
> --- 56,65 ----
>                 tf = open(tfName, "w")
>                 save(tf, None, self.seqs, None)
>                 tf.close()
> !               import os, os.path
> !               chimeraRoot = os.environ.get("CHIMERA")
> !               command = os.path.join(chimeraRoot, 'bin', 'al2co') + \
> !                       " -i %s -f %d -c %d -w %d -g %g" % (tfName,
>                         prefs[AL2CO_FREQ], prefs[AL2CO_CONS],
>                         prefs[AL2CO_WINDOW], prefs[AL2CO_GAP])
>                 if prefs[AL2CO_CONS] == 2:
> 


From pett at cgl.ucsf.edu  Tue Aug  9 13:45:32 2005
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 9 Aug 2005 13:45:32 -0700
Subject: [Chimera-users]
In-Reply-To: <42F91407.3050003@vanderbilt.edu>
References: <1123607085.42f8e22d33abc@vuwebmail.vanderbilt.edu>
	<B906CE49-8E62-4FFF-BBB0-C721B27CDEE9@cgl.ucsf.edu>
	<42F90A38.5080003@vanderbilt.edu>
	<3513A6DE-B433-4B5C-9E8C-A7A581AB7043@cgl.ucsf.edu>
	<42F91407.3050003@vanderbilt.edu>
Message-ID: <03161A1E-C602-4443-86D3-1BE8D7E37702@cgl.ucsf.edu>

Hi Sabuj,
     It is the indentation.  In Python, indentation is meaningful and  
statements at the same "level" have to have the same indentation.   
I've appended the critical part below.  Note the the  
"self.rulerTexts..." and "x += ..." statements are indented one space  
further than the preceding if/else and "text = ..." statements.  To  
Python, the extra space starts a new indented block of statements,  
which is only legal after 'if' statements and so forth.  Take a space  
away from the front of the last two statements and I think things  
will work.

--Eric



                 for chunkStart in range(self.seqOffset, end, 10):
                        seq1index = self.seqs[0].gapped2ungapped  
(chunkStart)
                        if seq1index is None:
                                dispText = "?"
                        else:
                                dispText = str(seq1index+1)
                        text = self.mainCanvas.create_text(x, y,   
anchor='s',
                                font=self.font, text="%s" % (dispText))
                         self.rulerTexts.append(text)
                         x += self.chunkGap + 10 * (self.fontPixels[0]
                                                         +   
self.letterGaps[0])


From sabuj.pattanayek at vanderbilt.edu  Tue Aug  9 14:01:16 2005
From: sabuj.pattanayek at vanderbilt.edu (Sabuj Pattanayek)
Date: Tue, 09 Aug 2005 16:01:16 -0500
Subject: [Chimera-users]
In-Reply-To: <03161A1E-C602-4443-86D3-1BE8D7E37702@cgl.ucsf.edu>
References: <1123607085.42f8e22d33abc@vuwebmail.vanderbilt.edu>
	<B906CE49-8E62-4FFF-BBB0-C721B27CDEE9@cgl.ucsf.edu>
	<42F90A38.5080003@vanderbilt.edu>
	<3513A6DE-B433-4B5C-9E8C-A7A581AB7043@cgl.ucsf.edu>
	<42F91407.3050003@vanderbilt.edu>
	<03161A1E-C602-4443-86D3-1BE8D7E37702@cgl.ucsf.edu>
Message-ID: <42F9199C.6030407@vanderbilt.edu>

Hi,

Yeah, I just remembered a second ago and googled to make sure this was 
the problem.

http://www.secnetix.de/~olli/Python/block_indentation.hawk

..i need to learn python..

It works perfectly now. There was only one slight cosmetic error when I 
loaded the fasta file in the multi-align viewer. It showed the Consensus 
and Conservation rows but in the Analysis settings under preferences 
both were set to "None". Setting it to something besides "None" and 
setting it back to "None" fixed it.

Thanks for your help,
..Sabuj

Eric Pettersen wrote:
> Hi Sabuj,
>     It is the indentation.  In Python, indentation is meaningful and  
> statements at the same "level" have to have the same indentation.   I've 
> appended the critical part below.  Note the the  "self.rulerTexts..." 
> and "x += ..." statements are indented one space  further than the 
> preceding if/else and "text = ..." statements.  To  Python, the extra 
> space starts a new indented block of statements,  which is only legal 
> after 'if' statements and so forth.  Take a space  away from the front 
> of the last two statements and I think things  will work.
> 
> --Eric
> 
> 
> 
>                 for chunkStart in range(self.seqOffset, end, 10):
>                        seq1index = self.seqs[0].gapped2ungapped  
> (chunkStart)
>                        if seq1index is None:
>                                dispText = "?"
>                        else:
>                                dispText = str(seq1index+1)
>                        text = self.mainCanvas.create_text(x, y,   
> anchor='s',
>                                font=self.font, text="%s" % (dispText))
>                         self.rulerTexts.append(text)
>                         x += self.chunkGap + 10 * (self.fontPixels[0]
>                                                         +   
> self.letterGaps[0])
> 


From sabuj.pattanayek at vanderbilt.edu  Wed Aug 17 13:48:53 2005
From: sabuj.pattanayek at vanderbilt.edu (Sabuj Pattanayek)
Date: Wed, 17 Aug 2005 15:48:53 -0500
Subject: [Chimera-users] 
 ATI catalyst 5.7 drivers with R9600SE video card crash winxp when
 creating surfaces (or running surface benchmark) in chimera-1.2143
Message-ID: <4303A2B5.1000202@vanderbilt.edu>

Hi,

I had upgraded ATI's catalyst drivers from 5.4 (or 5.5) to 5.7 for my 
R9600SE video card under winxp sp2. In Chimera-1.2143 when I tried to 
create a surface representation or tried the surface benchmark the 
screen would go black (monitor led goes from green to orange) and the 
system would crash (no longer responds to pings).

Downgrading to catalyst 5.6 fixed the problem. I sent a trouble ticket 
to ATI. Has anyone had a similar problem with Radeon (non-firegl) cards?

Thanks,
Sabuj Pattanayek



From sabuj.pattanayek at vanderbilt.edu  Wed Aug 17 14:00:54 2005
From: sabuj.pattanayek at vanderbilt.edu (Sabuj Pattanayek)
Date: Wed, 17 Aug 2005 16:00:54 -0500
Subject: [Chimera-users]  ATI catalyst 5.7 drivers with R9600SE video
 card crash winxp when creating surfaces (or running surface benchmark) in
 chimera-1.2143
In-Reply-To: <4303A2B5.1000202@vanderbilt.edu>
References: <4303A2B5.1000202@vanderbilt.edu>
Message-ID: <4303A586.3020108@vanderbilt.edu>

Oops, just realized Catalyst is now at 5.8 (just released today). I'll 
try that and let you guys know if the problem persists.

Thanks

Sabuj Pattanayek wrote:
> Hi,
> 
> I had upgraded ATI's catalyst drivers from 5.4 (or 5.5) to 5.7 for my 
> R9600SE video card under winxp sp2. In Chimera-1.2143 when I tried to 
> create a surface representation or tried the surface benchmark the 
> screen would go black (monitor led goes from green to orange) and the 
> system would crash (no longer responds to pings).
> 
> Downgrading to catalyst 5.6 fixed the problem. I sent a trouble ticket 
> to ATI. Has anyone had a similar problem with Radeon (non-firegl) cards?
> 
> Thanks,
> Sabuj Pattanayek
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users


From pett at cgl.ucsf.edu  Thu Aug 18 15:37:56 2005
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 18 Aug 2005 15:37:56 -0700
Subject: [Chimera-users] Re: [chimera-dev] accelerators and stereo
In-Reply-To: <22efaf653eac012eac9a5cd63a1b5a43@osu.edu>
References: <22efaf653eac012eac9a5cd63a1b5a43@osu.edu>
Message-ID: <1CD129BF-1FC6-4B79-8C3F-53EC9D5193F4@cgl.ucsf.edu>

Hi Justin,
     Chimera doesn't have a function to directly save a stereo  
image.  Instead, what you do is save separate left-eye and right-eye  
images and place them appropriately in your presentation or paper --  
for a cross-eye image that would be the left-eye on the right and  
vice versa.  You save the images by bringing up the Side View (under  
Favorites) and clicking on the "Camera" tab.  There is a "camera  
mode" menu under that tab that lets you select left-eye/right-eye  
views.  Then just use the regular image-saving process.
     This is also described in the Images tutorial (near the end):   
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
frameimages.html
     We want to make this easier to do but haven't gotten to it yet.

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu


On Aug 18, 2005, at 7:06 AM, Justin Wu wrote:

> Hi
> Would you please let me know how to make a cross-eye figure from  
> Chimera?  I do not where to look for this function.
> Thanks
> Justin
> ************************************************
> Justin Wu
> Rm 752, Biological Science Building
> 484 West 12th Ave,
> Columbus, OH 43210
> Tel: (614)247-5040, Fax: (614)292-6773
> ************************************************
>
> _______________________________________________
> Chimera-dev mailing list
> Chimera-dev at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
>

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From sabuj.pattanayek at vanderbilt.edu  Mon Aug 22 09:34:46 2005
From: sabuj.pattanayek at vanderbilt.edu (Sabuj Pattanayek)
Date: Mon, 22 Aug 2005 11:34:46 -0500
Subject: [Chimera-users]  ATI catalyst 5.7 drivers with R9600SE video
 card crash winxp when creating surfaces (or running surface benchmark) in
 chimera-1.2143
In-Reply-To: <4303A586.3020108@vanderbilt.edu>
References: <4303A2B5.1000202@vanderbilt.edu>
	<4303A586.3020108@vanderbilt.edu>
Message-ID: <4309FEA6.5050203@vanderbilt.edu>

Same problem with Catalyst 5.8 . Has anyone noticed the same problem on 
non-firegl cards?

Sabuj Pattanayek wrote:
> Oops, just realized Catalyst is now at 5.8 (just released today). I'll 
> try that and let you guys know if the problem persists.
> 
> Thanks
> 
> Sabuj Pattanayek wrote:
> 
>> Hi,
>>
>> I had upgraded ATI's catalyst drivers from 5.4 (or 5.5) to 5.7 for my 
>> R9600SE video card under winxp sp2. In Chimera-1.2143 when I tried to 
>> create a surface representation or tried the surface benchmark the 
>> screen would go black (monitor led goes from green to orange) and the 
>> system would crash (no longer responds to pings).
>>
>> Downgrading to catalyst 5.6 fixed the problem. I sent a trouble ticket 
>> to ATI. Has anyone had a similar problem with Radeon (non-firegl) cards?
>>
>> Thanks,
>> Sabuj Pattanayek
>>
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users


From goddard at cgl.ucsf.edu  Mon Aug 22 10:48:27 2005
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 22 Aug 2005 10:48:27 -0700 (PDT)
Subject: [Chimera-users]  ATI catalyst 5.7 drivers with R9600SE video
 card crash winxp when creating surfaces (or running surface benchmark) in
 chimera-1.2143
In-Reply-To: <4309FEA6.5050203@vanderbilt.edu> (message from Sabuj Pattanayek
	on Mon, 22 Aug 2005 11:34:46 -0500)
References: <4303A2B5.1000202@vanderbilt.edu>
	<4303A586.3020108@vanderbilt.edu> <4309FEA6.5050203@vanderbilt.edu>
Message-ID: <200508221748.j7MHmRFH1683148@guanine.cgl.ucsf.edu>

Hi Sabuj,

  We use Chimera with an ATI Radeon 9800 Pro on Win XP.  I'm not sure
we have tried Chimera version 1.2143 (the machine is down now) -- could
be 1.2129 was the last version we tried on that machine.  Also the drivers
on that machine are probably a year old.  If you are interested I can get
more definitive information about that machine when we get it running again.

     Tom

From sabuj.pattanayek at vanderbilt.edu  Mon Aug 22 11:30:57 2005
From: sabuj.pattanayek at vanderbilt.edu (sabuj pattanayek)
Date: Mon, 22 Aug 2005 13:30:57 -0500
Subject: [Chimera-users]  ATI catalyst 5.7 drivers with R9600SE video
 card crash winxp when creating surfaces (or running surface benchmark) in
 chimera-1.2143
In-Reply-To: <200508221748.j7MHmRFH1683148@guanine.cgl.ucsf.edu>
References: <4303A2B5.1000202@vanderbilt.edu>
	<4303A586.3020108@vanderbilt.edu> <4309FEA6.5050203@vanderbilt.edu>
	<200508221748.j7MHmRFH1683148@guanine.cgl.ucsf.edu>
Message-ID: <430A19E1.5070506@vanderbilt.edu>

Hi,

No rush, but thanks for checking.

Also I have another question regarding the benchmark scores in linux vs 
WinXP on the same machine.

The surface benchmark under WinXP seems to be almost twice as high as 
that in linux, but everything else is higher in linux:

Chimera-1.2154, Linux-2.6.12.5, ATI Mobility Radeon 9600 (128MB), 
fglrx-8.16.20 drivers, ECS G736 laptop, 1G RAM, P4 3.2GHz

Surface rendering
  size      rate
    32      249.0
    64       76.5
   128       20.0
   179       10.3
   250        5.3
   214        7.2
   196        8.6
   187        9.4
   183        9.9
   181       10.1
   182       10.0
Surface rendering benchmark: 181
Mesh rendering
  size      rate
    32      249.5
    64       74.1
   128       19.7
   179       10.2
   250        5.3
   214        7.2
   196        8.5
   187        9.4
   183        9.8
   181       10.0
   182        9.9
Mesh rendering benchmark: 181
Contouring
  size      rate
    32      371.8
    64       70.4
   128       13.4
   179        6.4
   153        9.1
   140       11.6
   146       10.1
   149        9.6
   147        9.9
Contouring benchmark: 146
Solid rendering
  size      rate
    32       76.7
    64       38.2
   128       19.2
   179       13.9
   250        9.8
   214       11.5
   232       10.6
   241       10.1
   245       10.0
   243       10.1
   244       10.0
Solid rendering benchmark: 244
Recoloring
  size      rate
    32      145.6
    64       43.9
   128        8.1
    96       17.2
   112       11.6
   120        9.7
   116       10.6
   118       10.1
   119        9.9
Recoloring benchmark: 118
Benchmark scores
surface 181  mesh 181  contour 146  solid 244  recolor 118

Chimera-1.2143, WinXP SP1, ATI Mobility Radeon 9600 (128MB), driver 
6.14.10.6436, ECS G736 laptop, 1G RAM, P4 3.2GHz

Surface rendering
  size      rate
    32      256.0
    64      130.0
   128       27.5
   179       39.0
   250       29.8
   350       26.5
   489        1.6
   419        1.3
   384        1.7
   367        1.9
   358        1.9
   354        2.0
   352        1.8
   351        2.0
Surface rendering benchmark: 350
Mesh rendering
  size      rate
    32      135.0
    64       49.0
   128       15.0
   179        7.4
   153        9.1
   140       11.6
   146       11.6
   149       11.3
   151        9.9
   150       11.0
Mesh rendering benchmark: 150
Contouring
  size      rate
    32      169.0
    64       35.0
   128        6.7
    96       15.8
   112        9.0
   104       12.0
   108       11.3
   110       13.0
   111        8.0
Contouring benchmark: 110
Solid rendering
  size      rate
    32       59.7
    64       55.1
   128       14.5
   179       32.0
   250        7.5
   214        8.6
   196       29.3
   205       30.5
   209        8.7
   207       29.6
   208       30.0
Solid rendering benchmark: 208
Recoloring
  size      rate
    32       75.0
    64       14.8
   128        1.7
    96        4.7
    80        5.7
    72        9.0
    68       11.6
    70       11.6
    71        9.7
Recoloring benchmark: 70
Benchmark scores
surface 350  mesh 150  contour 110  solid 208  recolor 70

If you add up the scores you get for linux = 870 and for WinXP = 888. 
The difference I notice in the surface benchmark is that under linux 
after a surface size of 250 is rendered it renders a size of 214, 
whereas in WinXP it attempts a higher size of 350. How does it decide to 
attempt a higher or lower size? Is this a bug or some sort of malloc 
error in linux? It seems to me that if the linux surface score is >= the 
WinXP score, the overall score under linux would be much greater.

Thanks for your help,
Sabuj Pattanayek

Thomas Goddard wrote:
> Hi Sabuj,
> 
>   We use Chimera with an ATI Radeon 9800 Pro on Win XP.  I'm not sure
> we have tried Chimera version 1.2143 (the machine is down now) -- could
> be 1.2129 was the last version we tried on that machine.  Also the drivers
> on that machine are probably a year old.  If you are interested I can get
> more definitive information about that machine when we get it running again.
> 
>      Tom


From goddard at cgl.ucsf.edu  Mon Aug 22 11:48:53 2005
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Mon, 22 Aug 2005 11:48:53 -0700 (PDT)
Subject: [Chimera-users]  ATI catalyst 5.7 drivers with R9600SE video
 card crash winxp when creating surfaces (or running surface benchmark) in
 chimera-1.2143
In-Reply-To: <430A19E1.5070506@vanderbilt.edu> (message from sabuj pattanayek
	on Mon, 22 Aug 2005 13:30:57 -0500)
References: <4303A2B5.1000202@vanderbilt.edu>
	<4303A586.3020108@vanderbilt.edu> <4309FEA6.5050203@vanderbilt.edu>
	<430A19E1.5070506@vanderbilt.edu>
Message-ID: <200508221848.j7MImrZx1753092@guanine.cgl.ucsf.edu>

Hi Sabuj,

  I'm surprised how different your Chimera benchmark scores are running
Windows versus Linux on the same machine.

> Chimera-1.2143, WinXP SP1, ATI Mobility Radeon 9600 (128MB), driver 
> 6.14.10.6436, ECS G736 laptop, 1G RAM, P4 3.2GHz
> 
> Linux:   surface 181  mesh 181  contour 146  solid 244  recolor 118
> Windows: surface 350  mesh 150  contour 110  solid 208  recolor 70

The graphics drivers can make a big difference in the Surface / Mesh
scores.  I believe this has to do with the rules the graphics driver
uses to decide whether to put the surface geometry in the graphics
card memory (fast), or shuttle it from the main computer memory for each
drawing (slow).

The difference you see in contouring scores (146 vs 110) is hard to
fathom.  This is not using any graphics -- it is just a calculation done
on the computer CPU.  Do you get close to the same number if you run the
benchmarks twice?  It could be that Windows is much slower at allocating
memory -- that is also done during the contour calculation.

I would definitely *not* add the scores to get an overall measure of
performance.  Some may be much more important to you than others.
Surface and contour are probably most important for looking at density
maps.  Surface is probably most important for looking at large molecular
models.  Recolor is relatively unimportant (it concerns recoloring of
solid volume renderings).

The benchmark code works by increasing the volume data set size until
the drawing or contour calculation speed drops below 10 times per second
(considered "interactive").  Then uses bisection to find exactly what size
volume data set can be handled at 10 frames per second.

See the Chimera User's Guide page for more info about the benchmarks.
It's in the Tools section under Benchmark.

	http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/benchmark/benchmark.html

We are currently enhancing the benchmarking tool to time display of
molecular models.

  Tom

From sabuj.pattanayek at vanderbilt.edu  Mon Aug 22 12:19:22 2005
From: sabuj.pattanayek at vanderbilt.edu (Sabuj Pattanayek)
Date: Mon, 22 Aug 2005 14:19:22 -0500
Subject: [Chimera-users]  ATI catalyst 5.7 drivers with R9600SE video
 card crash winxp when creating surfaces (or running surface benchmark) in
 chimera-1.2143
In-Reply-To: <200508221848.j7MImrZx1753092@guanine.cgl.ucsf.edu>
References: <4303A2B5.1000202@vanderbilt.edu>
	<4303A586.3020108@vanderbilt.edu> <4309FEA6.5050203@vanderbilt.edu>
	<200508221748.j7MHmRFH1683148@guanine.cgl.ucsf.edu>
	<430A19E1.5070506@vanderbilt.edu>
	<200508221848.j7MImrZx1753092@guanine.cgl.ucsf.edu>
Message-ID: <430A253A.702@vanderbilt.edu>

Hi,

On multiple tests of the contour benchmark under WinXP I get anywhere 
from 108 to 120 with the mode being 115 or 116.

Under linux I always get a score of 146 no matter how many times I run 
it consecutively.

..Sabuj

Thomas Goddard wrote:
> Hi Sabuj,
> 
>   I'm surprised how different your Chimera benchmark scores are running
> Windows versus Linux on the same machine.
> 
> 
>>Chimera-1.2143, WinXP SP1, ATI Mobility Radeon 9600 (128MB), driver 
>>6.14.10.6436, ECS G736 laptop, 1G RAM, P4 3.2GHz
>>
>>Linux:   surface 181  mesh 181  contour 146  solid 244  recolor 118
>>Windows: surface 350  mesh 150  contour 110  solid 208  recolor 70
> 
> 
> The graphics drivers can make a big difference in the Surface / Mesh
> scores.  I believe this has to do with the rules the graphics driver
> uses to decide whether to put the surface geometry in the graphics
> card memory (fast), or shuttle it from the main computer memory for each
> drawing (slow).
> 
> The difference you see in contouring scores (146 vs 110) is hard to
> fathom.  This is not using any graphics -- it is just a calculation done
> on the computer CPU.  Do you get close to the same number if you run the
> benchmarks twice?  It could be that Windows is much slower at allocating
> memory -- that is also done during the contour calculation.
> 
> I would definitely *not* add the scores to get an overall measure of
> performance.  Some may be much more important to you than others.
> Surface and contour are probably most important for looking at density
> maps.  Surface is probably most important for looking at large molecular
> models.  Recolor is relatively unimportant (it concerns recoloring of
> solid volume renderings).
> 
> The benchmark code works by increasing the volume data set size until
> the drawing or contour calculation speed drops below 10 times per second
> (considered "interactive").  Then uses bisection to find exactly what size
> volume data set can be handled at 10 frames per second.
> 
> See the Chimera User's Guide page for more info about the benchmarks.
> It's in the Tools section under Benchmark.
> 
> 	http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/benchmark/benchmark.html
> 
> We are currently enhancing the benchmarking tool to time display of
> molecular models.
> 
>   Tom


From bshaanan at bgu.ac.il  Wed Aug 24 10:43:13 2005
From: bshaanan at bgu.ac.il (Boaz Shaanan)
Date: Wed, 24 Aug 2005 19:43:13 +0200
Subject: [Chimera-users] problems reading delphi phi map under XP
Message-ID: <430CB1B1.8040803@bgu.ac.il>

Hello,

 When I try to read a delphi phi map under XP I get the error message:
Return code: -2147483641 and the program exits.

 The same map would be read OK under linux and under Win2k. I'm using 
the latest win32 snapshot (the same happens with the official release 
though). I would appreciate if you could let me know what has gone wrong.

   Thanks,

            Boaz



From moumita_dutt2000 at yahoo.com  Wed Aug 24 05:06:34 2005
From: moumita_dutt2000 at yahoo.com (moumita dutta)
Date: Wed, 24 Aug 2005 05:06:34 -0700 (PDT)
Subject: [Chimera-users] regarding coloring
Message-ID: <20050824120634.79322.qmail@web32503.mail.mud.yahoo.com>

Dear Sir,
               How can I use more than one color to highlight different area  using the UCSF chimera software in a 3d refined model of a virus ?
 
 
Regards,
M.Dutta


		
---------------------------------
 Start your day with Yahoo! - make it your home page 
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From goddard at cgl.ucsf.edu  Wed Aug 24 11:10:19 2005
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Wed, 24 Aug 2005 11:10:19 -0700 (PDT)
Subject: [Chimera-users] problems reading delphi phi map under XP
In-Reply-To: <430CB1B1.8040803@bgu.ac.il> (message from Boaz Shaanan on Wed,
	24 Aug 2005 19:43:13 +0200)
References: <430CB1B1.8040803@bgu.ac.il>
Message-ID: <200508241810.j7OIAJLh1764486@guanine.cgl.ucsf.edu>

Hi Boaz,

  I'm not sure why reading the DelPhi map crashes Chimera on Windows XP but
not linux or win2k.  Could you email the map to me (if under 10 Mbytes) or
make it available to me on the web?  I can debug on my WinXP machine.
You can reply directly to me instead of chimera-users.

   Tom

From goddard at cgl.ucsf.edu  Wed Aug 24 11:22:48 2005
From: goddard at cgl.ucsf.edu (Thomas Goddard)
Date: Wed, 24 Aug 2005 11:22:48 -0700 (PDT)
Subject: [Chimera-users] regarding coloring
In-Reply-To: <20050824120634.79322.qmail@web32503.mail.mud.yahoo.com> (message
	from moumita dutta on Wed, 24 Aug 2005 05:06:34 -0700 (PDT))
References: <20050824120634.79322.qmail@web32503.mail.mud.yahoo.com>
Message-ID: <200508241822.j7OIMmLK1769432@guanine.cgl.ucsf.edu>

Hi M. Dutta,

  I'm not clear whether you want to color a density map of a virus,
or a PDB model.

  If you want to color the density map there is a new tool called
"Color Zone" (menu Tools / Volume Data / Color Zone) that lets you
color patches of surfaces near selected atoms or markers.  If you have
an atomic model docked to the map, you can color the atoms, select
them, then use Color Zone to color the surface within some specified
distance of the atoms.  If you don't have a docked model, you can
place markers on the density map using the Volume Path Tracer tool
(menu Tools / Volume Data / Volume Path Tracer).  The markers behave
just like atoms -- they can be colored and have their colors painted
onto nearby surface patches.

  This Color Zone tool is only in Chimera version 1.2154 (the latest
snapshot release) which is only available on Linux and Mac right now.
I could provide you the Color Zone tool separately to work with the
Windows Chimera version 1.2143 if needed.

  Documentation for Color Zone is available by pressing the Help button
on the Color Zone dialog.  We don't have online documentation for it yet.

	Tom

From agrosdidier_phd at yahoo.fr  Mon Aug 29 02:36:31 2005
From: agrosdidier_phd at yahoo.fr (Aurelien GROSDIDIER)
Date: Mon, 29 Aug 2005 11:36:31 +0200
Subject: [Chimera-users] [ViewDock] wrong bonds
Message-ID: <200508291136.31720.agrosdidier_phd@yahoo.fr>

Hi all !

I'm currently trying to use the ViewDock plugin to visualize results coming 
from our in house docking program, which dumps PDB files. These PDBs are them 
transformed into in a DOCK3/DOCK4 compliant format. First, I should say I 
haven't seen a clear description of this format, and the script gathering 
together PDB files is very empirical. The problem I see might come from a 
mistake of our docking program. Urls to fock3/4 specifications are thus 
welcome :)

Problem context:
----------------
The problem happens when dealing with ligands having several distinct residue 
numbers or if the docking coordinates do not consist only of a ligand, but 
also a set of sidechains of its receptor (also with distinct residue number).


Problem symptoms:
-----------------
The representation loaded using ViewDock show bonds between each and every 
atoms of the ligand (and the sidechains, if any), no matters their atom type 
or how far they are. This is kinda of weird, as the representation is perfect 
when these PDB are loaded from individual PDB files (not using ViewDock).

I am a newbie on this mailing list, and unfortunately this problem should be 
solved withing a few days or so. I would like to apologize in advance in case 
this help request should go somewhere else. And in case you need a clearer 
description of the problem (with figures, input files and so on), feel free 
to contact me either directly or using the ML :)

Thanks a lot for your help,

Aur?lien Grosdidier


From meng at cgl.ucsf.edu  Mon Aug 29 09:45:54 2005
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 29 Aug 2005 09:45:54 -0700
Subject: [Chimera-users] [ViewDock] wrong bonds
In-Reply-To: <200508291136.31720.agrosdidier_phd@yahoo.fr>
References: <200508291136.31720.agrosdidier_phd@yahoo.fr>
Message-ID: <A09565B7-3D03-4173-B865-634D551A435E@cgl.ucsf.edu>

Hi Aurelien,
Your question is somewhat for the DOCK developers.  Our understanding
of the format is only from relatively few examples, since (like you)
I don't think there is a formal specification on the web.  I think
they comply with the official PDB and MOL2 formats except with extra
information such as scores and molecule names in comment lines.

However, there are examples from DOCK4 in the ViewDock man page:

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/ 
framevd.html

The last section has links to the example files
(both PDB and MOL2 ligand output from DOCK4).
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/ 
viewdock.html#examples

These short examples just contain one molecule, but essentially multiple
copies concatenated together would comprise a ligand file.  The various
descriptors and scores are in the comment lines that start with ##.

There is also a ViewDock tutorial in the Chimera User's Guide
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html
that includes a multi-ligand example from DOCK4 in MOL2 format:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ras.mol2

The display of your files sounds very problematic.  Without an example,
I can only guess that they might have all the ligands with the same  
residue
number, or with the atom names in the wrong columns.

I hope this helps,
Elaine

On Aug 29, 2005, at 2:36 AM, Aurelien GROSDIDIER wrote:

> Hi all !
>
> I'm currently trying to use the ViewDock plugin to visualize  
> results coming
> from our in house docking program, which dumps PDB files. These  
> PDBs are them
> transformed into in a DOCK3/DOCK4 compliant format. First, I should  
> say I
> haven't seen a clear description of this format, and the script  
> gathering
> together PDB files is very empirical. The problem I see might come  
> from a
> mistake of our docking program. Urls to fock3/4 specifications are  
> thus
> welcome :)
>
> Problem context:
> ----------------
> The problem happens when dealing with ligands having several  
> distinct residue
> numbers or if the docking coordinates do not consist only of a  
> ligand, but
> also a set of sidechains of its receptor (also with distinct  
> residue number).
>
>
> Problem symptoms:
> -----------------
> The representation loaded using ViewDock show bonds between each  
> and every
> atoms of the ligand (and the sidechains, if any), no matters their  
> atom type
> or how far they are. This is kinda of weird, as the representation  
> is perfect
> when these PDB are loaded from individual PDB files (not using  
> ViewDock).
>
> I am a newbie on this mailing list, and unfortunately this problem  
> should be
> solved withing a few days or so. I would like to apologize in  
> advance in case
> this help request should go somewhere else. And in case you need a  
> clearer
> description of the problem (with figures, input files and so on),  
> feel free
> to contact me either directly or using the ML :)
>
> Thanks a lot for your help,
>
> Aur?lien Grosdidier
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>



From bshaanan at bgu.ac.il  Tue Aug 30 02:21:28 2005
From: bshaanan at bgu.ac.il (Boaz Shaanan)
Date: Tue, 30 Aug 2005 12:21:28 +0300
Subject: [Chimera-users] helices display in latest snapshots
Message-ID: <20050830090712.E913033E62@smtp2.bgu.ac.il>

Hello,

 I the latest snapshots (Windows 2143 and linux 2154) helices show up as thin worms when I ask for 'ribbons' under action (they used to look like nice ribbons in previous releases). I found the tools/depiction/ribbons display and managed somehow to change the look of the ribbons (still, they looked nicer before) but failed to change the look of the helices. Where can I do this now ?

   Thanks,

         Boaz


From meng at cgl.ucsf.edu  Tue Aug 30 11:21:35 2005
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 30 Aug 2005 11:21:35 -0700
Subject: [Chimera-users] helices display in latest snapshots
In-Reply-To: <20050830090712.E913033E62@smtp2.bgu.ac.il>
References: <20050830090712.E913033E62@smtp2.bgu.ac.il>
Message-ID: <CBE24D33-DA1C-454A-9BCA-C55E41B506D8@cgl.ucsf.edu>

Hi Boaz,
As far as we know, and in our testing, the ribbons are behaving  
normally in these
newer versions.  Some possibilities as to what is happening:

(A) a different scaling scheme is being used than the default.  Open  
Tools...
Depiction... Ribbon Style Editor, then under Ribbon Scaling, make  
sure it
is set to "Chimera default" and then click OK or Apply (without  
anything selected)
If someone had made different scalings before and saved them, one of  
those might
have been in use rather than the default.  Those are saved in the  
preferences file.

(B) secondary structure assignments:  are the helices known to be  
helices?
One way to check is to use the command
    select helix
and see if the areas you believe to be helices are selected.
(I'm assuming you are viewing a protein, not nucleic acids)
You can change assignments
      (a) manually (by selecting the desired parts, then clicking the  
button
reporting what is selected on the bottom right corner of the Chimera  
window
to open the Selection Inspector, Inspect "Residue" instead of "Atom,"  
setting
"in helix" to "true" and "in strand" to "false")
    OR
      (b) by running ksdssp with different parameters
(open Model Panel, which is under Favorites, then make sure the line
for your protein is chosen, change from "frequently used" to the
"infrequently used" list, click "compute SS" and set parameters as  
desired)

A final possibility if these methods (a,b) do not make what you want
into a helix is that there are some atom-naming or PDB format  
problems that
prevent the coordinates from being recognized correctly as peptide/ 
protein.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html



On Aug 30, 2005, at 2:21 AM, Boaz Shaanan wrote:

> Hello,
>
>  I the latest snapshots (Windows 2143 and linux 2154) helices show  
> up as thin worms when I ask for 'ribbons' under action (they used  
> to look like nice ribbons in previous releases). I found the tools/ 
> depiction/ribbons display and managed somehow to change the look of  
> the ribbons (still, they looked nicer before) but failed to change  
> the look of the helices. Where can I do this now ?
>
>    Thanks,
>
>          Boaz
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>


From pett at cgl.ucsf.edu  Tue Aug 30 11:31:45 2005
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 30 Aug 2005 11:31:45 -0700
Subject: [Chimera-users] helices display in latest snapshots
In-Reply-To: <CBE24D33-DA1C-454A-9BCA-C55E41B506D8@cgl.ucsf.edu>
References: <20050830090712.E913033E62@smtp2.bgu.ac.il>
	<CBE24D33-DA1C-454A-9BCA-C55E41B506D8@cgl.ucsf.edu>
Message-ID: <7B660F0C-D3FB-472C-9134-A5402B795345@cgl.ucsf.edu>

After the 1.2065 production release, a bug crept into the code that  
determines secondary structure when HELIX and SHEET records are  
absent.  I'm guessing your structure is lacking these records and  
therefore the helices aren't being properly identified.  You can  
manually identify them to Chimera by using the procedure Elaine  
outlined, quoted below.

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu
                         http://www.cgl.ucsf.edu

On Aug 30, 2005, at 11:21 AM, Elaine Meng wrote:

> You can change assignments
>      (a) manually (by selecting the desired parts, then clicking  
> the button
> reporting what is selected on the bottom right corner of the  
> Chimera window
> to open the Selection Inspector, Inspect "Residue" instead of  
> "Atom," setting
> "in helix" to "true" and "in strand" to "false")
>

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From gtseng at hsc.vcu.edu  Wed Aug 31 11:34:57 2005
From: gtseng at hsc.vcu.edu (Gea-Ny Tseng)
Date: Wed, 31 Aug 2005 14:34:57 -0400
Subject: [Chimera-users] Using the Chimera Tutorial
Message-ID: <4315F851.3010802@hsc.vcu.edu>

Dear Chimera creators:
    I am trying to learn how to use Chimera by using your on-line 
Tutorial. Is there a printable version of the Tutorial and User's Guide? 
I am not sure how to read the Tutorial and then try out the commands 
using one single monitor (that is all I have). Or did I miss something 
obvious? Your help is highly appreciated?

Gea-Ny Tseng, PhD
Physiology
Virginia Commonwealth University


From meng at cgl.ucsf.edu  Wed Aug 31 13:14:39 2005
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 31 Aug 2005 13:14:39 -0700
Subject: [Chimera-users] Using the Chimera Tutorial
In-Reply-To: <4315F851.3010802@hsc.vcu.edu>
References: <4315F851.3010802@hsc.vcu.edu>
Message-ID: <AFB6FBC2-3022-4330-8A6B-F257FABDFD7E@cgl.ucsf.edu>

Hello,
Sorry, there is no PDF version of the User's Guide (which includes  
the Tutorials).
I recommend opening the tutorial you are working on in a web browser,  
and then
using the web browser's print function.  This would also apply to any  
other parts
of the Guide you wanted in hard copy form.

The User's Guide is very nonlinear (each page has links to many other  
pages all
through the Guide), and it proved nearly impossible to produce a  
usable PDF version.
In the print form, you lose the ability to travel through the links.   
I can certainly
understand wanting a printout, however, especially if you don't have  
a large monitor.

You can write to me (meng at cgl.ucsf.edu) if you have trouble finding  
anything in
the User's Guide.  In our September release (coming soon), you will  
be able to
easily search the Guide using Help... Search Documentation in the  
Chimera menu.
Best wishes,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html



> Dear Chimera creators:
>    I am trying to learn how to use Chimera by using your on-line  
> Tutorial. Is there a printable version of the Tutorial and User's  
> Guide? I am not sure how to read the Tutorial and then try out the  
> commands using one single monitor (that is all I have). Or did I  
> miss something obvious? Your help is highly appreciated?
>
> Gea-Ny Tseng, PhD
> Physiology
> Virginia Commonwealth University
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>